WorldWideScience

Sample records for methods 5 alignment

  1. 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.

  2. 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.

  3. 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

  4. Control rod housing alignment and repair method

    International Nuclear Information System (INIS)

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

    1992-01-01

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

  5. Image correlation method for DNA sequence alignment.

    Science.gov (United States)

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

    2012-01-01

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

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

    International Nuclear Information System (INIS)

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

    2011-01-01

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

  7. 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.

  8. Novel method of aligning ATF-1 coils

    International Nuclear Information System (INIS)

    Rome, J.A.; Harris, J.H.; Neilson, G.H.; Jernigan, T.C.

    1983-08-01

    The coils for the Advanced Toroidal Facility (ATF-1) torsatron may be easily aligned before the machine is placed under vacuum. This is done by creating nulls in the magnetic field by energizing the coils in various configurations. All of the nulls in vertical bar B vector vertical bar occur on the z-axis. When the nulls coincide, the coils are properly aligned

  9. Aligned, plasma sprayed SmCo5 deposits

    International Nuclear Information System (INIS)

    Kumar, K.; Das, D.

    1986-01-01

    Highly aligned SmCo 5 deposits were produced using plasma spraying. c-axis alignment, normal to the plane of the deposit, was achieved by depositing the Sm-Co alloys on steel substrates maintained at high temperatures. The substrates were heated by the plasma flame to obtain the high temperatures. The attainment of a range of substrate temperatures was made possible through control over the geometry of the substrate

  10. Spent fuel container alignment device and method

    Science.gov (United States)

    Jones, Stewart D.; Chapek, George V.

    1996-01-01

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

  11. Sequence alignment visualization in HTML5 without Java.

    Science.gov (United States)

    Gille, Christoph; Birgit, Weyand; Gille, Andreas

    2014-01-01

    Java has been extensively used for the visualization of biological data in the web. However, the Java runtime environment is an additional layer of software with an own set of technical problems and security risks. HTML in its new version 5 provides features that for some tasks may render Java unnecessary. Alignment-To-HTML is the first HTML-based interactive visualization for annotated multiple sequence alignments. The server side script interpreter can perform all tasks like (i) sequence retrieval, (ii) alignment computation, (iii) rendering, (iv) identification of a homologous structural models and (v) communication with BioDAS-servers. The rendered alignment can be included in web pages and is displayed in all browsers on all platforms including touch screen tablets. The functionality of the user interface is similar to legacy Java applets and includes color schemes, highlighting of conserved and variable alignment positions, row reordering by drag and drop, interlinked 3D visualization and sequence groups. Novel features are (i) support for multiple overlapping residue annotations, such as chemical modifications, single nucleotide polymorphisms and mutations, (ii) mechanisms to quickly hide residue annotations, (iii) export to MS-Word and (iv) sequence icons. Alignment-To-HTML, the first interactive alignment visualization that runs in web browsers without additional software, confirms that to some extend HTML5 is already sufficient to display complex biological data. The low speed at which programs are executed in browsers is still the main obstacle. Nevertheless, we envision an increased use of HTML and JavaScript for interactive biological software. Under GPL at: http://www.bioinformatics.org/strap/toHTML/.

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

    International Nuclear Information System (INIS)

    Schuller, P.D.; Hatcher, D.C.; Caelli, T.M.; Eggert, F.M.; Yuzyk, J.

    1991-01-01

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

  13. A Global Network Alignment Method Using Discrete Particle Swarm Optimization.

    Science.gov (United States)

    Huang, Jiaxiang; Gong, Maoguo; Ma, Lijia

    2016-10-19

    Molecular interactions data increase exponentially with the advance of biotechnology. This makes it possible and necessary to comparatively analyse the different data at a network level. Global network alignment is an important network comparison approach to identify conserved subnetworks and get insight into evolutionary relationship across species. Network alignment which is analogous to subgraph isomorphism is known to be an NP-hard problem. In this paper, we introduce a novel heuristic Particle-Swarm-Optimization based Network Aligner (PSONA), which optimizes a weighted global alignment model considering both protein sequence similarity and interaction conservations. The particle statuses and status updating rules are redefined in a discrete form by using permutation. A seed-and-extend strategy is employed to guide the searching for the superior alignment. The proposed initialization method "seeds" matches with high sequence similarity into the alignment, which guarantees the functional coherence of the mapping nodes. A greedy local search method is designed as the "extension" procedure to iteratively optimize the edge conservations. PSONA is compared with several state-of-art methods on ten network pairs combined by five species. The experimental results demonstrate that the proposed aligner can map the proteins with high functional coherence and can be used as a booster to effectively refine the well-studied aligners.

  14. In-Flight Self-Alignment Method Aided by Geomagnetism for Moving Basement of Guided Munitions

    Directory of Open Access Journals (Sweden)

    Shuang-biao Zhang

    2015-01-01

    Full Text Available Due to power-after-launch mode of guided munitions of high rolling speed, initial attitude of munitions cannot be determined accurately, and this makes it difficult for navigation and control system to work effectively and validly. An in-flight self-alignment method aided by geomagnetism that includes a fast in-flight coarse alignment method and an in-flight alignment model based on Kalman theory is proposed in this paper. Firstly a fast in-flight coarse alignment method is developed by using gyros, magnetic sensors, and trajectory angles. Then, an in-flight alignment model is derived by investigation of the measurement errors and attitude errors, which regards attitude errors as state variables and geomagnetic components in navigation frame as observed variables. Finally, fight data of a spinning projectile is used to verify the performance of the in-flight self-alignment method. The satisfying results show that (1 the precision of coarse alignment can attain below 5°; (2 the attitude errors by in-flight alignment model converge to 24′ at early of the latter half of the flight; (3 the in-flight alignment model based on Kalman theory has better adaptability, and show satisfying performance.

  15. 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.

  16. 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

  17. 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

  18. Method for Providing Semiconductors Having Self-Aligned Ion Implant

    Science.gov (United States)

    Neudeck, Philip G. (Inventor)

    2014-01-01

    A method is disclosed that provides a self-aligned nitrogen-implant particularly suited for a Junction Field Effect Transistor (JFET) semiconductor device preferably comprised of a silicon carbide (SiC). This self-aligned nitrogen-implant allows for the realization of durable and stable electrical functionality of high temperature transistors such as JFETs. The method implements the self-aligned nitrogen-implant having predetermined dimensions, at a particular step in the fabrication process, so that the SiC junction field effect transistors are capable of being electrically operating continuously at 500.degree. C. for over 10,000 hours in an air ambient with less than a 10% change in operational transistor parameters.

  19. 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.

  20. 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.

  1. 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.

  2. An Automatic High Efficient Method for Dish Concentrator Alignment

    Directory of Open Access Journals (Sweden)

    Yong Wang

    2014-01-01

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

  3. GROUPING WEB ACCESS SEQUENCES uSING SEQUENCE ALIGNMENT METHOD

    OpenAIRE

    BHUPENDRA S CHORDIA; KRISHNAKANT P ADHIYA

    2011-01-01

    In web usage mining grouping of web access sequences can be used to determine the behavior or intent of a set of users. Grouping websessions is how to measure the similarity between web sessions. There are many shortcomings in traditional measurement methods. The taskof grouping web sessions based on similarity and consists of maximizing the intra-group similarity while minimizing the inter-groupsimilarity is done using sequence alignment method. This paper introduces a new method to group we...

  4. 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.

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

    DEFF Research Database (Denmark)

    Nielsen, Morten; Lundegaard, Claus; Lund, Ole

    2007-01-01

    the correct alignment of a peptide in the binding groove a crucial part of identifying the core of an MHC class II binding motif. Here, we present a novel stabilization matrix alignment method, SMM-align, that allows for direct prediction of peptide:MHC binding affinities. The predictive performance...... of the method is validated on a large MHC class II benchmark data set covering 14 HLA-DR (human MHC) and three mouse H2-IA alleles. RESULTS: The predictive performance of the SMM-align method was demonstrated to be superior to that of the Gibbs sampler, TEPITOPE, SVRMHC, and MHCpred methods. Cross validation...... 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...

  6. Interconnection blocks: a method for providing reusable, rapid, multiple, aligned and planar microfluidic interconnections

    International Nuclear Information System (INIS)

    Sabourin, D; Snakenborg, D; Dufva, M

    2009-01-01

    In this paper a method is presented for creating 'interconnection blocks' that are re-usable and provide multiple, aligned and planar microfluidic interconnections. Interconnection blocks made from polydimethylsiloxane allow rapid testing of microfluidic chips and unobstructed microfluidic observation. The interconnection block method is scalable, flexible and supports high interconnection density. The average pressure limit of the interconnection block was near 5.5 bar and all individual results were well above the 2 bar threshold considered applicable to most microfluidic applications

  7. Fabrication of Aligned Nanofibers by Manipulated Rotating Drum Method and Studying the Effective Parameters on Fibers Alignment by Image Processing

    Directory of Open Access Journals (Sweden)

    Zohreh Hadi

    2013-01-01

    Full Text Available Electrospinning is a known process to produce nanofibers through electrostatic forces. In a typical process, an electrical potential is applied between droplets of polymer solution or melt, held through a syringe needle and a grounded target. In general electrospinning fibers are collected on the grounded target as a random oriented web of nanofiber. Various research projects are attempted to obtain aligned electrospun fibers. This modified electrospinning method can be developed and used in a variety of nanofiber-based applications such as making of nanofibrous scaffolds for tissue engineering. In this study, an effective method has been developed to fabricate aligned nanofibers by manipulation of electrospinning system using two nozzles with opposite charges. Moreover, the effect of some parameters including take-up velocity, applied voltage and polymer solution concentration on alignment of produced nanofibers is investigated. The comparison of fibers alignment was carried out by programming and image processing in MATLAB. It is shown that take-up velocity and polymer solution concentration have significant effect on increasing the fibers alignment. Also, the alignment is increased with applied voltage at first and then, it is decreased. The analytical results and optical microscopic images are clear evidence of showing the maximum alignment of nanofibers obtained at 15% polymer solution concentration with take-up velocity of 600 rpm and 11 kV voltage.

  8. Initial alignment method for free space optics laser beam

    Science.gov (United States)

    Shimada, Yuta; Tashiro, Yuki; Izumi, Kiyotaka; Yoshida, Koichi; Tsujimura, Takeshi

    2016-08-01

    The authors have newly proposed and constructed an active free space optics transmission system. It is equipped with a motor driven laser emitting mechanism and positioning photodiodes, and it transmits a collimated thin laser beam and accurately steers the laser beam direction. It is necessary to introduce the laser beam within sensible range of the receiver in advance of laser beam tracking control. This paper studies an estimation method of laser reaching point for initial laser beam alignment. Distributed photodiodes detect laser luminescence at respective position, and the optical axis of laser beam is analytically presumed based on the Gaussian beam optics. Computer simulation evaluates the accuracy of the proposed estimation methods, and results disclose that the methods help us to guide the laser beam to a distant receiver.

  9. 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

  10. 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

  11. Proposal for an alignment method of the CLIC linear accelerator - From geodesic networks to the active pre-alignment

    International Nuclear Information System (INIS)

    Touze, T.

    2011-01-01

    The compact linear collider (CLIC) is the particle accelerator project proposed by the european organization for nuclear research (CERN) for high energy physics after the large hadron collider (LHC). Because of the nano-metric 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 before. 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 pre-alignment but shows the way to the last developments that have to be done for that purpose. A method is proposed. Based on the management of the Helmert transformations between Euclidean coordinate systems, from the geodetic networks to the metrological measurements, this method is likely to solve the CLIC pre-alignment problem. Large scale facilities have been built and Monte-Carlo simulations have been made in order to validate the mathematical modeling of the measurement systems and of the alignment references. When this is done, it will be possible to extrapolate the modeling to the entire CLIC length. It will be the last step towards the demonstration of the CLIC pre-alignment feasibility. (author)

  12. A direct method for computing extreme value (Gumbel) parameters for gapped biological sequence alignments.

    Science.gov (United States)

    Quinn, Terrance; Sinkala, Zachariah

    2014-01-01

    We develop a general method for computing extreme value distribution (Gumbel, 1958) parameters for gapped alignments. Our approach uses mixture distribution theory to obtain associated BLOSUM matrices for gapped alignments, which in turn are used for determining significance of gapped alignment scores for pairs of biological sequences. We compare our results with parameters already obtained in the literature.

  13. Warping methods for spectroscopic and chromatographic signal alignment: A tutorial

    Energy Technology Data Exchange (ETDEWEB)

    Bloemberg, Tom G., E-mail: T.Bloemberg@science.ru.nl [Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands); Radboud University Nijmegen, Education Institute for Molecular Sciences, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands); Gerretzen, Jan; Lunshof, Anton [Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands); Wehrens, Ron [Centre for Research and Innovation, Fondazione Edmund Mach, Via E. Mach, 1, 38010 San Michele all’Adige, TN (Italy); Buydens, Lutgarde M.C. [Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands)

    2013-06-05

    Highlights: •The concepts of warping and alignment are introduced. •The most important warping methods are critically reviewed and explained. •Reference selection, evaluation and place of warping in preprocessing are discussed. •Some pitfalls, especially for LC–MS and similar data, are addressed. •Examples are provided, together with programming scripts to rework and extend them. -- Abstract: Warping methods are an important class of methods that can correct for misalignments in (a.o.) chemical measurements. Their use in preprocessing of chromatographic, spectroscopic and spectrometric data has grown rapidly over the last decade. This tutorial review aims to give a critical introduction to the most important warping methods, the place of warping in preprocessing and current views on the related matters of reference selection, optimization, and evaluation. Some pitfalls in warping, notably for liquid chromatography–mass spectrometry (LC–MS) data and similar, will be discussed. Examples will be given of the application of a number of freely available warping methods to a nuclear magnetic resonance (NMR) spectroscopic dataset and a chromatographic dataset. As part of the Supporting Information, we provide a number of programming scripts in Matlab and R, allowing the reader to work the extended examples in detail and to reproduce the figures in this paper.

  14. Word aligned bitmap compression method, data structure, and apparatus

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Kesheng; Shoshani, Arie; Otoo, Ekow

    2004-12-14

    The Word-Aligned Hybrid (WAH) bitmap compression method and data structure is a relatively efficient method for searching and performing logical, counting, and pattern location operations upon large datasets. The technique is comprised of a data structure and methods that are optimized for computational efficiency by using the WAH compression method, which typically takes advantage of the target computing system's native word length. WAH is particularly apropos to infrequently varying databases, including those found in the on-line analytical processing (OLAP) industry, due to the increased computational efficiency of the WAH compressed bitmap index. Some commercial database products already include some version of a bitmap index, which could possibly be replaced by the WAH bitmap compression techniques for potentially increased operation speed, as well as increased efficiencies in constructing compressed bitmaps. Combined together, this technique may be particularly useful for real-time business intelligence. Additional WAH applications may include scientific modeling, such as climate and combustion simulations, to minimize search time for analysis and subsequent data visualization.

  15. Word aligned bitmap compression method, data structure, and apparatus

    Science.gov (United States)

    Wu, Kesheng; Shoshani, Arie; Otoo, Ekow

    2004-12-14

    The Word-Aligned Hybrid (WAH) bitmap compression method and data structure is a relatively efficient method for searching and performing logical, counting, and pattern location operations upon large datasets. The technique is comprised of a data structure and methods that are optimized for computational efficiency by using the WAH compression method, which typically takes advantage of the target computing system's native word length. WAH is particularly apropos to infrequently varying databases, including those found in the on-line analytical processing (OLAP) industry, due to the increased computational efficiency of the WAH compressed bitmap index. Some commercial database products already include some version of a bitmap index, which could possibly be replaced by the WAH bitmap compression techniques for potentially increased operation speed, as well as increased efficiencies in constructing compressed bitmaps. Combined together, this technique may be particularly useful for real-time business intelligence. Additional WAH applications may include scientific modeling, such as climate and combustion simulations, to minimize search time for analysis and subsequent data visualization.

  16. Method for the mechanical axis alignment of the linear induction accelerator

    International Nuclear Information System (INIS)

    Li Hong; China Academy of Engineering Physics, Mianyang; Yao Jin; Liu Yunlong; Zhang Linwen; Deng Jianjun

    2004-01-01

    Accurate mechanical axis alignment is a basic requirement for assembling a linear induction accelerator (LIA). The total length of an LIA is usually over thirty or fifty meters, and it consists of many induction cells. By using a laser tracker a new method of mechanical axis alignment for LIA is established to achieve the high accuracy. This paper introduces the method and gives implementation step and point position measure errors of the mechanical axis alignment. During the alignment process a 55 m-long alignment control survey net is built, and the theoretic revision of the coordinate of the control survey net is presented. (authors)

  17. Facile method to align crystalline needles composed of organic ...

    Indian Academy of Sciences (India)

    2017-09-23

    Sep 23, 2017 ... (using self-assembly) used for the purpose, its disadvantage is that a larger amount of the material dissolves in the solution than what ... Working hypothesis for aligning crystalline needles .... using a home-made equipment.

  18. Getting Your Peaks in Line: A Review of Alignment Methods for NMR Spectral Data

    Directory of Open Access Journals (Sweden)

    Trung Nghia Vu

    2013-04-01

    Full Text Available One of the most significant challenges in the comparative analysis of Nuclear Magnetic Resonance (NMR metabolome profiles is the occurrence of shifts between peaks across different spectra, for example caused by fluctuations in pH, temperature, instrument factors and ion content. Proper alignment of spectral peaks is therefore often a crucial preprocessing step prior to downstream quantitative analysis. Various alignment methods have been developed specifically for this purpose. Other methods were originally developed to align other data types (GC, LC, SELDI-MS, etc., but can also be applied to NMR data. This review discusses the available methods, as well as related problems such as reference determination or the evaluation of alignment quality. We present a generic alignment framework that allows for comparison and classification of different alignment approaches according to their algorithmic principles, and we discuss their performance.

  19. Vertically aligned carbon nanotube growth by pulsed laser deposition and thermal chemical vapor deposition methods

    International Nuclear Information System (INIS)

    Sohn, Jung Inn; Nam, Chunghee; Lee, Seonghoon

    2002-01-01

    We have grown vertically aligned carbon nanotubes on the various substrates such as a planar p-type Si(1 0 0) wafer, porous Si wafer, SiO 2 , Si 3 N 4 , Al 2 O 3 , and Cr by thermal chemical vapor deposition (CVD) at 800 deg.C, using C 2 H 2 gas as a carbon source and Fe catalyst films deposited by a pulsed laser on the substrates. The Fe films were deposited for 5 min by pulsed laser deposition (PLD). The advantage of Fe deposition by PLD over other deposition methods lies in the superior adhesion of Fe to a Si substrate due to high kinetic energies of the generated Fe species. Scanning electron microscopy (SEM) images show that vertically well-aligned carbon nanotubes are grown on Fe nanoparticles formed from the thermal annealing of the Fe film deposited by PLD on the various substrates. Atomic force microscopy (AFM) images show that the Fe film annealed at 800 deg.C is broken to Fe nanoparticles of 10-50 nm in size. We show that the appropriate density of Fe nanoparticles formed from the thermal annealing of the film deposited by PLD is crucial in growing vertically aligned carbon nanotubes. Using a PLD and a lift-off method, we developed the selective growth of carbon nanotubes on a patterned Fe-coated Si substrate

  20. Vertical periodontal ligament distraction--a new method for aligning ankylosed and displaced canines.

    Science.gov (United States)

    Wilmes, Benedict; Drescher, Dieter

    2009-05-01

    In the course of a clinical pilot study we tested the vertical periodontal ligament (V-PDL) distraction as a means of aligning ankylosed upper canines. The objective of this study was to analyze the appropriateness und effectiveness of this method. The ankylosed upper canines of five female patients aged between 16 und 19 years were surgically exposed, luxated, and after a latency period of 5 to 7 days, distracted at a rate of 0.5 mm per day. The installed distractors were borne by the periodontal-mucosa, the periodontal-mucosa and the bone, or by the bone exclusively. We evaluated the distraction distance and time and degree of hard and soft tissue generation present in the region surrounding the distracted teeth. All canines were aligned after a mean distraction period of 43.2 days (+/- 3.6 days). The mean distraction distance was 10.8 mm. Three canines had defects at the cemento-enamel junction, and one canine had to be extracted due to a large defect at the root. Vertical PDL distraction is a minimally-invasive therapy to align ankylosed impacted canines. Even if the long-term prognosis of distracted canines with defects is uncertain, the patient benefits from the vertical PDL distraction because both hard and soft tissues are generated in the vicinity of the distracted canine.

  1. Pattern recognition in complex activity travel patterns : comparison of Euclidean distance, signal-processing theoretical, and multidimensional sequence alignment methods

    NARCIS (Netherlands)

    Joh, C.H.; Arentze, T.A.; Timmermans, H.J.P.

    2001-01-01

    The application of a multidimensional sequence alignment method for classifying activity travel patterns is reported. The method was developed as an alternative to the existing classification methods suggested in the transportation literature. The relevance of the multidimensional sequence alignment

  2. A Fast and Specific Alignment Method for Minisatellite Maps

    Directory of Open Access Journals (Sweden)

    Eric Rivals

    2006-01-01

    Full Text Available Background: Variable minisatellites count among the most polymorphic markers of eukaryotic and prokaryotic genomes. This variability can affect gene coding regions, like in the prion protein gene, or gene regulation regions, like for the cystatin B gene, and be associated or implicated in diseases: the Creutzfeld-Jakob disease and the myoclonus epilepsy type 1, for our examples. When it affects neutrally evolving regions, the polymorphism in length (i.e., in number of copies of minisatellites proved useful in population genetics.Motivation: In these tandem repeat sequences, different mutational mechanisms let the number of copies, as well as the copies themselves, vary. Especially, the interspersion of events of tandem duplication/contraction and of punctual mutation makes the succession of variant repeats much more informative than the sole allele length. To exploit this information requires the ability to align minisatellite alleles by accounting for both punctual mutations and tandem duplications.Results: We propose a minisatellite maps alignment program that improves on previous solutions. Our new program is faster, simpler, considers an extended evolutionary model, and is available to the community. We test it on the data set of 609 alleles of the MSY1 (DYF155S1 human minisatellite and confirm its ability to recover known evolutionary signals. Our experiments highlight that the informativeness of minisatellites resides in their length and composition polymorphisms. Exploiting both simultaneously is critical to unravel the implications of variable minisatellites in the control of gene expression and diseases.Availability: Software is available at http://atgc.lirmm.fr/ms_align/

  3. A facile method to align carbon nanotubes on polymeric membrane substrate

    Science.gov (United States)

    Zhao, Haiyang; Zhou, Zhijun; Dong, Hang; Zhang, Lin; Chen, Huanlin; Hou, Lian

    2013-01-01

    The alignment of carbon nanotubes (CNT) is the fundamental requirement to ensure their excellent functions but seems to be desolated in recent years. A facile method, hot-press combined with peel-off (HPPO), is introduced here, through which CNT can be successfully vertically aligned on the polymeric membrane substrate. Shear force and mechanical stretch are proposed to be the main forces to align the tubes perpendicular to the substrate surface during the peel-off process. The alignment of CNT keeps its orientation in a thin hybrid membrane by dip-coating cellulose acetate dope solution. It is expected that the stable alignment of CNT by HPPO would contribute to the realization of its potential applications. PMID:24326297

  4. Composite Materials with Magnetically Aligned Carbon Nanoparticles and Methods of Preparation

    Science.gov (United States)

    Hong, Haiping (Inventor); Peterson, G.P. (Bud) (Inventor); Salem, David R. (Inventor)

    2018-01-01

    The present invention relates to magnetically aligned carbon nanoparticle composites and methods of preparing the same. The composites comprise carbon nanoparticles, host material, magnetically sensitive nanoparticles and surfactant. The composites may have enhanced mechanical, thermal, and/or electrical properties.

  5. Interconnection blocks: a method for providing reusable, rapid, multiple, aligned and planar microfluidic interconnections

    DEFF Research Database (Denmark)

    Sabourin, David; Snakenborg, Detlef; Dufva, Hans Martin

    2009-01-01

    In this paper a method is presented for creating 'interconnection blocks' that are re-usable and provide multiple, aligned and planar microfluidic interconnections. Interconnection blocks made from polydimethylsiloxane allow rapid testing of microfluidic chips and unobstructed microfluidic observ...

  6. 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

  7. An Advanced Electrospinning Method of Fabricating Nanofibrous Patterned Architectures with Controlled Deposition and Desired Alignment

    Science.gov (United States)

    Rasel, Sheikh Md

    We introduce a versatile advanced method of electrospinning for fabricating various kinds of nanofibrous patterns along with desired alignment, controlled amount of deposition and locally variable density into the architectures. In this method, we employed multiple electrodes whose potentials have been altered in milliseconds with the help of microprocessor based control system. Therefore, key success of this method was that the electrical field as well as charge carrying fibers could be switched shortly from one electrode's location to another, as a result, electrospun fibers could be deposited on the designated areas with desired alignment. A wide range of nanofibrous patterned architectures were constructed using proper arrangement of multiple electrodes. By controlling the concurrent activation time of two adjacent electrodes, we demonstrated that amount of fibers going into the pattern can be adjusted and desired alignment in electrospun fibers can be obtained. We also revealed that the deposition density of electrospun fibers in different areas of patterned architectures can be varied. We showed that by controlling the deposition time between two adjacent electrodes, a number of functionally graded patterns can be generated with uniaxial alignment. We also demonstrated that this handy method was capable of producing random, aligned, and multidirectional nanofibrous mats by engaging a number of electrodes and switching them in desired patterns. A comprehensive study using finite element method was carried out to understand the effects of electrical field. Simulation results revealed that electrical field strength alters shortly based on electrode control switch patterns. Nanofibrous polyvinyl alcohol (PVA) scaffolds and its composite reinforced with wollastonite and wood flour were fabricated using rotating drum electrospinning technique. Morphological, mechanical, and thermal, properties were characterized on PVA/wollastonite and PVA/wood flour nanocomposites

  8. Multiple alignment analysis on phylogenetic tree of the spread of SARS epidemic using distance method

    Science.gov (United States)

    Amiroch, S.; Pradana, M. S.; Irawan, M. I.; Mukhlash, I.

    2017-09-01

    Multiple Alignment (MA) is a particularly important tool for studying the viral genome and determine the evolutionary process of the specific virus. Application of MA in the case of the spread of the Severe acute respiratory syndrome (SARS) epidemic is an interesting thing because this virus epidemic a few years ago spread so quickly that medical attention in many countries. Although there has been a lot of software to process multiple sequences, but the use of pairwise alignment to process MA is very important to consider. In previous research, the alignment between the sequences to process MA algorithm, Super Pairwise Alignment, but in this study used a dynamic programming algorithm Needleman wunchs simulated in Matlab. From the analysis of MA obtained and stable region and unstable which indicates the position where the mutation occurs, the system network topology that produced the phylogenetic tree of the SARS epidemic distance method, and system area networks mutation.

  9. A method to align a bent crystal for channeling experiments by using quasichanneling oscillations

    Science.gov (United States)

    Sytov, A. I.; Guidi, V.; Tikhomirov, V. V.; Bandiera, L.; Bagli, E.; Germogli, G.; Mazzolari, A.; Romagnoni, M.

    2018-04-01

    A method to calculate both the bent crystal angle of alignment and radius of curvature by using only one distribution of deflection angles has been developed. The method is based on measuring of the angular position of recently predicted and observed quasichanneling oscillations in the deflection angle distribution and consequent fitting of both the radius and angular alignment by analytic formulae. In this paper this method is applied on the example of simulated angular distributions over a wide range of values of both radius and alignment for electrons. It is carried out through the example of (111) nonequidistant planes though this technique is general and could be applied to any kind of planes. In addition, the method application constraints are also discussed. It is shown by simulations that this method, being in fact a sort of beam diagnostics, allows one in a certain case to increase the crystal alignment accuracy as well as to control precisely the radius of curvature inside an accelerator tube without vacuum breaking. In addition, it speeds up the procedure of crystal alignment in channeling experiments, reducing beamtime consuming.

  10. Vertically aligned Ta3N5 nanorod arrays for solar-driven photoelectrochemical water splitting

    KAUST Repository

    Li, Yanbo

    2012-09-18

    A vertically aligned Ta3N5 nanorod photoelectrode is fabricated by through-mask anodization and nitridation for water splitting. The Ta3N5 nanorods, working as photoanodes of a photoelectrochemical cell, yield a high photocurrent density of 3.8 mA cm -2 at 1.23 V versus a reversible hydrogen electrode under AM 1.5G simulated sunlight and an incident photon-to-current conversion efficiency of 41.3% at 440 nm, one of the highest activities reported for photoanodes so far. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Vertically aligned Ta3N5 nanorod arrays for solar-driven photoelectrochemical water splitting

    KAUST Repository

    Li, Yanbo; Takata, Tsuyoshi; Cha, Dong Kyu; Takanabe, Kazuhiro; Minegishi, Tsutomu; Kubota, Jun; Domen, Kazunari

    2012-01-01

    A vertically aligned Ta3N5 nanorod photoelectrode is fabricated by through-mask anodization and nitridation for water splitting. The Ta3N5 nanorods, working as photoanodes of a photoelectrochemical cell, yield a high photocurrent density of 3.8 mA cm -2 at 1.23 V versus a reversible hydrogen electrode under AM 1.5G simulated sunlight and an incident photon-to-current conversion efficiency of 41.3% at 440 nm, one of the highest activities reported for photoanodes so far. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Evaporation-based method for preparing gelatin foams with aligned tubular pore structures

    International Nuclear Information System (INIS)

    Frazier, Shane D.; Srubar, Wil V.

    2016-01-01

    Gelatin-based foams with aligned tubular pore structures were prepared via liquid-to-gas vaporization of tightly bound water in dehydrated gelatin hydrogels. This study elucidates the mechanism of the foaming process by investigating the secondary (i.e., helical) structure, molecular interactions, and water content of gelatin films before and after foaming using X-ray diffraction, Fourier transform infrared (FTIR) spectroscopy, differential scanning calorimetry and thermogravimetric analysis (TGA), respectively. Experimental data from gelatin samples prepared at various gelatin-to-water concentrations (5–30 wt.%) substantiate that resulting foam structures are similar in pore diameter (approximately 350 μm), shape, and density (0.05–0.22 g/cm"3) to those fabricated using conventional methods (e.g., freeze-drying). Helical structures were identified in the films but were not evident in the foamed samples after vaporization (~ 150 °C), suggesting that the primary foaming mechanism is governed by the vaporization of water that is tightly bound in secondary structures (i.e., helices, β-turns, β-sheets) that are present in dehydrated gelatin films. FTIR and TGA data show that the foaming process leads to more disorder and reduced hydrogen bonding to hydroxyl groups in gelatin and that no thermal degradation of gelatin occurs before or after foaming. - Highlights: • A new method is presented for fabricating gelatin foams with aligned, tubular pores. • Gelatin hydrogels were dehydrated then heated to 150 °C to induce foaming. • Vaporization of tightly (vs. loosely) bound water is the primary foaming mechanism • Foaming induced no thermal degradation but caused disorder in secondary structures • Foam microstructures are similar to those prepared using conventional methods.

  13. Evaporation-based method for preparing gelatin foams with aligned tubular pore structures

    Energy Technology Data Exchange (ETDEWEB)

    Frazier, Shane D.; Srubar, Wil V., E-mail: wsrubar@colorado.edu

    2016-05-01

    Gelatin-based foams with aligned tubular pore structures were prepared via liquid-to-gas vaporization of tightly bound water in dehydrated gelatin hydrogels. This study elucidates the mechanism of the foaming process by investigating the secondary (i.e., helical) structure, molecular interactions, and water content of gelatin films before and after foaming using X-ray diffraction, Fourier transform infrared (FTIR) spectroscopy, differential scanning calorimetry and thermogravimetric analysis (TGA), respectively. Experimental data from gelatin samples prepared at various gelatin-to-water concentrations (5–30 wt.%) substantiate that resulting foam structures are similar in pore diameter (approximately 350 μm), shape, and density (0.05–0.22 g/cm{sup 3}) to those fabricated using conventional methods (e.g., freeze-drying). Helical structures were identified in the films but were not evident in the foamed samples after vaporization (~ 150 °C), suggesting that the primary foaming mechanism is governed by the vaporization of water that is tightly bound in secondary structures (i.e., helices, β-turns, β-sheets) that are present in dehydrated gelatin films. FTIR and TGA data show that the foaming process leads to more disorder and reduced hydrogen bonding to hydroxyl groups in gelatin and that no thermal degradation of gelatin occurs before or after foaming. - Highlights: • A new method is presented for fabricating gelatin foams with aligned, tubular pores. • Gelatin hydrogels were dehydrated then heated to 150 °C to induce foaming. • Vaporization of tightly (vs. loosely) bound water is the primary foaming mechanism • Foaming induced no thermal degradation but caused disorder in secondary structures • Foam microstructures are similar to those prepared using conventional methods.

  14. A comprehensive method for evaluating precision of transfer alignment on a moving base

    Science.gov (United States)

    Yin, Hongliang; Xu, Bo; Liu, Dezheng

    2017-09-01

    In this study, we propose the use of the Degree of Alignment (DOA) in engineering applications for evaluating the precision of and identifying the transfer alignment on a moving base. First, we derive the statistical formula on the basis of estimations. Next, we design a scheme for evaluating the transfer alignment on a moving base, for which the attitude error cannot be directly measured. Then, we build a mathematic estimation model and discuss Fixed Point Smoothing (FPS), Returns to Scale (RTS), Inverted Sequence Recursive Estimation (ISRE), and Kalman filter estimation methods, which can be used when evaluating alignment accuracy. Our theoretical calculations and simulated analyses show that the DOA reflects not only the alignment time and accuracy but also differences in the maneuver schemes, and is suitable for use as an integrated evaluation index. Furthermore, all four of these algorithms can be used to identify the transfer alignment and evaluate its accuracy. We recommend RTS in particular for engineering applications. Generalized DOAs should be calculated according to the tactical requirements.

  15. 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.

  16. A generalized method for alignment of block copolymer films: solvent vapor annealing with soft shear.

    Science.gov (United States)

    Qiang, Zhe; Zhang, Yuanzhong; Groff, Jesse A; Cavicchi, Kevin A; Vogt, Bryan D

    2014-08-28

    One of the key issues associated with the utilization of block copolymer (BCP) thin films in nanoscience and nanotechnology is control of their alignment and orientation over macroscopic dimensions. We have recently reported a method, solvent vapor annealing with soft shear (SVA-SS), for fabricating unidirectional alignment of cylindrical nanostructures. This method is a simple extension of the common SVA process by adhering a flat, crosslinked poly(dimethylsiloxane) (PDMS) pad to the BCP thin film. The impact of processing parameters, including annealing time, solvent removal rate and the physical properties of the PDMS pad, on the quality of alignment quantified by the Herman's orientational factor (S) is systematically examined for a model system of polystyrene-block-polyisoprene-block-polystyrene (SIS). As annealing time increases, the SIS morphology transitions from isotropic rods to highly aligned cylinders. Decreasing the rate of solvent removal, which impacts the shear rate imposed by the contraction of the PDMS, improves the orientation factor of the cylindrical domains; this suggests the nanostructure alignment is primarily induced by contraction of PDMS during solvent removal. Moreover, the physical properties of the PDMS controlled by the crosslink density impact the orientation factor by tuning its swelling extent during SVA-SS and elastic modulus. Decreasing the PDMS crosslink density increases S; this effect appears to be primarily driven by the changes in the solubility of the SVA-SS solvent in the PDMS. With this understanding of the critical processing parameters, SVA-SS has been successfully applied to align a wide variety of BCPs including polystyrene-block-polybutadiene-block-polystyrene (SBS), polystyrene-block-poly(N,N-dimethyl-n-octadecylammonium p-styrenesulfonate) (PS-b-PSS-DMODA), polystyrene-block-polydimethylsiloxane (PS-b-PDMS) and polystyrene-block-poly(2-vinlypyridine) (PS-b-P2VP). These results suggest that SVA-SS is a generalizable

  17. 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.

  18. Aligning ERP systems with companies' real needs: an `Operational Model Based' method

    Science.gov (United States)

    Mamoghli, Sarra; Goepp, Virginie; Botta-Genoulaz, Valérie

    2017-02-01

    Enterprise Resource Planning (ERP) systems offer standard functionalities that have to be configured and customised by a specific company depending on its own requirements. A consistent alignment is therefore an essential success factor of ERP projects. To manage this alignment, an 'Operational Model Based' method is proposed. It is based on the design and the matching of models, and conforms to the modelling views and constructs of the ISO 19439 and 19440 enterprise-modelling standards. It is characterised by: (1) a predefined design and matching order of the models; (2) the formalisation, in terms of modelling constructs, of alignment and misalignment situations; and (3) their association with a set of decisions in order to mitigate the misalignment risk. Thus, a comprehensive understanding of the alignment management during ERP projects is given. Unlike existing methods, this one includes decisions related to the organisational changes an ERP system can induce, as well as criteria on which the best decision can be based. In this way, it provides effective support and guidance to companies implementing ERP systems, as the alignment process is detailed and structured. The method is applied on the ERP project of a Small and Medium Enterprise, showing that it can be used even in contexts where the ERP project expertise level is low.

  19. Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer.

    Directory of Open Access Journals (Sweden)

    Raquel Bromberg

    2016-06-01

    Full Text Available Advances in sequencing have generated a large number of complete genomes. Traditionally, phylogenetic analysis relies on alignments of orthologs, but defining orthologs and separating them from paralogs is a complex task that may not always be suited to the large datasets of the future. An alternative to traditional, alignment-based approaches are whole-genome, alignment-free methods. These methods are scalable and require minimal manual intervention. We developed SlopeTree, a new alignment-free method that estimates evolutionary distances by measuring the decay of exact substring matches as a function of match length. SlopeTree corrects for horizontal gene transfer, for composition variation and low complexity sequences, and for branch-length nonlinearity caused by multiple mutations at the same site. We tested SlopeTree on 495 bacteria, 73 archaea, and 72 strains of Escherichia coli and Shigella. We compared our trees to the NCBI taxonomy, to trees based on concatenated alignments, and to trees produced by other alignment-free methods. The results were consistent with current knowledge about prokaryotic evolution. We assessed differences in tree topology over different methods and settings and found that the majority of bacteria and archaea have a core set of proteins that evolves by descent. In trees built from complete genomes rather than sets of core genes, we observed some grouping by phenotype rather than phylogeny, for instance with a cluster of sulfur-reducing thermophilic bacteria coming together irrespective of their phyla. The source-code for SlopeTree is available at: http://prodata.swmed.edu/download/pub/slopetree_v1/slopetree.tar.gz.

  20. Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer

    Science.gov (United States)

    Grishin, Nick V.; Otwinowski, Zbyszek

    2016-01-01

    Advances in sequencing have generated a large number of complete genomes. Traditionally, phylogenetic analysis relies on alignments of orthologs, but defining orthologs and separating them from paralogs is a complex task that may not always be suited to the large datasets of the future. An alternative to traditional, alignment-based approaches are whole-genome, alignment-free methods. These methods are scalable and require minimal manual intervention. We developed SlopeTree, a new alignment-free method that estimates evolutionary distances by measuring the decay of exact substring matches as a function of match length. SlopeTree corrects for horizontal gene transfer, for composition variation and low complexity sequences, and for branch-length nonlinearity caused by multiple mutations at the same site. We tested SlopeTree on 495 bacteria, 73 archaea, and 72 strains of Escherichia coli and Shigella. We compared our trees to the NCBI taxonomy, to trees based on concatenated alignments, and to trees produced by other alignment-free methods. The results were consistent with current knowledge about prokaryotic evolution. We assessed differences in tree topology over different methods and settings and found that the majority of bacteria and archaea have a core set of proteins that evolves by descent. In trees built from complete genomes rather than sets of core genes, we observed some grouping by phenotype rather than phylogeny, for instance with a cluster of sulfur-reducing thermophilic bacteria coming together irrespective of their phyla. The source-code for SlopeTree is available at: http://prodata.swmed.edu/download/pub/slopetree_v1/slopetree.tar.gz. PMID:27336403

  1. A Multi-Objective Method to Align Human Resource Allocation with University Strategy

    Science.gov (United States)

    Bouillard, Philippe

    2016-01-01

    Universities are currently under considerable pressure to reach their stakeholders' expectations. Management tools that use strategic plans, key performance indicators and quality assurance methods are increasingly deployed. This paper aims to demonstrate how resource allocation can be aligned with institutional strategic plans with a very simple…

  2. Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison

    Energy Technology Data Exchange (ETDEWEB)

    Ovacik, Meric A. [Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States); Androulakis, Ioannis P., E-mail: yannis@rci.rutgers.edu [Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States); Biomedical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States)

    2013-09-15

    Pathway-based information has become an important source of information for both establishing evolutionary relationships and understanding the mode of action of a chemical or pharmaceutical among species. Cross-species comparison of pathways can address two broad questions: comparison in order to inform evolutionary relationships and to extrapolate species differences used in a number of different applications including drug and toxicity testing. Cross-species comparison of metabolic pathways is complex as there are multiple features of a pathway that can be modeled and compared. Among the various methods that have been proposed, reaction alignment has emerged as the most successful at predicting phylogenetic relationships based on NCBI taxonomy. We propose an improvement of the reaction alignment method by accounting for sequence similarity in addition to reaction alignment method. Using nine species, including human and some model organisms and test species, we evaluate the standard and improved comparison methods by analyzing glycolysis and citrate cycle pathways conservation. In addition, we demonstrate how organism comparison can be conducted by accounting for the cumulative information retrieved from nine pathways in central metabolism as well as a more complete study involving 36 pathways common in all nine species. Our results indicate that reaction alignment with enzyme sequence similarity results in a more accurate representation of pathway specific cross-species similarities and differences based on NCBI taxonomy.

  3. Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison

    International Nuclear Information System (INIS)

    Ovacik, Meric A.; Androulakis, Ioannis P.

    2013-01-01

    Pathway-based information has become an important source of information for both establishing evolutionary relationships and understanding the mode of action of a chemical or pharmaceutical among species. Cross-species comparison of pathways can address two broad questions: comparison in order to inform evolutionary relationships and to extrapolate species differences used in a number of different applications including drug and toxicity testing. Cross-species comparison of metabolic pathways is complex as there are multiple features of a pathway that can be modeled and compared. Among the various methods that have been proposed, reaction alignment has emerged as the most successful at predicting phylogenetic relationships based on NCBI taxonomy. We propose an improvement of the reaction alignment method by accounting for sequence similarity in addition to reaction alignment method. Using nine species, including human and some model organisms and test species, we evaluate the standard and improved comparison methods by analyzing glycolysis and citrate cycle pathways conservation. In addition, we demonstrate how organism comparison can be conducted by accounting for the cumulative information retrieved from nine pathways in central metabolism as well as a more complete study involving 36 pathways common in all nine species. Our results indicate that reaction alignment with enzyme sequence similarity results in a more accurate representation of pathway specific cross-species similarities and differences based on NCBI taxonomy

  4. Time dependent growth of vertically aligned carbon nanotube forest using a laser activated catalytical CVD method

    NARCIS (Netherlands)

    Haluska, M.; Bellouard, Y.J.; Dietzel, A.H.

    2008-01-01

    We report the growth of vertically aligned single-wall and multi-wall carbon nanotube forest using a Laser Activated - Catalytic Chemical Vapor Deposition process. The experiments were performed in a cold-wall reactor filled with an ethylene-hydrogen-argon gas mixture in a 5:2:8 ratio at ambient

  5. GOSSIP: a method for fast and accurate global alignment of protein structures.

    Science.gov (United States)

    Kifer, I; Nussinov, R; Wolfson, H J

    2011-04-01

    The database of known protein structures (PDB) is increasing rapidly. This results in a growing need for methods that can cope with the vast amount of structural data. To analyze the accumulating data, it is important to have a fast tool for identifying similar structures and clustering them by structural resemblance. Several excellent tools have been developed for the comparison of protein structures. These usually address the task of local structure alignment, an important yet computationally intensive problem due to its complexity. It is difficult to use such tools for comparing a large number of structures to each other at a reasonable time. Here we present GOSSIP, a novel method for a global all-against-all alignment of any set of protein structures. The method detects similarities between structures down to a certain cutoff (a parameter of the program), hence allowing it to detect similar structures at a much higher speed than local structure alignment methods. GOSSIP compares many structures in times which are several orders of magnitude faster than well-known available structure alignment servers, and it is also faster than a database scanning method. We evaluate GOSSIP both on a dataset of short structural fragments and on two large sequence-diverse structural benchmarks. Our conclusions are that for a threshold of 0.6 and above, the speed of GOSSIP is obtained with no compromise of the accuracy of the alignments or of the number of detected global similarities. A server, as well as an executable for download, are available at http://bioinfo3d.cs.tau.ac.il/gossip/.

  6. ATP Bioluminometers Analysis on the Surfaces of Removable Orthodontic Aligners after the Use of Different Cleaning Methods

    OpenAIRE

    Levrini, Luca; Mangano, Alessandro; Margherini, Silvia; Tenconi, Camilla; Vigetti, Davide; Muollo, Raffaele; Marco Abbate, Gian

    2016-01-01

    Purpose. The aim was to quantify the bacteria concentration on the surface of orthodontic clear aligners using three different cleaning methods. Furthermore the objective was to validate the efficacy of the bioluminometer in assessing the bacteria concentration. Materials and Methods. Twenty subjects (six males and fourteen females) undergoing orthodontic therapy with clear aligners (Invisalign® Align Technology, Santa Clara, California) were enrolled in this study. The observation time was o...

  7. Space Technology 5 (ST-5) Observations of the Imbalance of Region 1 and 2 Field-Aligned Currents

    Science.gov (United States)

    Le, Guan

    2010-01-01

    Space Technology 5 (ST-5) is a three micro-satellite constellation deployed into a 300 x 4500 km, dawn-dusk, sun-synchronous polar orbit from March 22 to June 21, 2006, for technology validations. In this study, we use the in-situ magnetic field observations from Space Technology 5 mission to quantify the imbalance of Region 1 (R1) and Region 2 (R2) currents. During the three-month duration of the ST5 mission, geomagnetic conditions range from quiet to moderately active. We find that the R1 current intensity is consistently stronger than the R2 current intensity both for the dawnside and the duskside large-scale field-aligned current system. The net currents flowing into (out of) the ionosphere in the dawnside (duskside) are in the order of 5% of the total RI currents. We also find that the net currents flowing into or out of the ionosphere are controlled by the solar wind-magnetosphere interaction in the same way as the field-aligned currents themselves are. Since the net currents due to the imbalance of the R1 and R2 currents require that their closure currents flow across the polar cap from dawn to dusk as Pedersen currents, our results indicate that the total amount of the cross-polar cap Pedersen currents is in the order of approx. 0.1 MA. This study, although with a very limited dataset, is one of the first attempts to quantify the cross-polar cap Pedersen currents. Given the importance of the Joule heating due to Pedersen currents to the high-latitude ionospheric electrodynamics, quantifying the cross-polar cap Pedersen currents and associated Joule heating is needed for developing models of the magnetosphere-ionosphere coupling.

  8. An optimal beam alignment method for large-scale distributed space surveillance radar system

    Science.gov (United States)

    Huang, Jian; Wang, Dongya; Xia, Shuangzhi

    2018-06-01

    Large-scale distributed space surveillance radar is a very important ground-based equipment to maintain a complete catalogue for Low Earth Orbit (LEO) space debris. However, due to the thousands of kilometers distance between each sites of the distributed radar system, how to optimally implement the Transmitting/Receiving (T/R) beams alignment in a great space using the narrow beam, which proposed a special and considerable technical challenge in the space surveillance area. According to the common coordinate transformation model and the radar beam space model, we presented a two dimensional projection algorithm for T/R beam using the direction angles, which could visually describe and assess the beam alignment performance. Subsequently, the optimal mathematical models for the orientation angle of the antenna array, the site location and the T/R beam coverage are constructed, and also the beam alignment parameters are precisely solved. At last, we conducted the optimal beam alignment experiments base on the site parameters of Air Force Space Surveillance System (AFSSS). The simulation results demonstrate the correctness and effectiveness of our novel method, which can significantly stimulate the construction for the LEO space debris surveillance equipment.

  9. 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

  10. The alignment of the LHC low beta triplets. Review of instrumentation and methods

    International Nuclear Information System (INIS)

    Coosemans, W.; Mainaud Durand, H.; Marin, A.; Quesnel, J-P.

    2003-01-01

    Alignment tolerances for the LHC insertions are particularly stringent regarding the low beta quadrupoles, which induce strict positioning tolerances, in a severe environment (high radiation fluxes and magnetic fields): positioning of one inner triplet with respect to the other (left/right side): ±0.5 mm (3σ), stability of the positioning of one quadrupole inside its triplet: a few microns. We propose to continuously monitor the relative position of the quadrupoles of one inner triplet with respect to a reference frame materialized by a wire and a water surface, and to use common references to link a triplet on one side to the triplet on the other side of the experiment. When the offset between real and reference position becomes too great, the quadrupole will be moved using remote motorized jacks. Instrumentation (HLS, WPS, radial measuring system, etc.) and methods will be detailed as well as the first results obtained on a cryo-magnet prototype named TAP used as test facility. The TAP is equipped with HLS linked by two types of hydraulic networks (two pipes with air and water separated, one pipe half filled), WPS and one inclinometer. It is installed on three polyurethane motorized jacks in order to study and compare servo positioning using the different sensors. (author)

  11. 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.

  12. Effects of posttreatment skeletal maturity measured with the cervical vertebral maturation method on incisor alignment relapse.

    Science.gov (United States)

    Fudalej, Piotr; Rothe, Laura E; Bollen, Anne-Marie

    2008-08-01

    Our aim was to test the hypothesis that relapse of incisor alignment is associated with skeletal maturity at the end of treatment, as assessed with the cervical vertebral maturation (CVM) method. This was a case-control study with information from the postretention database at the University of Washington. Mandibular incisor irregularity (II) at least 10 years out of retention (T3) was used to define the subjects (II >6 mm, relapse group) and the controls (II 0.05). Pretreatment II and postretention time were found to be correlated with long-term incisor stability (P = 0.007 and 0.034, respectively). Sex was not related to relapse (P = 0.33). Maturity of craniofacial structures at the end of treatment evaluated with the CVM method is not associated with long-term stability of incisor alignment.

  13. A Facile Method to Fabricate Anisotropic Hydrogels with Perfectly Aligned Hierarchical Fibrous Structures.

    Science.gov (United States)

    Mredha, Md Tariful Islam; Guo, Yun Zhou; Nonoyama, Takayuki; Nakajima, Tasuku; Kurokawa, Takayuki; Gong, Jian Ping

    2018-03-01

    Natural structural materials (such as tendons and ligaments) are comprised of multiscale hierarchical architectures, with dimensions ranging from nano- to macroscale, which are difficult to mimic synthetically. Here a bioinspired, facile method to fabricate anisotropic hydrogels with perfectly aligned multiscale hierarchical fibrous structures similar to those of tendons and ligaments is reported. The method includes drying a diluted physical hydrogel in air by confining its length direction. During this process, sufficiently high tensile stress is built along the length direction to align the polymer chains and multiscale fibrous structures (from nano- to submicro- to microscale) are spontaneously formed in the bulk material, which are well-retained in the reswollen gel. The method is useful for relatively rigid polymers (such as alginate and cellulose), which are susceptible to mechanical signal. By controlling the drying with or without prestretching, the degree of alignment, size of superstructures, and the strength of supramolecular interactions can be tuned, which sensitively influence the strength and toughness of the hydrogels. The mechanical properties are comparable with those of natural ligaments. This study provides a general strategy for designing hydrogels with highly ordered hierarchical structures, which opens routes for the development of many functional biomimetic materials for biomedical applications. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Coordinate alignment of combined measurement systems using a modified common points method

    Science.gov (United States)

    Zhao, G.; Zhang, P.; Xiao, W.

    2018-03-01

    The co-ordinate metrology has been extensively researched for its outstanding advantages in measurement range and accuracy. The alignment of different measurement systems is usually achieved by integrating local coordinates via common points before measurement. The alignment errors would accumulate and significantly reduce the global accuracy, thus need to be minimized. In this thesis, a modified common points method (MCPM) is proposed to combine different traceable system errors of the cooperating machines, and optimize the global accuracy by introducing mutual geometric constraints. The geometric constraints, obtained by measuring the common points in individual local coordinate systems, provide the possibility to reduce the local measuring uncertainty whereby enhance the global measuring certainty. A simulation system is developed in Matlab to analyze the feature of MCPM using the Monto-Carlo method. An exemplary setup is constructed to verify the feasibility and efficiency of the proposed method associated with laser tracker and indoor iGPS systems. Experimental results show that MCPM could significantly improve the alignment accuracy.

  15. Improved image alignment method in application to X-ray images and biological images.

    Science.gov (United States)

    Wang, Ching-Wei; Chen, Hsiang-Chou

    2013-08-01

    Alignment of medical images is a vital component of a large number of applications throughout the clinical track of events; not only within clinical diagnostic settings, but prominently so in the area of planning, consummation and evaluation of surgical and radiotherapeutical procedures. However, image registration of medical images is challenging because of variations on data appearance, imaging artifacts and complex data deformation problems. Hence, the aim of this study is to develop a robust image alignment method for medical images. An improved image registration method is proposed, and the method is evaluated with two types of medical data, including biological microscopic tissue images and dental X-ray images and compared with five state-of-the-art image registration techniques. The experimental results show that the presented method consistently performs well on both types of medical images, achieving 88.44 and 88.93% averaged registration accuracies for biological tissue images and X-ray images, respectively, and outperforms the benchmark methods. Based on the Tukey's honestly significant difference test and Fisher's least square difference test tests, the presented method performs significantly better than all existing methods (P ≤ 0.001) for tissue image alignment, and for the X-ray image registration, the proposed method performs significantly better than the two benchmark b-spline approaches (P < 0.001). The software implementation of the presented method and the data used in this study are made publicly available for scientific communities to use (http://www-o.ntust.edu.tw/∼cweiwang/ImprovedImageRegistration/). cweiwang@mail.ntust.edu.tw.

  16. 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.

  17. Ingenious method of external fixator use to maintain alignment for nailing a proximal tibial shaft fracture.

    Science.gov (United States)

    Behera, Prateek; Aggarwal, Sameer; Kumar, Vishal; Kumar Meena, Umesh; Saibaba, Balaji

    2015-09-01

    Fractures of the tibia are one of the most commonly seen orthopedic injuries. Most of them result from a high velocity trauma. While intramedullary nailing of tibial diaphyseal fractures is considered as the golden standard form of treatment for such cases, many metaphyseal and metaphyseal-diaphyseal junction fractures can also be managed by nailing. Maintenance of alignment of such fractures during surgical procedure is often challenging as the pull of patellar tendon tends to extend the proximal fragment as soon as one flexes the knee for the surgical procedure. Numerous technical modifications have been described in the literature for successfully nailing such fractures including semi extended nailing, use of medial plates and external fixators among others. In this study, it was aimed to report two cases in which we used our ingenious method of applying external fixator for maintaining alignment of the fracture and aiding in the entire process of closed intramedullary nailing of metaphyseal tibial fractures by the conventional method. We were able to get good alignment during and after the closed surgery as observed on post-operative radiographs and believe that further evaluation of this technique may be of help to surgeons who want to avoid other techniques.

  18. Enhanced method of magnetic powder alignment for production of PLP Nd-Fe-B magnets

    Energy Technology Data Exchange (ETDEWEB)

    Popov, A.G. [M.N. Miheev Institute of Metal Physics of Ural Branch of Russian Academy of Sciences, Str. S. Kovalevskoy, 18, 620137 Ekaterinburg (Russian Federation); Institute of Natural Sciences and Mathematics, Ural Federal University, Av. Mira, 19, 620002 Ekaterinburg (Russian Federation); Golovnia, O.A., E-mail: golovnya@imp.uran.ru [M.N. Miheev Institute of Metal Physics of Ural Branch of Russian Academy of Sciences, Str. S. Kovalevskoy, 18, 620137 Ekaterinburg (Russian Federation); Institute of Natural Sciences and Mathematics, Ural Federal University, Av. Mira, 19, 620002 Ekaterinburg (Russian Federation); Protasov, A.V. [M.N. Miheev Institute of Metal Physics of Ural Branch of Russian Academy of Sciences, Str. S. Kovalevskoy, 18, 620137 Ekaterinburg (Russian Federation); Institute of Natural Sciences and Mathematics, Ural Federal University, Av. Mira, 19, 620002 Ekaterinburg (Russian Federation)

    2017-04-15

    It is demonstrated how the high degree of powder alignment in PLP magnets can be achieved by loading the powder into a container placed in a magnetic field of moderate strength. The strip-cast alloy with a composition of 30.00 Nd, 1.95 Dy, 66.42 Fe, 0.99 B, 0.54 Co, 0.1 Ga (wt%) was subjected to hydrogen decrepitation and then milled in a vibratory mill in toluene to an average particle size of 2.9 µm determined by the FSSS method. The powder was compacted in the magnetic field of 0.2 – 1.2 T to the filling density 2.6 – 3.2×10{sup 3} kg/m{sup 3}. It is shown that loading the powder into a container placed in a magnetic field enhances the degree of powder alignment in sintered Nd-Fe-B magnets produced from non-pressed powder. At the filling density less than 3.2×10{sup 3} kg/m{sup 3}, the density of magnets is high but insufficient, because of the formation of magnetostatic chains of particles, which impedes the powder compaction. The simulation by the discrete-element method qualitatively proves that the magnetostatic interaction of the chains of particles that are formed in the course of loading in the magnetic field stimulates a decrease in the density of the sintered magnets and its non-uniform distribution over the sample. As a result of the optimization of the parameters of the alignment and compaction of the powder loaded in a magnetic field, PLP magnets with B{sub r} ≥1.34 T, H{sub c} ≥950 kA/m, (BH){sub max} ≥340 kJ/m{sup 3}, and the degree of alignment exceeding 96% were produced. - Highlights: • The pressless process (PLP) in magnet production is studied. • A new method of the loading of powder in an applied DC magnetic field is suggested. • The method allows achieving higher degree of alignment in moderate magnetic field. • Density of sintered magnets is studied experimentally and via DEM simulation. • Low density is caused by the formation of magnetostatic chains of powder particles.

  19. Enhanced method of magnetic powder alignment for production of PLP Nd-Fe-B magnets

    International Nuclear Information System (INIS)

    Popov, A.G.; Golovnia, O.A.; Protasov, A.V.

    2017-01-01

    It is demonstrated how the high degree of powder alignment in PLP magnets can be achieved by loading the powder into a container placed in a magnetic field of moderate strength. The strip-cast alloy with a composition of 30.00 Nd, 1.95 Dy, 66.42 Fe, 0.99 B, 0.54 Co, 0.1 Ga (wt%) was subjected to hydrogen decrepitation and then milled in a vibratory mill in toluene to an average particle size of 2.9 µm determined by the FSSS method. The powder was compacted in the magnetic field of 0.2 – 1.2 T to the filling density 2.6 – 3.2×10 3 kg/m 3 . It is shown that loading the powder into a container placed in a magnetic field enhances the degree of powder alignment in sintered Nd-Fe-B magnets produced from non-pressed powder. At the filling density less than 3.2×10 3 kg/m 3 , the density of magnets is high but insufficient, because of the formation of magnetostatic chains of particles, which impedes the powder compaction. The simulation by the discrete-element method qualitatively proves that the magnetostatic interaction of the chains of particles that are formed in the course of loading in the magnetic field stimulates a decrease in the density of the sintered magnets and its non-uniform distribution over the sample. As a result of the optimization of the parameters of the alignment and compaction of the powder loaded in a magnetic field, PLP magnets with B r ≥1.34 T, H c ≥950 kA/m, (BH) max ≥340 kJ/m 3 , and the degree of alignment exceeding 96% were produced. - Highlights: • The pressless process (PLP) in magnet production is studied. • A new method of the loading of powder in an applied DC magnetic field is suggested. • The method allows achieving higher degree of alignment in moderate magnetic field. • Density of sintered magnets is studied experimentally and via DEM simulation. • Low density is caused by the formation of magnetostatic chains of powder particles.

  20. Dynamic evaluation method of lower limbs joint alignment (MADAAMI for dancers during the plié

    Directory of Open Access Journals (Sweden)

    Kaanda Nabilla Souza Gontijo

    Full Text Available Abstract In classical ballet, the joint misalignments during the plié can generate various injuries. To evaluate potential misalignments during the plié the aim of this study was to present a method for dynamic evaluation of lower limb alignment articulation (called MADAAMI. MADAAMI was validated by 12 experts, and for the evaluation of its reproducibility and for agreement with 3D kinematics, 20 dancers were assessed using a video recording of their plié. For statistical analysis we used the Kappa coefficient (k (p 0.40 and C > 80%, and it is a suitable and valid method for use by the same examiner.

  1. A method for optical ground station reduce alignment error in satellite-ground quantum experiments

    Science.gov (United States)

    He, Dong; Wang, Qiang; Zhou, Jian-Wei; Song, Zhi-Jun; Zhong, Dai-Jun; Jiang, Yu; Liu, Wan-Sheng; Huang, Yong-Mei

    2018-03-01

    A satellite dedicated for quantum science experiments, has been developed and successfully launched from Jiuquan, China, on August 16, 2016. Two new optical ground stations (OGSs) were built to cooperate with the satellite to complete satellite-ground quantum experiments. OGS corrected its pointing direction by satellite trajectory error to coarse tracking system and uplink beacon sight, therefore fine tracking CCD and uplink beacon optical axis alignment accuracy was to ensure that beacon could cover the quantum satellite in all time when it passed the OGSs. Unfortunately, when we tested specifications of the OGSs, due to the coarse tracking optical system was commercial telescopes, the change of position of the target in the coarse CCD was up to 600μrad along with the change of elevation angle. In this paper, a method of reduce alignment error between beacon beam and fine tracking CCD is proposed. Firstly, OGS fitted the curve of target positions in coarse CCD along with the change of elevation angle. Secondly, OGS fitted the curve of hexapod secondary mirror positions along with the change of elevation angle. Thirdly, when tracking satellite, the fine tracking error unloaded on the real-time zero point position of coarse CCD which computed by the firstly calibration data. Simultaneously the positions of the hexapod secondary mirror were adjusted by the secondly calibration data. Finally the experiment result is proposed. Results show that the alignment error is less than 50μrad.

  2. Pembangunan Tools Audit Sistem Informasi Berdasarkan COBIT 5 pada Domain Align, Plan, And Organize (APO

    Directory of Open Access Journals (Sweden)

    Mukhammad Ilham Nur Faizin

    2015-10-01

    Full Text Available Fast growth of information technology (IT encourages the implementation of IT governance processes to achieve its purposes. To determine its achievement, several tools in a checklist form is required to ease the measurement of purpose achievement and process capability level. This study aims to develop capability level measurement tools which can help in information system audit process based on COBIT 5 in domain of Align, Plan, and Organize (APO. The development of capability level measurement tools was done in four stages. The first stage was the analysis about variables or indicators needed in the making of the measurement checklist based on COBIT 5 and Panduan Tata Kelola TIK Nasional (National ITC Governance Guide. The second stage was the content and the tools design. The third stage was building the tools using a spreadsheet software. The fourth stage was the tools evaluation by giving a questionnaire to its users. Respondents involved were the staff of Directorate Information System of Airlangga University. The components of evaluated tools consisted of its contents, interfaces, as well as its functions and operations. The result was used as a base for tools improvements. This study produces tools that gives outcomes in the form of current process capability level and improvement advices to achieve the expected capability level. Evaluation result shows that 86% of users agree that the tools have understandable contents and good interface, and 81% of users agrees that the tools have good functions and operations.

  3. Sub-5 nm, globally aligned graphene nanoribbons on Ge(001)

    Energy Technology Data Exchange (ETDEWEB)

    Kiraly, Brian; Mannix, Andrew J. [Center for Nanoscale Materials, Argonne National Laboratory, 9700 South Cass Avenue, Building 440, Argonne, Illinois 60439 (United States); Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208 (United States); Jacobberger, Robert M.; Arnold, Michael S. [Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706 (United States); Fisher, Brandon L.; Guisinger, Nathan P., E-mail: nguisinger@anl.gov, E-mail: m-hersam@northwestern.edu [Center for Nanoscale Materials, Argonne National Laboratory, 9700 South Cass Avenue, Building 440, Argonne, Illinois 60439 (United States); Hersam, Mark C., E-mail: nguisinger@anl.gov, E-mail: m-hersam@northwestern.edu [Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208 (United States); Department of Chemistry, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208 (United States)

    2016-05-23

    Graphene nanoribbons (GNRs) hold great promise for future electronics because of their edge and width dependent electronic bandgaps and exceptional transport properties. While significant progress toward GNR devices has been made, the field has been limited by difficulties achieving narrow widths, global alignment, and atomically pristine GNR edges on technologically relevant substrates. A recent advance has challenged these limits by using Ge(001) substrates to direct the bottom-up growth of GNRs with nearly pristine armchair edges and widths near ∼10 nm via atmospheric pressure chemical vapor deposition. In this work, the growth of GNRs on Ge(001) is extended to ultra-high vacuum conditions, resulting in the realization of GNRs with widths narrower than 5 nm. Armchair graphene nanoribbons oriented along Ge 〈110〉 surface directions are achieved with excellent width control and relatively large bandgaps. The bandgap magnitude and electronic uniformity of these sub-5 nm GNRs are well-suited for emerging nanoelectronic applications.

  4. Note: Non-invasive optical method for rapid determination of alignment degree of oriented nanofibrous layers

    Energy Technology Data Exchange (ETDEWEB)

    Pokorny, M.; Rebicek, J. [R& D Department, Contipro Biotech s.r.o., 561 02 Dolni Dobrouc (Czech Republic); Klemes, J. [R& D Department, Contipro Pharma a.s., 561 02 Dolni Dobrouc (Czech Republic); Kotzianova, A. [R& D Department, Contipro Pharma a.s., 561 02 Dolni Dobrouc (Czech Republic); Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno (Czech Republic); Velebny, V. [R& D Department, Contipro Biotech s.r.o., 561 02 Dolni Dobrouc (Czech Republic); R& D Department, Contipro Pharma a.s., 561 02 Dolni Dobrouc (Czech Republic)

    2015-10-15

    This paper presents a rapid non-destructive method that provides information on the anisotropic internal structure of nanofibrous layers. A laser beam of a wavelength of 632.8 nm is directed at and passes through a nanofibrous layer prepared by electrostatic spinning. Information about the structural arrangement of nanofibers in the layer is directly visible in the form of a diffraction image formed on a projection screen or obtained from measured intensities of the laser beam passing through the sample which are determined by the dependency of the angle of the main direction of polarization of the laser beam on the axis of alignment of nanofibers in the sample. Both optical methods were verified on Polyvinyl alcohol (PVA) nanofibrous layers (fiber diameter of 470 nm) with random, single-axis aligned and crossed structures. The obtained results match the results of commonly used methods which apply the analysis of electron microscope images. The presented simple method not only allows samples to be analysed much more rapidly and without damaging them but it also makes possible the analysis of much larger areas, up to several square millimetres, at the same time.

  5. Note: Non-invasive optical method for rapid determination of alignment degree of oriented nanofibrous layers

    International Nuclear Information System (INIS)

    Pokorny, M.; Rebicek, J.; Klemes, J.; Kotzianova, A.; Velebny, V.

    2015-01-01

    This paper presents a rapid non-destructive method that provides information on the anisotropic internal structure of nanofibrous layers. A laser beam of a wavelength of 632.8 nm is directed at and passes through a nanofibrous layer prepared by electrostatic spinning. Information about the structural arrangement of nanofibers in the layer is directly visible in the form of a diffraction image formed on a projection screen or obtained from measured intensities of the laser beam passing through the sample which are determined by the dependency of the angle of the main direction of polarization of the laser beam on the axis of alignment of nanofibers in the sample. Both optical methods were verified on Polyvinyl alcohol (PVA) nanofibrous layers (fiber diameter of 470 nm) with random, single-axis aligned and crossed structures. The obtained results match the results of commonly used methods which apply the analysis of electron microscope images. The presented simple method not only allows samples to be analysed much more rapidly and without damaging them but it also makes possible the analysis of much larger areas, up to several square millimetres, at the same time

  6. An IMU-to-Body Alignment Method Applied to Human Gait Analysis

    Directory of Open Access Journals (Sweden)

    Laura Susana Vargas-Valencia

    2016-12-01

    Full Text Available This paper presents a novel calibration procedure as a simple, yet powerful, method to place and align inertial sensors with body segments. The calibration can be easily replicated without the need of any additional tools. The proposed method is validated in three different applications: a computer mathematical simulation; a simplified joint composed of two semi-spheres interconnected by a universal goniometer; and a real gait test with five able-bodied subjects. Simulation results demonstrate that, after the calibration method is applied, the joint angles are correctly measured independently of previous sensor placement on the joint, thus validating the proposed procedure. In the cases of a simplified joint and a real gait test with human volunteers, the method also performs correctly, although secondary plane errors appear when compared with the simulation results. We believe that such errors are caused by limitations of the current inertial measurement unit (IMU technology and fusion algorithms. In conclusion, the presented calibration procedure is an interesting option to solve the alignment problem when using IMUs for gait analysis.

  7. SRF cavity alignment detection method using beam-induced HOM with curved beam orbit

    Science.gov (United States)

    Hattori, Ayaka; Hayano, Hitoshi

    2017-09-01

    We have developed a method to obtain mechanical centers of nine cell superconducting radio frequency (SRF) cavities from localized dipole modes, that is one of the higher order modes (HOM) induced by low-energy beams. It is to be noted that low-energy beams, which are used as alignment probes, are easy to bend in fringe fields of accelerator cavities. The estimation of the beam passing orbit is important because only information about the beam positions measured by beam position monitors outside the cavities is available. In this case, the alignment information about the cavities can be obtained by optimizing the parameters of the acceleration components over the beam orbit simulation to consistently represent the position of the beam position monitors measured at every beam sweep. We discuss details of the orbit estimation method, and estimate the mechanical center of the localized modes through experiments performed at the STF accelerator. The mechanical center is determined as (x , y) =(0 . 44 ± 0 . 56 mm , - 1 . 95 ± 0 . 40 mm) . We also discuss the error and the applicable range of this method.

  8. 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.

  9. An alignment-free method to find similarity among protein sequences via the general form of Chou's pseudo amino acid composition.

    Science.gov (United States)

    Gupta, M K; Niyogi, R; Misra, M

    2013-01-01

    In this paper, we propose a method to create the 60-dimensional feature vector for protein sequences via the general form of pseudo amino acid composition. The construction of the feature vector is based on the contents of amino acids, total distance of each amino acid from the first amino acid in the protein sequence and the distribution of 20 amino acids. The obtained cosine distance metric (also called the similarity matrix) is used to construct the phylogenetic tree by the neighbour joining method. In order to show the applicability of our approach, we tested it on three proteins: 1) ND5 protein sequences from nine species, 2) ND6 protein sequences from eight species, and 3) 50 coronavirus spike proteins. The results are in agreement with known history and the output from the multiple sequence alignment program ClustalW, which is widely used. We have also compared our phylogenetic results with six other recently proposed alignment-free methods. These comparisons show that our proposed method gives a more consistent biological relationship than the others. In addition, the time complexity is linear and space required is less as compared with other alignment-free methods that use graphical representation. It should be noted that the multiple sequence alignment method has exponential time complexity.

  10. Reliability of lower limb alignment measures using an established landmark-based method with a customized computer software program

    Science.gov (United States)

    Sled, Elizabeth A.; Sheehy, Lisa M.; Felson, David T.; Costigan, Patrick A.; Lam, Miu; Cooke, T. Derek V.

    2010-01-01

    The objective of the study was to evaluate the reliability of frontal plane lower limb alignment measures using a landmark-based method by (1) comparing inter- and intra-reader reliability between measurements of alignment obtained manually with those using a computer program, and (2) determining inter- and intra-reader reliability of computer-assisted alignment measures from full-limb radiographs. An established method for measuring alignment was used, involving selection of 10 femoral and tibial bone landmarks. 1) To compare manual and computer methods, we used digital images and matching paper copies of five alignment patterns simulating healthy and malaligned limbs drawn using AutoCAD. Seven readers were trained in each system. Paper copies were measured manually and repeat measurements were performed daily for 3 days, followed by a similar routine with the digital images using the computer. 2) To examine the reliability of computer-assisted measures from full-limb radiographs, 100 images (200 limbs) were selected as a random sample from 1,500 full-limb digital radiographs which were part of the Multicenter Osteoarthritis (MOST) Study. Three trained readers used the software program to measure alignment twice from the batch of 100 images, with two or more weeks between batch handling. Manual and computer measures of alignment showed excellent agreement (intraclass correlations [ICCs] 0.977 – 0.999 for computer analysis; 0.820 – 0.995 for manual measures). The computer program applied to full-limb radiographs produced alignment measurements with high inter- and intra-reader reliability (ICCs 0.839 – 0.998). In conclusion, alignment measures using a bone landmark-based approach and a computer program were highly reliable between multiple readers. PMID:19882339

  11. Novel method for the production of spin-aligned RI beams in projectile fragmentation reaction with the dispersion matching technique

    Energy Technology Data Exchange (ETDEWEB)

    Ichikawa, Y., E-mail: yuichikawa@phys.titech.ac.jp [Tokyo Institute of Technology, Department of Physics (Japan); Ueno, H. [RIKEN Nishina Center (Japan); Ishii, Y. [Tokyo Institute of Technology, Department of Physics (Japan); Furukawa, T. [Tokyo Metropolitan University, Department of Physics (Japan); Yoshimi, A. [Okayama University, Research Core for Extreme Quantum World (Japan); Kameda, D.; Watanabe, H.; Aoi, N. [RIKEN Nishina Center (Japan); Asahi, K. [Tokyo Institute of Technology, Department of Physics (Japan); Balabanski, D. L. [Bulgarian Academy of Sciences, Institute for Nuclear Research and Nuclear Energy (Bulgaria); Chevrier, R.; Daugas, J. M. [CEA, DAM, DIF (France); Fukuda, N. [RIKEN Nishina Center (Japan); Georgiev, G. [CSNSM, IN2P3-CNRS, Universite Paris-sud (France); Hayashi, H.; Iijima, H. [Tokyo Institute of Technology, Department of Physics (Japan); Inabe, N. [RIKEN Nishina Center (Japan); Inoue, T. [Tokyo Institute of Technology, Department of Physics (Japan); Ishihara, M.; Kubo, T. [RIKEN Nishina Center (Japan); and others

    2013-05-15

    A novel method to produce spin-aligned rare-isotope (RI) beam has been developed, that is the two-step projectile fragmentation method with a technique of dispersion matching. The present method was verified in an experiment at the RIKEN RIBF, where an RI beam of {sup 32}Al with spin alignment of 8(1) % was successfully produced from a primary beam of {sup 48}Ca, with {sup 33}Al as an intermediate nucleus. Figure of merit of the present method was found to be improved by a factor larger than 50 compared with a conventional method employing single-step projectile fragmentation.

  12. Quality control methods for linear accelerator radiation and mechanical axes alignment.

    Science.gov (United States)

    Létourneau, Daniel; Keller, Harald; Becker, Nathan; Amin, Md Nurul; Norrlinger, Bernhard; Jaffray, David A

    2018-06-01

    The delivery accuracy of highly conformal dose distributions generated using intensity modulation and collimator, gantry, and couch degrees of freedom is directly affected by the quality of the alignment between the radiation beam and the mechanical axes of a linear accelerator. For this purpose, quality control (QC) guidelines recommend a tolerance of ±1 mm for the coincidence of the radiation and mechanical isocenters. Traditional QC methods for assessment of radiation and mechanical axes alignment (based on pointer alignment) are time consuming and complex tasks that provide limited accuracy. In this work, an automated test suite based on an analytical model of the linear accelerator motions was developed to streamline the QC of radiation and mechanical axes alignment. The proposed method used the automated analysis of megavoltage images of two simple task-specific phantoms acquired at different linear accelerator settings to determine the coincidence of the radiation and mechanical isocenters. The sensitivity and accuracy of the test suite were validated by introducing actual misalignments on a linear accelerator between the radiation axis and the mechanical axes using both beam steering and mechanical adjustments of the gantry and couch. The validation demonstrated that the new QC method can detect sub-millimeter misalignment between the radiation axis and the three mechanical axes of rotation. A displacement of the radiation source of 0.2 mm using beam steering parameters was easily detectable with the proposed collimator rotation axis test. Mechanical misalignments of the gantry and couch rotation axes of the same magnitude (0.2 mm) were also detectable using the new gantry and couch rotation axis tests. For the couch rotation axis, the phantom and test design allow detection of both translational and tilt misalignments with the radiation beam axis. For the collimator rotation axis, the test can isolate the misalignment between the beam radiation axis

  13. ATP Bioluminometers Analysis on the Surfaces of Removable Orthodontic Aligners after the Use of Different Cleaning Methods

    Directory of Open Access Journals (Sweden)

    Luca Levrini

    2016-01-01

    Full Text Available Purpose. The aim was to quantify the bacteria concentration on the surface of orthodontic clear aligners using three different cleaning methods. Furthermore the objective was to validate the efficacy of the bioluminometer in assessing the bacteria concentration. Materials and Methods. Twenty subjects (six males and fourteen females undergoing orthodontic therapy with clear aligners (Invisalign® Align Technology, Santa Clara, California were enrolled in this study. The observation time was of six weeks. The patients were instructed to use different cleaning methods (water, brushing with toothpaste, and brushing with toothpaste and use of sodium carbonate and sulphate tablet. At the end of each phase a microbiological analysis was performed using the bioluminometer. Results. The highest bacteria concentration was found on aligners cleaned using only water (583 relative light units; a value of 189 relative light units was found on aligners cleaned with brushing and toothpaste. The lowest bacteria concentration was recorded on aligners cleaned with brushing and toothpaste and the use of sodium carbonate and sulfate tablet. Conclusions. The mechanical removal of the bacterial biofilm proved to be effective with brushing and toothpaste. The best results in terms of bacteria concentration were achieved adding the use of sodium carbonate and sulfate tablet.

  14. ATP Bioluminometers Analysis on the Surfaces of Removable Orthodontic Aligners after the Use of Different Cleaning Methods.

    Science.gov (United States)

    Levrini, Luca; Mangano, Alessandro; Margherini, Silvia; Tenconi, Camilla; Vigetti, Davide; Muollo, Raffaele; Marco Abbate, Gian

    2016-01-01

    Purpose. The aim was to quantify the bacteria concentration on the surface of orthodontic clear aligners using three different cleaning methods. Furthermore the objective was to validate the efficacy of the bioluminometer in assessing the bacteria concentration. Materials and Methods. Twenty subjects (six males and fourteen females) undergoing orthodontic therapy with clear aligners (Invisalign® Align Technology, Santa Clara, California) were enrolled in this study. The observation time was of six weeks. The patients were instructed to use different cleaning methods (water, brushing with toothpaste, and brushing with toothpaste and use of sodium carbonate and sulphate tablet). At the end of each phase a microbiological analysis was performed using the bioluminometer. Results. The highest bacteria concentration was found on aligners cleaned using only water (583 relative light units); a value of 189 relative light units was found on aligners cleaned with brushing and toothpaste. The lowest bacteria concentration was recorded on aligners cleaned with brushing and toothpaste and the use of sodium carbonate and sulfate tablet. Conclusions. The mechanical removal of the bacterial biofilm proved to be effective with brushing and toothpaste. The best results in terms of bacteria concentration were achieved adding the use of sodium carbonate and sulfate tablet.

  15. Alignment and position visualization methods for the biomedical imaging and therapy (BMIT) MRT lift

    International Nuclear Information System (INIS)

    Bree, Michael; Miller, Denise; Kerr, Graham; Belev, George; Wysokinski, Tomasz W.; Dolton, Wade

    2016-01-01

    The Microbeam Radiation Therapy (MRT) Lift is an eight stage positioning and scanning system at the Canadian Light Source’s BMIT Facility. Alignment of the sample with the beam using the MRT Lift is a time consuming and challenging task. The BMIT Group has developed a Python-based MRT Lift positioning and control program that uses a combination of computational and iterative methods to independently adjust the sample’s X, Y, Z, pitch and roll positions. The program offers “1-Click” alignment of the sample to the beam. Use of a wireframe visualization technique enables even minute movements to be illustrated. Proposed movements and the resulting MRT Lift position can be manually verified before being applied. Optional integration with the SolidWorks modelling platform allows high quality renderings of the MRT Lift in its current or proposed position to be displayed in real time. Human factors principles are incorporated into the program with the objective of delivering easy to use controls for this complex device.

  16. Alignment and position visualization methods for the biomedical imaging and therapy (BMIT) MRT lift

    Energy Technology Data Exchange (ETDEWEB)

    Bree, Michael, E-mail: michael.bree@lightsource.ca; Miller, Denise; Kerr, Graham; Belev, George; Wysokinski, Tomasz W.; Dolton, Wade [Canadian Light Source Inc., 44 Innovation Blvd, Saskatoon, SK S7N 2V3 Canada (Canada)

    2016-07-27

    The Microbeam Radiation Therapy (MRT) Lift is an eight stage positioning and scanning system at the Canadian Light Source’s BMIT Facility. Alignment of the sample with the beam using the MRT Lift is a time consuming and challenging task. The BMIT Group has developed a Python-based MRT Lift positioning and control program that uses a combination of computational and iterative methods to independently adjust the sample’s X, Y, Z, pitch and roll positions. The program offers “1-Click” alignment of the sample to the beam. Use of a wireframe visualization technique enables even minute movements to be illustrated. Proposed movements and the resulting MRT Lift position can be manually verified before being applied. Optional integration with the SolidWorks modelling platform allows high quality renderings of the MRT Lift in its current or proposed position to be displayed in real time. Human factors principles are incorporated into the program with the objective of delivering easy to use controls for this complex device.

  17. Synthesis and assessment methods for an edge-alignment-free hybrid image

    Science.gov (United States)

    Sripian, Peeraya; Yamaguchi, Yasushi

    2017-07-01

    A hybrid image allows multiple image interpretations to be modulated by the viewing distance. It can be constructed on the basis of the multiscale perceptual mechanisms of the human visual system by combining the low and high spatial frequencies of two different images. The hybrid image was introduced as an experimental tool for visual recognition study in terms of spatial frequency perception. To produce a compelling hybrid image, the original hybrid image synthesis method could only use similar shapes of source images that were aligned in the edges. If any two different images can be hybrid, it would be beneficial as a new experimental tool. In addition, there is no measure for the actual perception of spatial frequency, whether a single spatial frequency or both spatial frequencies are perceived from the hybrid stimulus. This paper describes two methods for synthesizing a hybrid image from dissimilar shape images or unaligned images; this hybrid image is known as an "edge-alignment-free hybrid image." A noise-inserted method can be done by intentionally inserting and enhancing noises into the high-frequency image. With this method, the low-frequency blobs are covered with high-frequency noises when viewed up close. A color-inserted method uses complementary color gratings in the background of the high-frequency image to emphasize the high-frequency image when viewed up close, whereas the gratings disappear when viewed from far away. To ascertain that our approach successfully separates the spatial frequency at each viewing distance, we measured this property using our proposed assessment method. Our proposed method allows the experimenter to quantify the probability of perceiving both spatial frequencies and a single spatial frequency in a hybrid image. The experimental results confirmed that our proposed synthesis methods successfully hid the low-frequency image and emphasized the high-frequency image at a close viewing distance. At the same time, the

  18. System and method for aligning heliostats of a solar power tower

    Science.gov (United States)

    Convery, Mark R.

    2013-01-01

    Disclosed is a solar power tower heliostat alignment system and method that includes a solar power tower with a focal area, a plurality of heliostats that each reflect sunlight towards the focal area of the solar power tower, an off-focal area location substantially close to the focal area of the solar power tower, a communication link between the off-focal area location and a misaligned heliostat, and a processor that interprets the communication between the off-focal area location and the misaligned heliostat to identify the misaligned heliostat from the plurality of heliostats and that determines a correction for the identified misaligned heliostat to realign the misaligned heliostat to reflect sunlight towards the focal area of the solar power tower.

  19. Genomic signal processing methods for computation of alignment-free distances from DNA sequences.

    Science.gov (United States)

    Borrayo, Ernesto; Mendizabal-Ruiz, E Gerardo; Vélez-Pérez, Hugo; Romo-Vázquez, Rebeca; Mendizabal, Adriana P; Morales, J Alejandro

    2014-01-01

    Genomic signal processing (GSP) refers to the use of digital signal processing (DSP) tools for analyzing genomic data such as DNA sequences. A possible application of GSP that has not been fully explored is the computation of the distance between a pair of sequences. In this work we present GAFD, a novel GSP alignment-free distance computation method. We introduce a DNA sequence-to-signal mapping function based on the employment of doublet values, which increases the number of possible amplitude values for the generated signal. Additionally, we explore the use of three DSP distance metrics as descriptors for categorizing DNA signal fragments. Our results indicate the feasibility of employing GAFD for computing sequence distances and the use of descriptors for characterizing DNA fragments.

  20. Transducer-actuator systems and methods for performing on-machine measurements and automatic part alignment

    Science.gov (United States)

    Barkman, William E.; Dow, Thomas A.; Garrard, Kenneth P.; Marston, Zachary

    2016-07-12

    Systems and methods for performing on-machine measurements and automatic part alignment, including: a measurement component operable for determining the position of a part on a machine; and an actuation component operable for adjusting the position of the part by contacting the part with a predetermined force responsive to the determined position of the part. The measurement component consists of a transducer. The actuation component consists of a linear actuator. Optionally, the measurement component and the actuation component consist of a single linear actuator operable for contacting the part with a first lighter force for determining the position of the part and with a second harder force for adjusting the position of the part. The actuation component is utilized in a substantially horizontal configuration and the effects of gravitational drop of the part are accounted for in the force applied and the timing of the contact.

  1. 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

  2. Simple method of testing polymer leaching from thermoplastic sheets used for clear aligner

    Directory of Open Access Journals (Sweden)

    Shuvana Altaf Ansari

    2014-01-01

    Full Text Available Objective: With the increasing popularity of clear aligners, newer materials are introduced in the form of thermoplastic sheets. Long-term studies testing the biocompatibility of these sheets are not available. The purpose of this study is to provide a simple, yet effective method to evaluate their leaching potential. Materials and Methods: Using the oxidation reduction reaction taking place in the presence of two different concentrations of potassium permanganate, five different samples were tested. The sequence of colour change from purple to red to brown to yellow to clear was used to determine the amount of leaching. This is the result of a stoichiometric relation between the oxidizing agent and the reducing sample. Color changes were observed through naked eyes over a period of 24 h. Photographs were taken at 15 min, 8 h and 24 h using D-SLR1000 Canon camera. Photos were evaluated separately. Result: Diluted solution showed faster change in color, due to the lesser amount of reagent. 3A Medes (Korea was the first to leach, followed by CA (Scheu, Germany EVA (Endent Private Limited, Delhi, India, Ultradent (United States and Avac R (Jaypee, Kerela, India. Conclusion: "Do it yourself" test is a repeatable and reproducible method that can be modified and used in clinical practice as a chair side method.

  3. NGSS-Aligned, K-12 Climate Science Curricula, taught with citizen science and teacher-led inquiry methods

    Science.gov (United States)

    Zainfeld, S.

    2017-12-01

    Teacher-led inquiry into student learning is a promising method of formative assessment to gain insight into student achievement. NGSS-aligned K-12 Climate Science curricula taught with citizen science and teacher-led inquiry methods are described, along with results from a scientist-teacher collaboration survey.

  4. Wet etch methods for InAs nanowire patterning and self-aligned electrical contacts

    Science.gov (United States)

    Fülöp, G.; d'Hollosy, S.; Hofstetter, L.; Baumgartner, A.; Nygård, J.; Schönenberger, C.; Csonka, S.

    2016-05-01

    Advanced synthesis of semiconductor nanowires (NWs) enables their application in diverse fields, notably in chemical and electrical sensing, photovoltaics, or quantum electronic devices. In particular, indium arsenide (InAs) NWs are an ideal platform for quantum devices, e.g. they may host topological Majorana states. While the synthesis has been continously perfected, only a few techniques have been developed to tailor individual NWs after growth. Here we present three wet chemical etch methods for the post-growth morphological engineering of InAs NWs on the sub-100 nm scale. The first two methods allow the formation of self-aligned electrical contacts to etched NWs, while the third method results in conical shaped NW profiles ideal for creating smooth electrical potential gradients and shallow barriers. Low temperature experiments show that NWs with etched segments have stable transport characteristics and can serve as building blocks of quantum electronic devices. As an example we report the formation of a single electrically stable quantum dot between two etched NW segments.

  5. A Method for Functional Task Alignment Analysis of an Arthrocentesis Simulator.

    Science.gov (United States)

    Adams, Reid A; Gilbert, Gregory E; Buckley, Lisa A; Nino Fong, Rodolfo; Fuentealba, I Carmen; Little, Erika L

    2018-05-16

    During simulation-based education, simulators are subjected to procedures composed of a variety of tasks and processes. Simulators should functionally represent a patient in response to the physical action of these tasks. The aim of this work was to describe a method for determining whether a simulator does or does not have sufficient functional task alignment (FTA) to be used in a simulation. Potential performance checklist items were gathered from published arthrocentesis guidelines and aggregated into a performance checklist using Lawshe's method. An expert panel used this performance checklist and an FTA analysis questionnaire to evaluate a simulator's ability to respond to the physical actions required by the performance checklist. Thirteen items, from a pool of 39, were included on the performance checklist. Experts had mixed reviews of the simulator's FTA and its suitability for use in simulation. Unexpectedly, some positive FTA was found for several tasks where the simulator lacked functionality. By developing a detailed list of specific tasks required to complete a clinical procedure, and surveying experts on the simulator's response to those actions, educators can gain insight into the simulator's clinical accuracy and suitability. Unexpected of positive FTA ratings of function deficits suggest that further revision of the survey method is required.

  6. Application of Improved 5th-Cubature Kalman Filter in Initial Strapdown Inertial Navigation System Alignment for Large Misalignment Angles.

    Science.gov (United States)

    Wang, Wei; Chen, Xiyuan

    2018-02-23

    In view of the fact the accuracy of the third-degree Cubature Kalman Filter (CKF) used for initial alignment under large misalignment angle conditions is insufficient, an improved fifth-degree CKF algorithm is proposed in this paper. In order to make full use of the innovation on filtering, the innovation covariance matrix is calculated recursively by an innovative sequence with an exponent fading factor. Then a new adaptive error covariance matrix scaling algorithm is proposed. The Singular Value Decomposition (SVD) method is used for improving the numerical stability of the fifth-degree CKF in this paper. In order to avoid the overshoot caused by excessive scaling of error covariance matrix during the convergence stage, the scaling scheme is terminated when the gradient of azimuth reaches the maximum. The experimental results show that the improved algorithm has better alignment accuracy with large misalignment angles than the traditional algorithm.

  7. Grain alignment in bulk YBa2Cu3Ox superconductor by a low temperature phase transformation method

    International Nuclear Information System (INIS)

    Selvamanickam, V.; Goyal, A.; Kroeger, D.M.

    1994-01-01

    A quench and directional phase transformation process has been developed to achieve grain alignment in bulk YBa 2 Cu 3 O x superconductors at temperatures about 100 degree C below the peritectic temperature. Isothermal phase transformation of quenched precursors at 890 degree C for 3 min is found to result in the formation of more than 75% of YBa 2 Cu 3 O x phase without any formation of Y 2 BaCuO 5 . Phase transformation at higher temperatures leads to rapid formation of Y 2 BaCuO 5 in addition to YBa 2 Cu 3 O x . A well-aligned microstructure is achieved by directional phase transformation of the quenched compacts as a rate of 10 mm/h. The magnetic field dependence of the critical current density at 77 K of the directionally phase transformed material compares well with that of melt-textured YBCO and is superior to that of magnetically aligned and sintered YBCO

  8. Development and preliminary evaluation of a new anatomically based prosthetic alignment method for below-knee prosthesis.

    Science.gov (United States)

    Tafti, Nahid; Karimlou, Masoud; Mardani, Mohammad Ali; Jafarpisheh, Amir Salar; Aminian, Gholam Reza; Safari, Reza

    2018-04-20

    The objectives of current study were to a) assess similarities and relationships between anatomical landmark-based angles and distances of lower limbs in unilateral transtibial amputees and b) develop and evaluate a new anatomically based static prosthetic alignment method. First sub-study assessed the anthropometrical differences and relationships between the lower limbs in the photographs taken from amputees. Data were analysed via paired t-test and regression analysis. Results show no significant differences in frontal and transverse planes. In the sagittal plane, the anthropometric parameters of the amputated limb were significantly correlated to the corresponding variables of the sound limb. The results served as bases for the development of a new prosthetic alignment method. The method was evaluated on a single subject study. Prosthetic alignment carried out by an experienced prosthetist was compared with such alignment adjusted by an inexperienced prosthetist but with the use of the developed method. In sagittal and frontal planes, the socket angle was tuned with respect to the shin angle, and the position of the prosthetic foot was tuned in relation to the pelvic landmarks. Further study is needed to assess the proposed method on a larger sample of amputees and prosthetists.

  9. Composite Materials with Magnetically Aligned Carbon Nanoparticles Having Enhanced Electrical Properties and Methods of Preparation

    Science.gov (United States)

    Hong, Haiping (Inventor); Peterson, G.P. (Bud) (Inventor); Salem, David R. (Inventor)

    2016-01-01

    Magnetically aligned carbon nanoparticle composites have enhanced electrical properties. The composites comprise carbon nanoparticles, a host material, magnetically sensitive nanoparticles and a surfactant. In addition to enhanced electrical properties, the composites can have enhanced mechanical and thermal properties.

  10. Constrained-DFT method for accurate energy-level alignment of metal/molecule interfaces

    KAUST Repository

    Souza, A. M.

    2013-10-07

    We present a computational scheme for extracting the energy-level alignment of a metal/molecule interface, based on constrained density functional theory and local exchange and correlation functionals. The method, applied here to benzene on Li(100), allows us to evaluate charge-transfer energies, as well as the spatial distribution of the image charge induced on the metal surface. We systematically study the energies for charge transfer from the molecule to the substrate as function of the molecule-substrate distance, and investigate the effects arising from image-charge confinement and local charge neutrality violation. For benzene on Li(100) we find that the image-charge plane is located at about 1.8 Å above the Li surface, and that our calculated charge-transfer energies compare perfectly with those obtained with a classical electrostatic model having the image plane located at the same position. The methodology outlined here can be applied to study any metal/organic interface in the weak coupling limit at the computational cost of a total energy calculation. Most importantly, as the scheme is based on total energies and not on correcting the Kohn-Sham quasiparticle spectrum, accurate results can be obtained with local/semilocal exchange and correlation functionals. This enables a systematic approach to convergence.

  11. Constrained-DFT method for accurate energy-level alignment of metal/molecule interfaces

    KAUST Repository

    Souza, A. M.; Rungger, I.; Pemmaraju, C. D.; Schwingenschlö gl, Udo; Sanvito, S.

    2013-01-01

    We present a computational scheme for extracting the energy-level alignment of a metal/molecule interface, based on constrained density functional theory and local exchange and correlation functionals. The method, applied here to benzene on Li(100), allows us to evaluate charge-transfer energies, as well as the spatial distribution of the image charge induced on the metal surface. We systematically study the energies for charge transfer from the molecule to the substrate as function of the molecule-substrate distance, and investigate the effects arising from image-charge confinement and local charge neutrality violation. For benzene on Li(100) we find that the image-charge plane is located at about 1.8 Å above the Li surface, and that our calculated charge-transfer energies compare perfectly with those obtained with a classical electrostatic model having the image plane located at the same position. The methodology outlined here can be applied to study any metal/organic interface in the weak coupling limit at the computational cost of a total energy calculation. Most importantly, as the scheme is based on total energies and not on correcting the Kohn-Sham quasiparticle spectrum, accurate results can be obtained with local/semilocal exchange and correlation functionals. This enables a systematic approach to convergence.

  12. 5 CFR 950.602 - Solicitation methods.

    Science.gov (United States)

    2010-01-01

    ... 5 Administrative Personnel 2 2010-01-01 2010-01-01 false Solicitation methods. 950.602 Section 950... VOLUNTARY ORGANIZATIONS Miscellaneous Provisions § 950.602 Solicitation methods. (a) Employee solicitations shall be conducted during duty hours using methods that permit true voluntary giving and shall reserve...

  13. 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.

  14. Optical Alignment of the Chromospheric Lyman-Alpha SpectroPolarimeter using Sophisticated Methods to Minimize Activities under Vacuum

    Science.gov (United States)

    Giono, G.; Katsukawa, Y.; Ishikawa, R.; Narukage, N.; Kano, R.; Kubo, M.; Ishikawa, S.; Bando, T.; Hara, H.; Suematsu, Y.; hide

    2016-01-01

    The Chromospheric Lyman-Alpha Spectro-Polarimeter (CLASP) is a sounding-rocket instrument developed at the National Astronomical Observatory of Japan (NAOJ) as a part of an international collaboration. The in- strument main scientific goal is to achieve polarization measurement of the Lyman-alpha line at 121.56 nm emitted from the solar upper-chromosphere and transition region with an unprecedented 0.1% accuracy. For this purpose, the optics are composed of a Cassegrain telescope coated with a "cold mirror" coating optimized for UV reflection and a dual-channel spectrograph allowing for simultaneous observation of the two orthogonal states of polarization. Although the polarization sensitivity is the most important aspect of the instrument, the spatial and spectral resolutions of the instrument are also crucial to observe the chromospheric features and resolve the Ly- pro les. A precise alignment of the optics is required to ensure the resolutions, but experiments under vacuum conditions are needed since Ly-alpha is absorbed by air, making the alignment experiments difficult. To bypass this issue, we developed methods to align the telescope and the spectrograph separately in visible light. We will explain these methods and present the results for the optical alignment of the CLASP telescope and spectrograph. We will then discuss the combined performances of both parts to derive the expected resolutions of the instrument, and compare them with the flight observations performed on September 3rd 2015.

  15. Using lexical and logical methods for the alignment of medical terminologies

    NARCIS (Netherlands)

    Klein, Michel; Aleksovski, Zharko

    2005-01-01

    Standardized medical terminologies are often used for the registration of patient data. In several situations there is a need to align these terminologies to other terminologies. Even when the terminologies cover the same domain, this is often a non-trivial task. The task is even more complicated

  16. Enterprise strategic alignment method: a cross-disciplinary capability-driven approach

    NARCIS (Netherlands)

    Aldea, Adina

    2017-01-01

    The environment of organisations is changing more rapidly in the recent years, which makes it increasingly more difficult to stay competitive. Organisations need to ensure that when they make transformations, they focus on maintaining or improving their strategic alignment. However, the current

  17. The analysis of the accuracy of the wheel alignment inspection method on the side-slip plate stand

    Science.gov (United States)

    Gajek, A.; Strzępek, P.

    2016-09-01

    The article presents the theoretical basis and the results of the examination of the wheel alignment inspection method on the slide slip plate stand. It is obligatory test during periodic technical inspection of the vehicle. The measurement is executed in the dynamic conditions. The dependence between the lateral displacement of the plate and toe-in of the tested wheels has been shown. If the diameter of the wheel rim is known then the value of the toe-in can be calculated. The comparison of the toe-in measurements on the plate stand and on the four heads device for the wheel alignment inspection has been carried out. The accuracy of the measurements and the influence of the conditions of the tests on the plate stand (the way of passing through the plate) were estimated. The conclusions about the accuracy of this method are presented.

  18. 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 ...

  19. How Do DSM-5 Personality Traits Align With Schema Therapy Constructs?

    Science.gov (United States)

    Bach, Bo; Lee, Christopher; Mortensen, Erik Lykke; Simonsen, Erik

    2016-08-01

    DSM-5 offers an alternative model of personality pathology that includes 25 traits. Although personality disorders are mostly treated with psychotherapy, the correspondence between DSM-5 traits and concepts in evidence-based psychotherapy has not yet been evaluated adequately. Suitably, schema therapy was developed for treating personality disorders, and it has achieved promising evidence. The authors examined associations between DSM-5 traits and schema therapy constructs in a mixed sample of 662 adults, including 312 clinical participants. Associations were investigated in terms of factor loadings and regression coefficients in relation to five domains, followed by specific correlations among all constructs. The results indicated conceptually coherent associations, and 15 of 25 traits were strongly related to relevant schema therapy constructs. Conclusively, DSM-5 traits may be considered expressions of schema therapy constructs, which psychotherapists might take advantage of in terms of case formulation and targets of treatment. In turn, schema therapy constructs add theoretical understanding to DSM-5 traits.

  20. How Do DSM-5 Personality Traits Align With Schema Therapy Constructs?

    DEFF Research Database (Denmark)

    Bach, Bo; Lee, Christopher; Mortensen, Erik Lykke

    2016-01-01

    therapy was developed for treating personality disorders, and it has achieved promising evidence. The authors examined associations between DSM-5 traits and schema therapy constructs in a mixed sample of 662 adults, including 312 clinical participants. Associations were investigated in terms of factor......DSM-5 offers an alternative model of personality pathology that includes 25 traits. Although personality disorders are mostly treated with psychotherapy, the correspondence between DSM-5 traits and concepts in evidence-based psychotherapy has not yet been evaluated adequately. Suitably, schema...

  1. A new standard method for the surveying and alignment of beamline facilities at GSI

    Energy Technology Data Exchange (ETDEWEB)

    Wirth, H. [Metronom, Gesellschaft fuer Industrievermessung mbH, Mainz (Germany); Moritz, G.

    1996-01-01

    The GSI institute of heavy ion research is financed by the country of Germany. Founded in 1969, the main emphasis of the institute`s work is the research of the characteristics of atomic nuclei. The Universal Linear Accelerator UNILAC was built first and in 1987 new facilities were added to the setup. The GSI accelarators allow acceleration of all atomic nuclei up to Uranium to an energy of 20 MeV/u. In 1993 Metronome started working on a new alignment concept for the GSI`s accelerators. Metronome has developed the TASA concept. TSAS stands for Techeometric Accelerator Surveying and Alignment and is based on the new generation of high-precision total stations. One feature included in the TASA Concept, has been the replacement of all mobile plates by fixed consoles. An immense advantage of new fixed consoles, welded onto every component, is that they can be positioned to locations where they can be easily measured, simply by taking measuring conditions (lines of sight, heights of stands, error-figures, configuration, etc.) into consideration. The TASA Concept can be used for all alignments of the different GSI accelerators. For all accelerators a special investigation was carried out to check if it is possible to position a new pillar system and to install new consoles on the components. The free positioning of fiducial points makes it possible to use polar measurements for all components. This is an enormous advantage and a step forward for alignment procedures at GSI. Furthermore, use of a total station as opposed to the ECDS System means that one operator less is needed. (S.Y.)

  2. Electron re-scattering from aligned linear molecules using the R-matrix method

    International Nuclear Information System (INIS)

    Harvey, A G; Tennyson, J

    2009-01-01

    Electron re-scattering in a strong laser field provides an important probe of molecular structure and processes. The laser field drives the ionization of the molecule, followed by acceleration and subsequent recollision of the electron with the parent molecular ion, the scattered electrons carry information about the nuclear geometry and electronic states of the molecular ion. It is advantageous in strong field experiments to work with aligned molecules, which introduces extra physics compared to the standard gas-phase, electron-molecule scattering problem. The formalism for scattering from oriented linear molecules is presented and applied to H 2 and CO 2 . Differential cross sections are presented for (re-)scattering by these systems concentrating on the most common, linear alignment. In H 2 these cross sections show significant angular structure which, particularly for a scattering angle of 90 deg., are predicted to vary significantly between re-collisions stimulated by an even or an odd number of photons. In CO 2 these cross sections are zero indicating the necessity of using non-parallel alignment with this molecule.

  3. The ion capturing effect of 5° SiOx alignment films in liquid crystal devices

    Science.gov (United States)

    Huang, Yi; Bos, Philip J.; Bhowmik, Achintya

    2010-09-01

    We show that SiOx, deposited at 5° to the interior surface of a liquid crystal cell allows for a surprisingly substantial reduction in the ion concentration of liquid crystal devices. We have investigated this effect and found that this type of film, due to its surface morphology, captures ions from the liquid crystal material. Ion adsorption on 5° SiOx film obeys the Langmuir isotherm. Experimental results shown allow estimation of the ion capturing capacity of these films to be more than an order of 10 000/μm2. These types of materials are useful for new types of very low power liquid crystal devices such as e-books.

  4. Structural and photoluminescence properties of aligned Sb-doped ZnO nanocolumns synthesized by the hydrothermal method

    Energy Technology Data Exchange (ETDEWEB)

    Fang Xuan [School of Science, Changchun University of Science and Technology, 7089-WeiXing Road, Changchun, 130022 (China); Key Laboratory of Excited State Processes, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, 16 East Nan-Hu Road, Open Economic Zone Changchun, 130033 (China); Li Jinhua [School of Science, Changchun University of Science and Technology, 7089-WeiXing Road, Changchun, 130022 (China); Zhao Dongxu, E-mail: dxzhao2000@yahoo.com.c [Key Laboratory of Excited State Processes, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, 16 East Nan-Hu Road, Open Economic Zone Changchun, 130033 (China); Li Binghui; Zhang Zhenzhong; Shen Dezhen [Key Laboratory of Excited State Processes, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, 16 East Nan-Hu Road, Open Economic Zone Changchun, 130033 (China); Wang Xiaohua; Wei Zhipeng [School of Science, Changchun University of Science and Technology, 7089-WeiXing Road, Changchun, 130022 (China)

    2010-08-02

    Aligned Sb-doped ZnO nanocolumns were synthesized by a simple hydrothermal method. Based on the analyses of the X-ray diffraction and photoluminescence result, it could be confirmed that the Sb has successfully doped in the ZnO crystal lattices to form an accepter energy level. At 85 K, the recombination of the acceptor-bound exciton was predominant in PL spectrum, which was attributed to the transition of the (Sb{sub Zn}-2V{sub Zn}) complex bound exciton. The acceptor binding energy had been calculated to be 123 meV.

  5. Structural and photoluminescence properties of aligned Sb-doped ZnO nanocolumns synthesized by the hydrothermal method

    International Nuclear Information System (INIS)

    Fang Xuan; Li Jinhua; Zhao Dongxu; Li Binghui; Zhang Zhenzhong; Shen Dezhen; Wang Xiaohua; Wei Zhipeng

    2010-01-01

    Aligned Sb-doped ZnO nanocolumns were synthesized by a simple hydrothermal method. Based on the analyses of the X-ray diffraction and photoluminescence result, it could be confirmed that the Sb has successfully doped in the ZnO crystal lattices to form an accepter energy level. At 85 K, the recombination of the acceptor-bound exciton was predominant in PL spectrum, which was attributed to the transition of the (Sb Zn -2V Zn ) complex bound exciton. The acceptor binding energy had been calculated to be 123 meV.

  6. Standard test method for verifying the alignment of X-Ray diffraction instrumentation for residual stress measurement

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    2010-01-01

    1.1 This test method covers the preparation and use of a flat stress-free test specimen for the purpose of checking the systematic error caused by instrument misalignment or sample positioning in X-ray diffraction residual stress measurement, or both. 1.2 This test method is applicable to apparatus intended for X-ray diffraction macroscopic residual stress measurement in polycrystalline samples employing measurement of a diffraction peak position in the high-back reflection region, and in which the θ, 2θ, and ψ rotation axes can be made to coincide (see Fig. 1). 1.3 This test method describes the use of iron powder which has been investigated in round-robin studies for the purpose of verifying the alignment of instrumentation intended for stress measurement in ferritic or martensitic steels. To verify instrument alignment prior to stress measurement in other metallic alloys and ceramics, powder having the same or lower diffraction angle as the material to be measured should be prepared in similar fashion...

  7. Thin concentrator photovoltaic module with micro-solar cells which are mounted by self-align method using surface tension of melted solder

    Science.gov (United States)

    Hayashi, Nobuhiko; Terauchi, Masaharu; Aya, Youichirou; Kanayama, Shutetsu; Nishitani, Hikaru; Nakagawa, Tohru; Takase, Michihiko

    2017-09-01

    We are developing a thin and lightweight CPV module using small size lens system made from poly methyl methacrylate (PMMA) with a short focal length and micro-solar cells to decrease the transporting and the installing costs of CPV systems. In order to achieve high conversion efficiency in CPV modules using micro-solar cells, the micro-solar cells need to be mounted accurately to the irradiated region of the concentrated sunlight. In this study, we have successfully developed self-align method thanks to the surface tension of the melted solder even utilizing commercially available surface-mounting technology (SMT). Solar cells were self-aligned to the specified positions of the circuit board by this self-align method with accuracy within ±10 µm. We actually fabricated CPV modules using this self-align method and demonstrated high conversion efficiency of our CPV module.

  8. Innovative electron transport methods in EGS5

    International Nuclear Information System (INIS)

    Bielajew, A.F.; Wilderman, S.J.

    2000-01-01

    The initial formulation of a Monte Carlo scheme for the transport of high-energy (>≅ 100 keV) electrons was established by Berger in 1963. Calling his method the 'condensed history theory', Berger combined the theoretical results of the previous generation of research into developing approximate solutions of the Boltzmann transport equation with numerical algorithms for exploiting the power of computers to permit iterative, piece-wise solution of the transport equation in a computationally intensive but much less approximate fashion. The methods devised by Berger, with comparatively little modification, provide the foundation of all present day Monte Carlo electron transport simulation algorithms. Only in the last 15 years, beginning with the development and publication of the PRESTA algorithm, has there been a significant revisitation of the problem of simulating electron transport within the condensed history framework. Research in this area is ongoing, highly active, and far from complete. It presents an enormous challenge, demanding derivation of new analytical transport solutions based on underlying fundamental interaction mechanisms, intuitive insight in the development of computer algorithms, and state of the art computer science skills in order to permit deployment of these techniques in an efficient manner. The EGS5 project, a modern ground-up rewrite of the EGS4 code, is now in the design phase. EGS5 will take modern photon and electron transport algorithms and deploy them in an easy-to-maintain, modern computer language-ANSI-standard C ++. Moreover, the well-known difficulties of applying EGS4 to practical geometries (geometry code development, tally routine design) should be made easier and more intuitive through the use of a visual user interface being designed by Quantum Research, Inc., work that is presented elsewhere in this conference. This report commences with a historical review of electron transport models culminating with the proposal of a

  9. 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

  10. Scanning electron microscopy analysis of the growth of dental plaque on the surfaces of removable orthodontic aligners after the use of different cleaning methods

    Directory of Open Access Journals (Sweden)

    Levrini L

    2015-12-01

    Full Text Available Luca Levrini, Francesca Novara, Silvia Margherini, Camilla Tenconi, Mario Raspanti Department of Surgical and Morphological Sciences, Dental Hygiene School, Research Centre Cranio Facial Disease and Medicine, University of Insubria, Varese, Italy Background: Advances in orthodontics are leading to the use of minimally invasive technologies, such as transparent removable aligners, and are able to meet high demands in terms of performance and esthetics. However, the most correct method of cleaning these appliances, in order to minimize the effects of microbial colonization, remains to be determined. Purpose: The aim of the present study was to identify the most effective method of cleaning removable orthodontic aligners, analyzing the growth of dental plaque as observed under scanning electron microscopy. Methods: Twelve subjects were selected for the study. All were free from caries and periodontal disease and were candidates for orthodontic therapy with invisible orthodontic aligners. The trial had a duration of 6 weeks, divided into three 2-week stages, during which three sets of aligners were used. In each stage, the subjects were asked to use a different method of cleaning their aligners: 1 running water (control condition; 2 effervescent tablets containing sodium carbonate and sulfate crystals followed by brushing with a toothbrush; and 3 brushing alone (with a toothbrush and toothpaste. At the end of each 2-week stage, the surfaces of the aligners were analyzed under scanning electron microscopy. Results: The best results were obtained with brushing combined with the use of sodium carbonate and sulfate crystals; brushing alone gave slightly inferior results. Conclusion: On the basis of previous literature results relating to devices in resin, studies evaluating the reliability of domestic ultrasonic baths for domestic use should be encouraged. At present, pending the availability of experimental evidence, it can be suggested that dental

  11. An Alignment Method for the Integration of Underwater 3D Data Captured by a Stereovision System and an Acoustic Camera

    Directory of Open Access Journals (Sweden)

    Antonio Lagudi

    2016-04-01

    Full Text Available The integration of underwater 3D data captured by acoustic and optical systems is a promising technique in various applications such as mapping or vehicle navigation. It allows for compensating the drawbacks of the low resolution of acoustic sensors and the limitations of optical sensors in bad visibility conditions. Aligning these data is a challenging problem, as it is hard to make a point-to-point correspondence. This paper presents a multi-sensor registration for the automatic integration of 3D data acquired from a stereovision system and a 3D acoustic camera in close-range acquisition. An appropriate rig has been used in the laboratory tests to determine the relative position between the two sensor frames. The experimental results show that our alignment approach, based on the acquisition of a rig in several poses, can be adopted to estimate the rigid transformation between the two heterogeneous sensors. A first estimation of the unknown geometric transformation is obtained by a registration of the two 3D point clouds, but it ends up to be strongly affected by noise and data dispersion. A robust and optimal estimation is obtained by a statistical processing of the transformations computed for each pose. The effectiveness of the method has been demonstrated in this first experimentation of the proposed 3D opto-acoustic camera.

  12. A fully automated and scalable timing probe-based method for time alignment of the LabPET II scanners

    Science.gov (United States)

    Samson, Arnaud; Thibaudeau, Christian; Bouchard, Jonathan; Gaudin, Émilie; Paulin, Caroline; Lecomte, Roger; Fontaine, Réjean

    2018-05-01

    A fully automated time alignment method based on a positron timing probe was developed to correct the channel-to-channel coincidence time dispersion of the LabPET II avalanche photodiode-based positron emission tomography (PET) scanners. The timing probe was designed to directly detect positrons and generate an absolute time reference. The probe-to-channel coincidences are recorded and processed using firmware embedded in the scanner hardware to compute the time differences between detector channels. The time corrections are then applied in real-time to each event in every channel during PET data acquisition to align all coincidence time spectra, thus enhancing the scanner time resolution. When applied to the mouse version of the LabPET II scanner, the calibration of 6 144 channels was performed in less than 15 min and showed a 47% improvement on the overall time resolution of the scanner, decreasing from 7 ns to 3.7 ns full width at half maximum (FWHM).

  13. Low temperature superconductor and aligned high temperature superconductor magnetic dipole system and method for producing high magnetic fields

    Science.gov (United States)

    Gupta, Ramesh; Scanlan, Ronald; Ghosh, Arup K.; Weggel, Robert J.; Palmer, Robert; Anerella, Michael D.; Schmalzle, Jesse

    2017-10-17

    A dipole-magnet system and method for producing high-magnetic-fields, including an open-region located in a radially-central-region to allow particle-beam transport and other uses, low-temperature-superconducting-coils comprised of low-temperature-superconducting-wire located in radially-outward-regions to generate high magnetic-fields, high-temperature-superconducting-coils comprised of high-temperature-superconducting-tape located in radially-inward-regions to generate even higher magnetic-fields and to reduce erroneous fields, support-structures to support the coils against large Lorentz-forces, a liquid-helium-system to cool the coils, and electrical-contacts to allow electric-current into and out of the coils. The high-temperature-superconducting-tape may be comprised of bismuth-strontium-calcium-copper-oxide or rare-earth-metal, barium-copper-oxide (ReBCO) where the rare-earth-metal may be yttrium, samarium, neodymium, or gadolinium. Advantageously, alignment of the large-dimension of the rectangular-cross-section or curved-cross-section of the high-temperature-superconducting-tape with the high-magnetic-field minimizes unwanted erroneous magnetic fields. Alignment may be accomplished by proper positioning, tilting the high-temperature-superconducting-coils, forming the high-temperature-superconducting-coils into a curved-cross-section, placing nonconducting wedge-shaped-material between windings, placing nonconducting curved-and-wedge-shaped-material between windings, or by a combination of these techniques.

  14. A simple method for fabrication of electrospun fibers with controlled degree of alignment having potential for nerve regeneration applications

    Energy Technology Data Exchange (ETDEWEB)

    Vimal, Sunil Kumar; Ahamad, Nadim; Katti, Dhirendra S., E-mail: dsk@iitk.ac.in

    2016-06-01

    In peripheral nerve injuries where direct suturing of nerve endings is not feasible, nerve regeneration has been facilitated through the use of artificially aligned fibrous scaffolds that provide directional growth of neurons to bridge the gap. The degree of fiber alignment is crucial and can impact the directionality of cells in a fibrous scaffold. While there have been multiple approaches that have been used for controlling fiber alignment, however, they have been associated with a compromised control on other properties, such as diameter, morphology, curvature, and topology of fibers. Therefore, the present study demonstrates a modified electrospinning set-up, that enabled fabrication of electrospun fibers with controlled degree of alignment from non-aligned (NA), moderately aligned (MA, 75%) to highly aligned (HA, 95%) sub-micron fibers while keeping other physical properties unchanged. The results demonstrate that the aligned fibers (MA and HA) facilitated directional growth of human astrocytoma cells (U373), wherein the aspect ratio of cells was found to increase with an increase in degree of fibers alignment. In contrast to NA and MA fibers, the HA fibers showed improved contact guidance to U373 cells that was demonstrated by a significantly higher cell aspect ratio and nuclear aspect ratio. In conclusion, the present study demonstrated a modified electrospinning setup to fabricate differentially aligned fibrous scaffolds with the HA fibers showing potential for use in neural tissue engineering. - Highlights: • Modified electrospinning set-up for fabrication of fibers with controlled alignment • Three parameter-based control on the degree of alignment of fibers • The aligned fibers enhanced cell elongation and cell-cell contact. • The aligned fibers show potential for use in nerve regeneration.

  15. One dimensional well-aligned CdO nanocrystal by solvothermal method

    International Nuclear Information System (INIS)

    Kaviyarasu, K.; Manikandan, E.; Paulraj, P.; Mohamed, S.B.; Kennedy, J.

    2014-01-01

    Graphical abstract: - Highlights: • Cadmium oxide (CdO) emerged as one of the important semiconducting materials. • Iodine concentration increases intensity of the peak around 300 cm −1 becomes stronger. • Surface morphology of these crystals has been modified by varying complexing agent. • Nanofibers structure like CdO crystals first time achieved. • The diameters of these nanofibers range mostly between 40 nm and 70 nm. - Abstract: Cadmium oxide (CdO) is a category of the practical semiconductor metal oxides, which is widely applied in various scientific and industrial fields because of its catalytic, optical, and electrical properties. CdO nanocrystal was successfully synthesized by a virtue of a single source precursor method at mild reaction conditions between cadmium oxide, and element iodine by a solvothermal route. X-ray powder diffraction (XRD), ultraviolet spectroscopy studies (UV–vis), Fourier Transform Infrared analysis (FTIR), scanning electron microscopy (SEM), μ-Raman spectroscopy and cyclic voltammogram (CV) were used to characterize the CdO nanocrystals. The ultra-violet visible absorption peaks of CdO exhibited a large blue shift and the luminescent spectra had a strong and broad emission band centered at 228 nm. The various functional groups present in the CdO nanocrystals were identified by FTIR analysis. Intense PL was also observed with some spectral tuning possibly giving a range of emission photon energies approximately spanning from 2.5 to 3.4 eV. Scanning electron microscopy and μ-Raman microscopy images indicated that the morphology of the product is spherical nanoparticles with an average particle size of 46 nm with standard deviation. The electrochemical response of CdO which is proved the nano-cadmium has high functionality due to the small size and it has higher electrochemical activity without any modifications. The above studies demonstrate the potential for the utilization of cadmium nitrite nanocrystal in visible

  16. Field-aligned structure of the storm time Pc 5 wave of November 14-15, 1979

    International Nuclear Information System (INIS)

    Takahashi, K.; Higbie, P.R.; Fennell, J.F.; Amata, E.

    1987-01-01

    Magnetic field data from the four satellites SCATHA (P78-2), GOES 2, GOES 3, and GEOS 2 have been analyzed to examine the magnetic field-aligned structure of a storm time Pc 5 wave that occurred on November 14-15, 1979. The wave had both transverse and compressional components. At a given instance the compressional and the radial components oscillated in phase of 180 degree out of phase, and the compressional and the azimuthal components oscillated +90 degree or -90 degree out of phase. In addition, each component changed its amplitude with magnetic latitude: the compressional component had a minimum at the magnetic equator, whereas the transverse components had a maximum at the equator and minima several degrees off the equator. A 180 degree relative phase switching among the components occurred across the latitudes of amplitude minima. From these observations the field line displacement of the wave is confirmed to have an antisymmetric standing structure about the magnetic equator with a parallel wave length of a few earth radii. The authors also observed other intriguing properties of the wave such as different parallel wave lengths of different field components and small-amplitude second harmonics near the nodes. A dielectric tensor appropriate for the ring current plasma is found to give an explanation for the relation between the polarization and the propagation of the wave. However, plasma data available from SCATHA does not support either the drift mirror instability of A. Hasegawa (1969) or the coupling between a drift mirror wave and a shear Alfven wave as discussed by A.D.M. Walker et al. (1982)

  17. 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...

  18. Engineering survey planning for the alignment of a particle accelerator: part I. Proposition of an assessment method

    Science.gov (United States)

    Junqueira Leão, Rodrigo; Raffaelo Baldo, Crhistian; Collucci da Costa Reis, Maria Luisa; Alves Trabanco, Jorge Luiz

    2018-03-01

    The performance of particle accelerators depends highly on the relative alignment between their components. The position and orientation of the magnetic lenses that form the trajectory of the charged beam is kept to micrometric tolerances in a range of hundreds of meters of the length of the machines. Therefore, the alignment problem is fundamentally of a dimensional metrology nature. There is no common way of expressing these tolerances in terms of terminology and alignment concept. The alignment needs for a certain machine is normally given in terms of deviations between the position of any magnet in the accelerator and the fitted line that relates the actual position of the magnets’ assembly. Root mean square errors and standard deviations are normally used interchangeably and measurement uncertainty is often neglected. Although some solutions have been employed successfully in several accelerators, there is no off-the-shelf solution to perform the alignment. Also, each alignment campaign makes use of different measuring instruments to achieve the desired results, which makes the alignment process a complex measurement chain. This paper explores these issues by reviewing the tolerances specified for the alignment of particle accelerators, and proposes a metric to assess the quality of the alignment. The metric has the advantage of fully integrating the measurement uncertainty in the process.

  19. Aligning professional skills and active learning methods: an application for information and communications technology engineering

    Science.gov (United States)

    Llorens, Ariadna; Berbegal-Mirabent, Jasmina; Llinàs-Audet, Xavier

    2017-07-01

    Engineering education is facing new challenges to effectively provide the appropriate skills to future engineering professionals according to market demands. This study proposes a model based on active learning methods, which is expected to facilitate the acquisition of the professional skills most highly valued in the information and communications technology (ICT) market. The theoretical foundations of the study are based on the specific literature on active learning methodologies. The Delphi method is used to establish the fit between learning methods and generic skills required by the ICT sector. An innovative proposition is therefore presented that groups the required skills in relation to the teaching method that best develops them. The qualitative research suggests that a combination of project-based learning and the learning contract is sufficient to ensure a satisfactory skills level for this profile of engineers.

  20. Scanning electron microscopy analysis of the growth of dental plaque on the surfaces of removable orthodontic aligners after the use of different cleaning methods.

    Science.gov (United States)

    Levrini, Luca; Novara, Francesca; Margherini, Silvia; Tenconi, Camilla; Raspanti, Mario

    2015-01-01

    Advances in orthodontics are leading to the use of minimally invasive technologies, such as transparent removable aligners, and are able to meet high demands in terms of performance and esthetics. However, the most correct method of cleaning these appliances, in order to minimize the effects of microbial colonization, remains to be determined. The aim of the present study was to identify the most effective method of cleaning removable orthodontic aligners, analyzing the growth of dental plaque as observed under scanning electron microscopy. Twelve subjects were selected for the study. All were free from caries and periodontal disease and were candidates for orthodontic therapy with invisible orthodontic aligners. The trial had a duration of 6 weeks, divided into three 2-week stages, during which three sets of aligners were used. In each stage, the subjects were asked to use a different method of cleaning their aligners: 1) running water (control condition); 2) effervescent tablets containing sodium carbonate and sulfate crystals followed by brushing with a toothbrush; and 3) brushing alone (with a toothbrush and toothpaste). At the end of each 2-week stage, the surfaces of the aligners were analyzed under scanning electron microscopy. The best results were obtained with brushing combined with the use of sodium carbonate and sulfate crystals; brushing alone gave slightly inferior results. On the basis of previous literature results relating to devices in resin, studies evaluating the reliability of domestic ultrasonic baths for domestic use should be encouraged. At present, pending the availability of experimental evidence, it can be suggested that dental hygienists should strongly advise patients wearing orthodontic aligners to clean them using a combination of brushing and commercially available tablets for cleaning oral appliances.

  1. A fast alignment method for breast MRI follow-up studies using automated breast segmentation and current-prior registration

    Science.gov (United States)

    Wang, Lei; Strehlow, Jan; Rühaak, Jan; Weiler, Florian; Diez, Yago; Gubern-Merida, Albert; Diekmann, Susanne; Laue, Hendrik; Hahn, Horst K.

    2015-03-01

    In breast cancer screening for high-risk women, follow-up magnetic resonance images (MRI) are acquired with a time interval ranging from several months up to a few years. Prior MRI studies may provide additional clinical value when examining the current one and thus have the potential to increase sensitivity and specificity of screening. To build a spatial correlation between suspicious findings in both current and prior studies, a reliable alignment method between follow-up studies is desirable. However, long time interval, different scanners and imaging protocols, and varying breast compression can result in a large deformation, which challenges the registration process. In this work, we present a fast and robust spatial alignment framework, which combines automated breast segmentation and current-prior registration techniques in a multi-level fashion. First, fully automatic breast segmentation is applied to extract the breast masks that are used to obtain an initial affine transform. Then, a non-rigid registration algorithm using normalized gradient fields as similarity measure together with curvature regularization is applied. A total of 29 subjects and 58 breast MR images were collected for performance assessment. To evaluate the global registration accuracy, the volume overlap and boundary surface distance metrics are calculated, resulting in an average Dice Similarity Coefficient (DSC) of 0.96 and root mean square distance (RMSD) of 1.64 mm. In addition, to measure local registration accuracy, for each subject a radiologist annotated 10 pairs of markers in the current and prior studies representing corresponding anatomical locations. The average distance error of marker pairs dropped from 67.37 mm to 10.86 mm after applying registration.

  2. 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.

  3. Aligning Order Picking Methods, Incentive Systems, and Regulatory Focus to Increase Performance

    NARCIS (Netherlands)

    de Vries, J.; de Koster, R.; Stam, D.

    2016-01-01

    A controlled field experiment investigates order picking performance in terms of productivity. We examined three manual picker-to-parts order picking methods (parallel, zone, and dynamic zone picking) under two different incentive systems (competition-based vs. cooperation-based) for pickers with

  4. Aligning order picking methods, incentive systems, and regulatory focus to increase performance

    NARCIS (Netherlands)

    J. de Vries (Jelle); M.B.M. de Koster (René); D.A. Stam (Daan)

    2015-01-01

    textabstractA unique controlled field experiment investigates order picking performance (in terms of productivity and quality). We examined three manual picker-to-parts order picking methods (parallel, zone, and dynamic zone picking) under two different incentive systems (competition- based versus

  5. Aligning Professional Skills and Active Learning Methods: An Application for Information and Communications Technology Engineering

    Science.gov (United States)

    Llorens, Ariadna; Berbegal-Mirabent, Jasmina; Llinàs-Audet, Xavier

    2017-01-01

    Engineering education is facing new challenges to effectively provide the appropriate skills to future engineering professionals according to market demands. This study proposes a model based on active learning methods, which is expected to facilitate the acquisition of the professional skills most highly valued in the information and…

  6. The bridge of dreams: : Towards a method for operational performance alignment in IT-enabled service supply chains

    NARCIS (Netherlands)

    Wang, Yan

    2016-01-01

    Concerns on performance alignment, especially on business-IT alignment, have been around for three decades. It is still considered to be one of the most important driving forces for business success, as well as one of the top concerns of many practitioners and organizational researchers. It is also

  7. Embedded arrays of vertically aligned carbon nanotube carpets and methods for making them

    Science.gov (United States)

    Kim, Myung Jong; Nicholas, Nolan Walker; Kittrell, W. Carter; Schmidt, Howard K.

    2015-06-30

    According to some embodiments, the present invention provides a system and method for supporting a carbon nanotube array that involve an entangled carbon nanotube mat integral with the array, where the mat is embedded in an embedding material. The embedding material may be depositable on a carbon nanotube. A depositable material may be metallic or nonmetallic. The embedding material may be an adhesive material. The adhesive material may optionally be mixed with a metal powder. The embedding material may be supported by a substrate or self-supportive. The embedding material may be conductive or nonconductive. The system and method provide superior mechanical and, when applicable, electrical, contact between the carbon nanotubes in the array and the embedding material. The optional use of a conductive material for the embedding material provides a mechanism useful for integration of carbon nanotube arrays into electronic devices.

  8. Automated method and system for the alignment and correlation of images from two different modalities

    Science.gov (United States)

    Giger, Maryellen L.; Chen, Chin-Tu; Armato, Samuel; Doi, Kunio

    1999-10-26

    A method and system for the computerized registration of radionuclide images with radiographic images, including generating image data from radiographic and radionuclide images of the thorax. Techniques include contouring the lung regions in each type of chest image, scaling and registration of the contours based on location of lung apices, and superimposition after appropriate shifting of the images. Specific applications are given for the automated registration of radionuclide lungs scans with chest radiographs. The method in the example given yields a system that spatially registers and correlates digitized chest radiographs with V/Q scans in order to correlate V/Q functional information with the greater structural detail of chest radiographs. Final output could be the computer-determined contours from each type of image superimposed on any of the original images, or superimposition of the radionuclide image data, which contains high activity, onto the radiographic chest image.

  9. Eight piece quadrupole magnet, method for aligning quadrupole magent pole tips

    Science.gov (United States)

    Jaski, Mark S.; Liu, Jie; Donnelly, Aric T.; Downey, Joshua S.; Nudell, Jeremy J.; Jain, Animesh

    2018-01-30

    The invention provides an alternative to the standard 2-piece or 4-piece quadrupole. For example, an 8-piece and a 10-piece quadrupole are provided whereby the tips of each pole may be adjustable. Also provided is a method for producing a quadrupole using standard machining techniques but which results in a final tolerance accuracy of the resulting construct which is better than that obtained using standard machining techniques.

  10. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez

    2011-01-01

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

  11. Methods and Application of Phonetic Label Alignment in Speech Processing Tasks

    Directory of Open Access Journals (Sweden)

    M. Myslivec

    2000-12-01

    Full Text Available The paper deals with the problem of automatic phonetic segmentation ofspeech signals, namely for speech analysis and recognition purposes.Several methods and approaches are described and evaluated from thepoint of view of their accuracy. A complete instruction for creating anannotated database for training a Czech speech recognition system isprovided together with the authors' own experience. The results of thework have found practical applications, for example, in developing atool for semi-automatic speech segmentation, building alarge-vocabulary phoneme-based speech recognition system and designingan aid for learning and practicing pronunciation of words or phrases inthe native or a foreign language.

  12. Student evaluation of the flipped classroom instruction method: is it aligned with Problem-Based Learning?

    DEFF Research Database (Denmark)

    Triantafyllou, Evangelia; Timcenko, Olga; Kofoed, Lise

    2017-01-01

    The flipped classroom approach is an instructional method that has gained momentum in the last years. In a flipped classroom the traditional lecture and homework sessions are inverted. We believe that the flipped classroom, which employs computer-based individual instruction outside the classroom...... presents data from the second year, where we conducted a survey study among students participating in the flipped statistics course. This study consisted of two surveys designed to gather student perceptions on the out-of-classroom preparation material (videos and quizzes) and the flipped classroom...

  13. Chemical solution deposition method of fabricating highly aligned MgO templates

    Science.gov (United States)

    Paranthaman, Mariappan Parans [Knoxville, TN; Sathyamurthy, Srivatsan [Knoxville, TN; Aytug, Tolga [Knoxville, TN; Arendt, Paul N [Los Alamos, NM; Stan, Liliana [Los Alamos, NM; Foltyn, Stephen R [Los Alamos, NM

    2012-01-03

    A superconducting article includes a substrate having an untextured metal surface; an untextured barrier layer of La.sub.2Zr.sub.2O.sub.7 or Gd.sub.2Zr.sub.2O.sub.7 supported by and in contact with the surface of the substrate; a biaxially textured buffer layer supported by the untextured barrier layer; and a biaxially textured superconducting layer supported by the biaxially textured buffer layer. Moreover, a method of forming a buffer layer on a metal substrate includes the steps of: providing a substrate having an untextured metal surface; coating the surface of the substrate with a barrier layer precursor; converting the precursor to an untextured barrier layer; and depositing a biaxially textured buffer layer above and supported by the untextured barrier layer.

  14. Assembly and alignment method for optimized spatial resolution of off-axis three-mirror fore optics of hyperspectral imager.

    Science.gov (United States)

    Kim, Youngsoo; Hong, Jinsuk; Choi, Byungin; Lee, Jong-Ung; Kim, Yeonsoo; Kim, Hyunsook

    2017-08-21

    A fore optics for the hyperspectral spectrometer is designed, manufactured, assembled, and aligned. The optics has a telecentric off-axis three-mirror configuration with a field of view wider than 14 degrees and an f-number as small as 2.3. The primary mirror (M1) and the secondary mirror (M2) are axially symmetric aspheric surfaces to minimize the sensitivity. The tertiary mirror (M3) is a decentered aspheric surface to minimize the coma and astigmatism aberration. The M2 also has a hole for the slit to maintain the optical performance while maximizing the telecentricity. To ensure the spatial resolution performance of the optical system, an alignment procedure is established to assemble and align the entrance slit of the spectrometer to the rear end of the fore optics. It has a great advantage to confirm and maintain the alignment integrity of the fore optics module throughout the alignment procedure. To perform the alignment procedure successfully, the precision movement control requirements are calculated and applied. As a result, the alignment goal of the RMS wave front error (WFE) to be smaller than 90 nm at all fields is achieved.

  15. DETERMINATION OF STEERING WHEEL ANGLES DURING CAR ALIGNMENT BY IMAGE ANALYSIS METHODS

    Directory of Open Access Journals (Sweden)

    M. Mueller

    2016-06-01

    Full Text Available Optical systems for automatic visual inspections are of increasing importance in the field of automation in the industrial domain. A new application is the determination of steering wheel angles during wheel track setting of the final inspection of car manufacturing. The camera has to be positioned outside the car to avoid interruptions of the processes and therefore, oblique images of the steering wheel must be acquired. Three different approaches of computer vision are considered in this paper, i.e. a 2D shape-based matching (by means of a plane to plane rectification of the oblique images and detection of a shape model with a particular rotation, a 3D shape-based matching approach (by means of a series of different perspectives of the spatial shape of the steering wheel derived from a CAD design model and a point-to-point matching (by means of the extraction of significant elements (e.g. multifunctional buttons of a steering wheel and a pairwise connection of these points to straight lines. The HALCON system (HALCON, 2016 was used for all software developments and necessary adaptions. As reference a mechanical balance with an accuracy of 0.1° was used. The quality assessment was based on two different approaches, a laboratory test and a test during production process. In the laboratory a standard deviation of ±0.035° (2D shape-based matching, ±0.12° (3D approach and ±0.029° (point-to-point matching could be obtained. The field test of 291 measurements (27 cars with varying poses and angles of the steering wheel results in a detection rate of 100% and ±0.48° (2D matching and ±0.24° (point-to-point matching. Both methods also fulfil the request of real time processing (three measurements per second.

  16. 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

  17. 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.

  18. Beyond Alignment

    DEFF Research Database (Denmark)

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

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

    Directory of Open Access Journals (Sweden)

    Daniels Noah M

    2012-10-01

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

  20. 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...

  1. The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies.

    Directory of Open Access Journals (Sweden)

    Patrick D Schloss

    Full Text Available Pyrosequencing of PCR-amplified fragments that target variable regions within the 16S rRNA gene has quickly become a powerful method for analyzing the membership and structure of microbial communities. This approach has revealed and introduced questions that were not fully appreciated by those carrying out traditional Sanger sequencing-based methods. These include the effects of alignment quality, the best method of calculating pairwise genetic distances for 16S rRNA genes, whether it is appropriate to filter variable regions, and how the choice of variable region relates to the genetic diversity observed in full-length sequences. I used a diverse collection of 13,501 high-quality full-length sequences to assess each of these questions. First, alignment quality had a significant impact on distance values and downstream analyses. Specifically, the greengenes alignment, which does a poor job of aligning variable regions, predicted higher genetic diversity, richness, and phylogenetic diversity than the SILVA and RDP-based alignments. Second, the effect of different gap treatments in determining pairwise genetic distances was strongly affected by the variation in sequence length for a region; however, the effect of different calculation methods was subtle when determining the sample's richness or phylogenetic diversity for a region. Third, applying a sequence mask to remove variable positions had a profound impact on genetic distances by muting the observed richness and phylogenetic diversity. Finally, the genetic distances calculated for each of the variable regions did a poor job of correlating with the full-length gene. Thus, while it is tempting to apply traditional cutoff levels derived for full-length sequences to these shorter sequences, it is not advisable. Analysis of beta-diversity metrics showed that each of these factors can have a significant impact on the comparison of community membership and structure. Taken together, these results

  2. 46 CFR 56.85-5 - Heating and cooling method.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 2 2010-10-01 2010-10-01 false Heating and cooling method. 56.85-5 Section 56.85-5... APPURTENANCES Heat Treatment of Welds § 56.85-5 Heating and cooling method. Heat treatment may be accomplished by a suitable heating method that will provide the desired heating and cooling rates, the required...

  3. Novel methods in track-based alignment to correct for time-dependent distortions of the ATLAS Inner Detector

    CERN Document Server

    Estrada Pastor, Oscar; The ATLAS collaboration

    2017-01-01

    ATLAS is a multipurpose experiment at the LHC proton-proton collider. Its physics goals require high resolution, unbiased measurement of all charged particle kinematic parameters. These critically depend on the layout and performance of the tracking system and the quality of its offline alignment. For the LHC Run II, the system has been upgraded with the installation of a new pixel layer, the Insertable B-layer (IBL). Offline track alignment of the ATLAS tracking system has to deal with about 700,000 degrees of freedom (DoF) defining its geometrical parameters, representing a considerable numerical challenge in terms of both CPU time and precision. An outline of the track based alignment approach and its implementation within the ATLAS software will be presented. Special attention will be paid to describe the techniques allowing to pinpoint and eliminate track parameters biases due to alignment. During Run-II, ATLAS Inner Detector Alignment framework has been adapted and upgraded to correct very short time sc...

  4. 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

  5. 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

  6. Optimization methods of pulse-to-pulse alignment using femtosecond pulse laser based on temporal coherence function for practical distance measurement

    Science.gov (United States)

    Liu, Yang; Yang, Linghui; Guo, Yin; Lin, Jiarui; Cui, Pengfei; Zhu, Jigui

    2018-02-01

    An interferometer technique based on temporal coherence function of femtosecond pulses is demonstrated for practical distance measurement. Here, the pulse-to-pulse alignment is analyzed for large delay distance measurement. Firstly, a temporal coherence function model between two femtosecond pulses is developed in the time domain for the dispersive unbalanced Michelson interferometer. Then, according to this model, the fringes analysis and the envelope extraction process are discussed. Meanwhile, optimization methods of pulse-to-pulse alignment for practical long distance measurement are presented. The order of the curve fitting and the selection of points for envelope extraction are analyzed. Furthermore, an averaging method based on the symmetry of the coherence function is demonstrated. Finally, the performance of the proposed methods is evaluated in the absolute distance measurement of 20 μ m with path length difference of 9 m. The improvement of standard deviation in experimental results shows that these approaches have the potential for practical distance measurement.

  7. 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.

  8. EXTENDED NEUTRAL HYDROGEN IN THE ALIGNED SHELL GALAXIES Arp 230 AND MCG -5-7-1: FORMATION OF DISKS IN MERGING GALAXIES?

    Energy Technology Data Exchange (ETDEWEB)

    Schiminovich, David; Van Gorkom, J. H. [Department of Astronomy, Columbia University, New York, NY 10027 (United States); Van der Hulst, J. M. [Kapteyn Astronomical Institute, 9700-AV Groningen (Netherlands)

    2013-02-01

    As part of an ongoing study of the neutral hydrogen (H I) morphology and kinematics of 'shell' elliptical galaxies, we present Very Large Array observations of two shell galaxies with aligned shells, Arp 230 and MCG -5-7-1. Our data provide the first H I images of Arp 230 and deeper images of MCG -5-7-1 than previously reported. Optical images of Arp 230 reveal a bright, aligned, interleaved shell system, making it an ideal candidate for 'phase-wrapped' shell formation following a radial encounter with a smaller companion. The fainter, non-interleaved shells of MCG -5-7-1 do not clearly favor a particular formation scenario. The H I we detect in both galaxies extends to nearly the same projected distance as the optical shells. In Arp 230 this gas appears to be anti-correlated with the aligned shells, consistent with our expectations for phase-wrapped shells produced in a radial encounter. In MCG -5-7-1, we observe gas associated with the shells making a 'spatial wrapping' or looping scenario more plausible. Although the extended gas component in both galaxies is unevenly distributed, the gas kinematics are surprisingly regular, looking almost like complete disks in rotation. We use the H I kinematics and optical data to determine mass-to-light ratios M/L{sub B} of 2.4{sup +3.0}{sub -0.5} (at 13.5 kpc, 4.5 R{sub e} ) for Arp 230 and M/L{sub B} of 30 {+-} 7 (at 40 kpc, 7 R{sub e} ) in MCG -5-7-1. In both systems we find that this ratio changes as a function of radius, indicating the presence of a dark halo. By comparing orbital and precession timescales, we conclude that the potentials are slightly flattened. We infer a 5%-10% flattening for Arp 230 and less flattening in the case of MCG -5-7-1. Finally, we present images of the H I associated with the inner disk or (polar) ring of each galaxy and discuss possible explanations for their different present-day star formation rates. We detect total H I masses of 1.1 Multiplication-Sign 10

  9. Novel methods in track-based alignment to correct for time-dependent distortions of the ATLAS Inner Detector

    CERN Document Server

    Estrada Pastor, Oscar; The ATLAS collaboration

    2017-01-01

    ATLAS is a multipurpose experiment at the LHC proton-proton collider. Its physics goals require high resolution and unbiased measurement of all charged particle kinematic parameters. These critically depend on the layout and performance of the tracking system and the quality of its alignment. For the LHC Run II, the system has been upgraded with the installation of a new pixel layer, the Insertable B-layer (IBL). The offline track alignment of the ATLAS tracking system has to deal with about 700,000 degrees of freedom (DoF) defining its geometrical parameters, representing a considerable numerical challenge in terms of both CPU time and precision. An outline of the track based alignment approach and its implementation within the ATLAS software is presented. Special attention is paid to describe the techniques allowing to pinpoint and eliminate track parameters biases. During Run-II, ATLAS Inner Detector Alignment framework has been adapted and upgraded to correct very short time scale movements of the sub-det...

  10. 7 CFR 220.5 - Method of payment to States.

    Science.gov (United States)

    2010-01-01

    ... reimbursement to School Food Authorities through presentation by designated State officials of a payment Voucher... 7 Agriculture 4 2010-01-01 2010-01-01 false Method of payment to States. 220.5 Section 220.5... AGRICULTURE CHILD NUTRITION PROGRAMS SCHOOL BREAKFAST PROGRAM § 220.5 Method of payment to States. Funds to be...

  11. A new data-mining method to search for behavioral properties that induce alignment and their involvement in social learning in medaka fish (Oryzias latipes.

    Directory of Open Access Journals (Sweden)

    Takashi Ochiai

    Full Text Available BACKGROUND: Coordinated movement in social animal groups via social learning facilitates foraging activity. Few studies have examined the behavioral cause-and-effect between group members that mediates this social learning. METHODOLOGY/PRINCIPAL FINDINGS: We first established a behavioral paradigm for visual food learning using medaka fish and demonstrated that a single fish can learn to associate a visual cue with a food reward. Grouped medaka fish (6 fish learn to respond to the visual cue more rapidly than a single fish, indicating that medaka fish undergo social learning. We then established a data-mining method based on Kullback-Leibler divergence (KLD to search for candidate behaviors that induce alignment and found that high-speed movement of a focal fish tended to induce alignment of the other members locally and transiently under free-swimming conditions without presentation of a visual cue. The high-speed movement of the informed and trained fish during visual cue presentation appeared to facilitate the alignment of naïve fish in response to some visual cues, thereby mediating social learning. Compared with naïve fish, the informed fish had a higher tendency to induce alignment of other naïve fish under free-swimming conditions without visual cue presentation, suggesting the involvement of individual recognition in social learning. CONCLUSIONS/SIGNIFICANCE: Behavioral cause-and-effect studies of the high-speed movement between fish group members will contribute to our understanding of the dynamics of social behaviors. The data-mining method used in the present study is a powerful method to search for candidates factors associated with inter-individual interactions using a dataset for time-series coordinate data of individuals.

  12. Automatic slice-alignment method in cardiac magnetic resonance imaging for evaluation of the right ventricle in patients with pulmonary hypertension

    Science.gov (United States)

    Yokoyama, Kenichi; Nitta, Shuhei; Kuhara, Shigehide; Ishimura, Rieko; Kariyasu, Toshiya; Imai, Masamichi; Nitatori, Toshiaki; Takeguchi, Tomoyuki; Shiodera, Taichiro

    2015-09-01

    We propose a new automatic slice-alignment method, which enables right ventricular scan planning in addition to the left ventricular scan planning developed in our previous work, to simplify right ventricular cardiac scan planning and assess its accuracy and the clinical acceptability of the acquired imaging planes in the evaluation of patients with pulmonary hypertension. Steady-state free precession (SSFP) sequences covering the whole heart in the end-diastolic phase with ECG gating were used to acquire 2D axial multislice images. To realize right ventricular scan planning, two morphological feature points are added to be detected and a total of eight morphological features of the heart were extracted from these series of images, and six left ventricular planes and four right ventricular planes were calculated simultaneously based on the extracted features. The subjects were 33 patients (25 with chronic thromboembolic pulmonary hypertension and 8 with idiopathic pulmonary arterial hypertension). The four right ventricular reference planes including right ventricular short-axis, 4-chamber, 2-chamber, and 3-chamber images were evaluated. The acceptability of the acquired imaging planes was visually evaluated using a 4-point scale, and the angular differences between the results obtained by this method and by conventional manual annotation were measured for each view. The average visual scores were 3.9±0.4 for short-axis images, 3.8±0.4 for 4-chamber images, 3.8±0.4 for 2-chamber images, and 3.5±0.6 for 3-chamber images. The average angular differences were 8.7±5.3, 8.3±4.9, 8.1±4.8, and 7.9±5.3 degrees, respectively. The processing time was less than 2.5 seconds in all subjects. The proposed method, which enables right ventricular scan planning in addition to the left ventricular scan planning developed in our previous work, can provide clinically acceptable planes in a short time and is useful because special proficiency in performing cardiac MR for

  13. Method of making a self-aligned schottky metal semi-conductor field effect transistor with buried source and drain

    International Nuclear Information System (INIS)

    Bol, I.

    1984-01-01

    A semi-conductor structure and particularly a high speed VLSI Self-Aligned Schottky Metal Semi-Conductor Field Effect Transistor with buried source and drain, fabricated by the ion implantation of source and drain areas at a predetermined range of depths followed by very localized laser annealing to electrically reactivate the amorphous buried source and drain areas thereby providing effective vertical separation of the channel from the buried source and drain respectively. Accordingly, spatial separations between the self-aligned gate-to-drain, and gate-to-source can be relatively very closely controlled by varying the doping intensity and duration of the implantation thereby reducing the series resistance and increasing the operating speed

  14. Blazed vector grating liquid crystal cells with photocrosslinkable polymeric alignment films fabricated by one-step polarizer rotation method

    Science.gov (United States)

    Kawai, Kotaro; Kuzuwata, Mitsuru; Sasaki, Tomoyuki; Noda, Kohei; Kawatsuki, Nobuhiro; Ono, Hiroshi

    2014-12-01

    Blazed vector grating liquid crystal (LC) cells, in which the directors of low-molar-mass LCs are antisymmetrically distributed, were fabricated by one-step exposure of an empty glass cell inner-coated with a photocrosslinkable polymer LC (PCLC) to UV light. By adopting a LC cell structure, twisted nematic (TN) and homogeneous (HOMO) alignments were obtained in the blazed vector grating LC cells. Moreover, the diffraction efficiency of the blazed vector grating LC cells was greatly improved by increasing the thickness of the device in comparison with that of a blazed vector grating with a thin film structure obtained in our previous study. In addition, the diffraction efficiency and polarization states of ±1st-order diffracted beams from the resultant blazed vector grating LC cells were controlled by designing a blazed pattern in the alignment films, and these diffraction properties were well explained on the basis of Jones calculus and the elastic continuum theory of nematic LCs.

  15. Rab5 GTPase controls chromosome alignment through Lamin disassembly and relocation of the NuMA-like protein Mud to the poles during mitosis

    Science.gov (United States)

    Capalbo, Luisa; D'Avino, Pier Paolo; Archambault, Vincent; Glover, David M.

    2011-01-01

    The small GTPase Rab5 is a conserved regulator of membrane trafficking; it regulates the formation of early endosomes, their transport along microtubules, and the fusion to the target organelles. Although several members of the endocytic pathway were recently implicated in spindle organization, it is unclear whether Rab5 has any role during mitosis. Here, we describe that Rab5 is required for proper chromosome alignment during Drosophila mitoses. We also found that Rab5 associated in vivo with nuclear Lamin and mushroom body defect (Mud), the Drosophila counterpart of nuclear mitotic apparatus protein (NuMA). Consistent with this finding, Rab5 was required for the disassembly of the nuclear envelope at mitotic entry and the accumulation of Mud at the spindle poles. Furthermore, Mud depletion caused chromosome misalignment defects that resembled the defects of Rab5 RNAi cells, and double-knockdown experiments indicated that the two proteins function in a linear pathway. Our results indicate a role for Rab5 in mitosis and reinforce the emerging view of the contributions made by cell membrane dynamics to spindle function. PMID:21987826

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

    Energy Technology Data Exchange (ETDEWEB)

    Stynes, J. K.; Ihas, B.

    2012-04-01

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

  17. Improvement in device performance from a mixture of a liquid crystal and photosensitive acrylic prepolymer with the photoinduced vertical alignment method

    Directory of Open Access Journals (Sweden)

    Czung-Yu Ho, Fa-Hsin Lin, Yu-Tai Tao and Jiunn-Yih Lee

    2011-01-01

    Full Text Available In a multicomponent nematic liquid crystal (NLC mixture of a liquid crystal (negative-type NLC and a photosensitive acrylic prepolymer, photopolymerization upon UV irradiation induces the separation of the LC and photosensitive acrylic prepolymer layers, thereby leading to a vertical arrangement of LC molecules. In this study, we propose a simple vertical alignment method for LC molecules, by adding a chiral smectic A (SmA* liquid crystal having homeotropic texture characteristics to an NLC mixture solution. Measurements of electro-optical properties revealed that the addition of the SmA* LC not only strengthened the anchoring force of the copolymer alignment film surface, but also significantly enhanced the contrast ratio (~73%, response time and grayscale switching performance of the device.

  18. Mango: multiple alignment with N gapped oligos.

    Science.gov (United States)

    Zhang, Zefeng; Lin, Hao; Li, Ming

    2008-06-01

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

  19. ST5 Observations of the Imbalance of Region 1 and 2 Field-Aligned Currents and Its Implication to the Cross-Polar Cap Pedersen Currents

    Science.gov (United States)

    Le, Guan; Slavin, J. A.; Strangeway, Robert

    2011-01-01

    In this study, we use the in-situ magnetic field observations from Space Technology 5 mission to quantify the imbalance of Region 1 (R1) and Region 2 (R2) currents. During the three-month duration of the ST5 mission, geomagnetic conditions range from quiet to moderately active. We find that the R1 current intensity is consistently stronger than the R2 current intensity both for the dawnside and the duskside large-scale field-aligned current system. The net currents flowing into (out of) the ionosphere in the dawnside (duskside) are in the order of 5% of the total R1 currents. We also find that the net currents flowing into or out of the ionosphere are controlled by the solar wind-magnetosphere interaction in the same way as the field-aligned currents themselves are. Since the net currents due to the imbalance of the R1 and R2 currents require that their closure currents flow across the polar cap from dawn to dusk as Pedersen currents, our results indicate that the total amount of the cross-polar cap Pedersen currents is in the order of 0.1 MA. This study, although with a very limited dataset, is one of the first attempts to quantify the cross-polar cap Pedersen currents. Given the importance of the Joule heating due to Pedersen currents to the high-latitude ionospheric electrodynamics, quantifying the cross-polar cap Pedersen currents and associated Joule heating is needed for developing models of the magnetosphere-ionosphere coupling.

  20. 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

  1. Discriminative Shape Alignment

    DEFF Research Database (Denmark)

    Loog, M.; de Bruijne, M.

    2009-01-01

    , not taking into account that eventually the shapes are to be assigned to two or more different classes. This work introduces a discriminative variation to well-known Procrustes alignment and demonstrates its benefit over this classical method in shape classification tasks. The focus is on two...

  2. CLINICAL STUDY OF THE CHRONOLOGICAL CHANGES IN KNEE ALIGNMENT PATTERN IN NORMAL SOUTH-EAST NIGERIAN CHILDREN AGED BETWEEN 0 AND 5 YEARS

    Directory of Open Access Journals (Sweden)

    Ezeuko V.C

    2010-01-01

    Full Text Available The purpose of this study is to establish the chronological changes in knee alignment pattern in normal South-East Nigerian children aged between 0 and 5 years. A total number of 1450 subjects (680 males and 770 females were used for the study. The intercondylar/intermalleolar distances were measured using a vernier caliper with the subjects standing erect in anatomical position to determine straight knee, genu valgum and genu varum. The data was analysed with Microsoft Excel version 2007. The prevalence was presented as percentage (%.The result showed that the subjects have varum by the first year of life, prevalently genu valgum in type by the second year, valgum by the third year, neutral by the fourth and fifth year.

  3. Intermixing, band alignment and charge transport in AgIn5S8/CuI heterojunctions

    International Nuclear Information System (INIS)

    Konovalov, I.; Makhova, L.; Hesse, R.; Szargan, R.

    2005-01-01

    Possibilities of creating photovoltaic devices using CuI/AgIn 5 S 8 heterojunctions are considered. Among other properties, preferential formation of polar (111) surfaces makes n-type AgIn 5 S 8 an attractive candidate for absorber layers of top cells in 4-terminal tandem structures. Cu-Ag exchange at the interface with p-type CuI was observed. This intermixing results in an additional component of Ag 3d5 photoelectron line after deposition of CuI, in the Cu (but not I) contamination of the surface after a chemical removal of CuI, and in a photoelectric sensitivity of the junction at energies below the band gaps. Valence band offsets of 0.4 and 0.5 eV (cliff) were found at interfaces with thin film and bulk AgIn 5 S 8 , supporting a conduction mechanism through interface recombination. Pinning conflict at the interface between materials with contradictory doping limitations is likely to promote the intermixing

  4. Alignment for new Subaru ring

    International Nuclear Information System (INIS)

    Zhang, Ch.; Matsui, S.; Hashimoto, S.

    1999-01-01

    The New SUBARU is a synchrotron light source being constructed at the SPring-8 site. The main facility is a 1.5 GeV electron storage ring that provides light beam in the region from VUV to soft X-ray using SPring-8's 1 GeV linac as an injector. The ring, with a circumference of about 119 meters, is composed of six bending cells. Each bending cell has two normal dipoles of 34 degree and one inverse dipole of -8 degree. The ring has six straight sections: two very long straight sections for a 11-m long undulator and an optical klystron, four short straight sections for a 2.3-m undulator, a super-conducting wiggler, rf cavity and injection, etc. The magnets of the storage ring are composed of 12 dipoles (BMs), 6 invert dipoles (BIs), 56 quadrupoles and 44 sextupoles, etc. For the magnet alignment, positions of the dipoles (the BMs and BIs) are determined by network survey method. The multipoles, which are mounted on girders between the dipoles, are aligned with a laser-CCD camera system. This article presents the methodology used to position the different components and particularly to assure the precise alignment of the multipoles. (authors)

  5. Individual Differences in the Alignment of Structural and Functional Markers of the V5/MT Complex in Primates

    DEFF Research Database (Denmark)

    Large, I.; Bridge, H.; Ahmed, B.

    2016-01-01

    Extrastriate visual area V5/MT in primates is defined both structurally by myeloarchitecture and functionally by distinct responses to visual motion. Myelination is directly identifiable from postmortem histology but also indirectly by image contrast with structural magnetic resonance imaging (s...

  6. Simultaneous AFM and fluorescence imaging: A method for aligning an AFM-tip with an excitation beam using a 2D galvanometer

    Science.gov (United States)

    Moores, A. N.; Cadby, A. J.

    2018-02-01

    Correlative fluorescence and atomic force microscopy (AFM) imaging is a highly attractive technique for use in biological imaging, enabling force and mechanical measurements of particular structures whose locations are known due to the specificity of fluorescence imaging. The ability to perform these two measurements simultaneously (rather than consecutively with post-processing correlation) is highly valuable because it would allow the mechanical properties of a structure to be tracked over time as changes in the sample occur. We present an instrument which allows simultaneous AFM and fluorescence imaging by aligning an incident fluorescence excitation beam with an AFM-tip. Alignment was performed by calibrating a 2D galvanometer present in the excitation beam path and using it to reposition the incident beam. Two programs were developed (one manual and one automated) which correlate sample features between the AFM and fluorescence images, calculating the distance required to translate the incident beam towards the AFM-tip. Using this method, we were able to obtain beam-tip alignment (and therefore field-of-view alignment) from an offset of >15 μm to within one micron in two iterations of the program. With the program running alongside data acquisition for real-time feedback between AFM and optical images, this offset was maintained over a time period of several hours. Not only does this eliminate the need to image large areas with both techniques to ensure that fields-of-view overlap, but it also raises the possibility of using this instrument for tip-enhanced fluorescence applications, a technique in which super-resolution images have previously been achieved.

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

    International Nuclear Information System (INIS)

    French, R.H.

    1991-01-01

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

  8. OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy

    Directory of Open Access Journals (Sweden)

    Searle Stephen MJ

    2003-10-01

    Full Text Available Abstract Background The alignment of two or more protein sequences provides a powerful guide in the prediction of the protein structure and in identifying key functional residues, however, the utility of any prediction is completely dependent on the accuracy of the alignment. In this paper we describe a suite of reference alignments derived from the comparison of protein three-dimensional structures together with evaluation measures and software that allow automatically generated alignments to be benchmarked. We test the OXBench benchmark suite on alignments generated by the AMPS multiple alignment method, then apply the suite to compare eight different multiple alignment algorithms. The benchmark shows the current state-of-the art for alignment accuracy and provides a baseline against which new alignment algorithms may be judged. Results The simple hierarchical multiple alignment algorithm, AMPS, performed as well as or better than more modern methods such as CLUSTALW once the PAM250 pair-score matrix was replaced by a BLOSUM series matrix. AMPS gave an accuracy in Structurally Conserved Regions (SCRs of 89.9% over a set of 672 alignments. The T-COFFEE method on a data set of families with http://www.compbio.dundee.ac.uk. Conclusions The OXBench suite of reference alignments, evaluation software and results database provide a convenient method to assess progress in sequence alignment techniques. Evaluation measures that were dependent on comparison to a reference alignment were found to give good discrimination between methods. The STAMP Sc Score which is independent of a reference alignment also gave good discrimination. Application of OXBench in this paper shows that with the exception of T-COFFEE, the majority of the improvement in alignment accuracy seen since 1985 stems from improved pair-score matrices rather than algorithmic refinements. The maximum theoretical alignment accuracy obtained by pooling results over all methods was 94.5

  9. Myristoylation as a general method for immobilization and alignment of soluble proteins for solid-state NMR structural studies

    International Nuclear Information System (INIS)

    Mesleh, M.F.; Valentine, K.G.; Opella, S.J.; Louis, J.M.; Gronenborn, A.M.

    2003-01-01

    N-terminal myristoylation of the immunoglobulin-binding domain of protein G (GB1) from group G Streptococcus provides the means to bind the protein to aligned phospholipid bilayers for solid-state NMR structural studies. The myristoylated protein is immobilized by its interactions with bilayers, and the sample alignment enables orientationally dependent 15 N chemical shifts and 1 H- 15 N-dipolar couplings to be measured. Spectra calculated for the average solution NMR structure of the protein at various orientations with respect to the magnetic field direction were compared to the experimental spectrum. The best fit identified the orientation of the myristoylated protein on the lipid bilayers, and demonstrated that the protein adopts a similar structure in both its myristoylated and non-myristoylated forms, and that the structure is not grossly distorted by its interaction with the phosholipid bilayer surface or by its location in the restricted aqueous space between bilayer leaflets. The protein is oriented such that its charged sides face the phosphatidylcholine headgroups of the lipids with the single amphiphilic helix running parallel to the bilayer surface

  10. A 3.5 V lithium-iodine hybrid redox battery with vertically aligned carbon nanotube current collector.

    Science.gov (United States)

    Zhao, Yu; Hong, Misun; Bonnet Mercier, Nadège; Yu, Guihua; Choi, Hee Cheul; Byon, Hye Ryung

    2014-02-12

    A lithium-iodine (Li-I2) cell using the triiodide/iodide (I3(-)/I(-)) redox couple in an aqueous cathode has superior gravimetric and volumetric energy densities (∼ 330 W h kg(-1) and ∼ 650 W h L(-1), respectively, from saturated I2 in an aqueous cathode) to the reported aqueous Li-ion batteries and aqueous cathode-type batteries, which provides an opportunity to construct cost-effective and high-performance energy storage. To apply this I3(-)/I(-) aqueous cathode for a portable and compact 3.5 V battery, unlike for grid-scale storage as general target of redox flow batteries, we use a three-dimensional and millimeter thick carbon nanotube current collector for the I3(-)/I(-) redox reaction, which can shorten the diffusion length of the redox couple and provide rapid electron transport. These endeavors allow the Li-I2 battery to enlarge its specific capacity, cycling retention, and maintain a stable potential, thereby demonstrating a promising candidate for an environmentally benign and reusable portable battery.

  11. Semiconductor band alignment from first principles: a new nonequilibrium Green's function method applied to the CZTSe/CdS interface for photovoltaics

    DEFF Research Database (Denmark)

    Palsgaard, Mattias Lau Nøhr; Crovetto, Andrea; Gunst, Tue

    2016-01-01

    In this paper we present a method to obtain the band offset of semiconductor heterointerfaces from Density Functional Theory together with the nonequilibrium Green's function method. Band alignment and detailed properties of the interface between Cu2ZnSnSe4 and CdS are extracted directly from first...... principles simulations. The interface is important for photovoltaics applications where in particular the band offsets are important for efficiency. The band bending pose a problem for accurate atomistic simulations of band offsets due to its long range. Here we investigate two different methods for dealing...... with band bending directly. One involves doping the materials to induce a shorter screening length. The other method is to apply a voltage bias across the interface to correct for the band bending. The calculated band offsets agree well with previous experimental and theoretical studies and, interestingly...

  12. Self-aligned BCB planarization method for high-frequency signal injection in a VCSEL with an integrated modulator

    Science.gov (United States)

    Marigo-Lombart, Ludovic; Doucet, Jean-Baptiste; Lecestre, Aurélie; Reig, Benjamin; Rousset, Bernard; Thienpont, Hugo; Panajotov, Krassimir; Almuneau, Guilhem

    2016-04-01

    The huge increase of datacom capacities requires lasers sources with more and more bandwidth performances. Vertical-Cavity Surface-Emitting Lasers (VCSEL) in direct modulation is a good candidate, already widely used for short communication links such as in datacenters. Recently several different approaches have been proposed to further extend the direct modulation bandwidth of these devices, by improving the VCSEL structure, or by combining the VCSEL with another high speed element such as lateral slow light modulator or transistor/laser based structure (TVCSEL). We propose to increase the modulation bandwidth by vertically integrating a continuous-wave VCSEL with a high-speed electro-modulator. This vertical structure implies multiple electrodes with sufficiently good electrical separation between the different input electrical signals. This high frequency modulation requires both good electrical insulation between metal electrodes and an optimized design of the coplanar lines. BenzoCyclobutene (BCB) thanks to its low dielectric constant, low losses, low moisture absorption and good thermal stability, is often used as insulating layer. Also, BCB planarization offers the advantages of simpler and more reliable technological process flow in such integrated VCSEL/modulator structures with important reliefs. As described by Burdeaux et al. a degree of planarization (DOP) of about 95% can be achieved by simple spin coating whatever the device thickness. In most of the cases, the BCB planarization process requires an additional photolithography step in order to open an access to the mesa surface, thus involving a tight mask alignment and resulting in a degraded planarization. In this paper, we propose a self-aligned process with improved BCB planarization by combining a hot isostatic pressing derived from nanoimprint techniques with a dry plasma etching step.

  13. Effect of orbital alignment on the forward and reverse electronic energy transfer Ca(4s5p 1P1)+Marrow-right-leftCa(4s5p 3P/sub J/)+M with rare gases

    International Nuclear Information System (INIS)

    Bussert, W.; Neuschaefer, D.; Leone, S.R.; Departments of Physics and Chemistry, University of Colorado, Boulder, Colorado 80309-0440)

    1987-01-01

    Effects of orbital alignment on the relative cross sections for electronic energy transfer are determined for the near resonant transfer between Ca(4s5p 1 P 1 ) and Ca(4s5p 3 P/sub J/) states with rare gas collision partners. The experiments are carried out by pulsed laser excitation in a crossed beam. The results for the forward direction, 1 P to 3 P, formulated in terms of the ratio of the maximum to minimum transfer probability are: 3 He 1.61 +- 0.05; He 1.60 +- 0.03; Ne 1.55 +- 0.10; Ar 1.52 +- 0.21; for Kr, transfer occurs, but no preference is distinguishable within 1 +- 0.2; Xe 1.44 +- 0.06. The results for He, Ne, and Ar indicate a clear preference in the transfer for the initially prepared molecular Pi state. For Xe the molecular Σ state is dominant. The energy transfer is also carried out in the reverse direction, 3 P 1 to 1 P, for He and Xe, obtaining 1.65 +- 0.10 and 1.94 +- 0.22, respectively. Analysis of the state preparation suggests that the reverse direction favors the asymptotic molecular Σ state for He and the molecular Pi state for Xe. These alignment results provide a first experimental determination of the dominant electronic states involved in a collisional energy transfer process

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

    Science.gov (United States)

    Zhang, Zefeng; Lin, Hao; Li, Ming

    2007-01-01

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

  15. 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

  16. 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...

  17. 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.

  18. Structure and method for controlling band offset and alignment at a crystalline oxide-on-semiconductor interface

    Science.gov (United States)

    McKee, Rodney A.; Walker, Frederick J.

    2003-11-25

    A crystalline oxide-on-semiconductor structure and a process for constructing the structure involves a substrate of silicon, germanium or a silicon-germanium alloy and an epitaxial thin film overlying the surface of the substrate wherein the thin film consists of a first epitaxial stratum of single atomic plane layers of an alkaline earth oxide designated generally as (AO).sub.n and a second stratum of single unit cell layers of an oxide material designated as (A'BO.sub.3).sub.m so that the multilayer film arranged upon the substrate surface is designated (AO).sub.n (A'BO.sub.3).sub.m wherein n is an integer repeat of single atomic plane layers of the alkaline earth oxide AO and m is an integer repeat of single unit cell layers of the A'BO.sub.3 oxide material. Within the multilayer film, the values of n and m have been selected to provide the structure with a desired electrical structure at the substrate/thin film interface that can be optimized to control band offset and alignment.

  19. Pairwise structure alignment specifically tuned for surface pockets and interaction interfaces

    KAUST Repository

    Cui, Xuefeng

    2015-09-09

    To detect and evaluate the similarities between the three-dimensional (3D) structures of two molecules, various kinds of methods have been proposed for the pairwise structure alignment problem [6, 9, 7, 11]. The problem plays important roles when studying the function and the evolution of biological molecules. Recently, pairwise structure alignment methods have been extended and applied on surface pocket structures [10, 3, 5] and interaction interface structures [8, 4]. The results show that, even when there are no global similarities discovered between the global sequences and the global structures, biological molecules or complexes could share similar functions because of well conserved pockets and interfaces. Thus, pairwise pocket and interface structure alignments are promising to unveil such shared functions that cannot be discovered by the well-studied global sequence and global structure alignments. State-of-the-art methods for pairwise pocket and interface structure alignments [4, 5] are direct extensions of the classic pairwise protein structure alignment methods, and thus such methods share a few limitations. First, the goal of the classic protein structure alignment methods is to align single-chain protein structures (i.e., a single fragment of residues connected by peptide bonds). However, we observed that pockets and interfaces tend to consist of tens of extremely short backbone fragments (i.e., three or fewer residues connected by peptide bonds). Thus, existing pocket and interface alignment methods based on the protein structure alignment methods still rely on the existence of long-enough backbone fragments, and the fragmentation issue of pockets and interfaces rises the risk of missing the optimal alignments. Moreover, existing interface structure alignment methods focus on protein-protein interfaces, and require a "blackbox preprocessing" before aligning protein-DNA and protein-RNA interfaces. Therefore, we introduce the PROtein STucture Alignment

  20. 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....

  1. MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

    Science.gov (United States)

    Tamura, Koichiro; Peterson, Daniel; Peterson, Nicholas; Stecher, Glen; Nei, Masatoshi; Kumar, Sudhir

    2011-01-01

    Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net. PMID:21546353

  2. Articular chondrocyte alignment in the rat after surgically induced osteoarthritis

    Science.gov (United States)

    Takahashi, Hideaki; Tamaki, Hiroyuki; Yamamoto, Noriaki; Onishi, Hideaki

    2017-01-01

    [Purpose] Chondrocytes in articular cartilage are aligned as columns from the joint surface. Notably, loss of chondrocyte and abnormalities of differentiation factors give rise to osteoarthritis (OA). However, the relationship between chondrocyte alignment and OA progression remains unclear. This study was performed to investigate temporal alterations in surgically-induced OA rats. [Subjects and Methods] Thirteen-week-old Wistar rats (n=30) underwent destabilized medial meniscus surgery in their right knee and sham surgery in their left knee. Specimens (n=5) were collected at 0, 1, 2, 4 and 8 weeks after surgery. Histological analysis with Osteoarthritis Research Society International (OARSI) scores, cell density ratios, cell alignments and correlation between OARSI scores and cell density/alignment was performed. [Results] OARSI scores were significantly higher at 1, 2, 4 and 8 weeks in the DMM group than in the control. Cell density ratios were decreased significantly in the DMM group at 2, 4 and 8 weeks compared with the control. Chondrocyte alignment was decreased significantly in the DMM group at 4 and 8 weeks. There were negative correlations between OA severity and cell density / cell alignment. [Conclusion] The results suggest a relationship between chondrocyte alignment and cartilage homeostasis, which plays an important role in OA progression. PMID:28533592

  3. Assimilation of GMS-5 satellite winds using nudging method with MM5

    Science.gov (United States)

    Gao, Shanhong; Wu, Zengmao; Yang, Bo

    2006-09-01

    With the aid of Meteorological Information Composite and Processing System (MICAPS), satellite wind vectors derived from the Geostationary Meteorological Statellite-5 (GMS-5) and retrieved by National Satellite Meteorology Center of China (NSMC) can be obtained. Based on the nudging method built in the fifth-generation Mesoscale Model (MM5) of Pennsylvania State University and National Center for Atmospheric Research, a data preprocessor is developed to convert these satellite wind vectors to those with specified format required in MM5. To examine the data preprocessor and evaluate the impact of satellite winds from GMS-5 on MM5 simulations, a series of numerical experimental forecasts consisting of four typhoon cases in 2002 are designed and implemented. The results show that the preprocessor can process satellite winds smoothly and MM5 model runs successfully with a little extra computational load during ingesting these winds, and that assimilation of satellite winds by MM5 nudging method can obviously improve typhoon track forecast but contributes a little to typhoon intensity forecast. The impact of the satellite winds depends heavily upon whether the typhoon bogussing scheme in MM5 was turned on or not. The data preprocessor developed in this paper not only can treat GMS-5 satellite winds but also has capability with little modification to process derived winds from other geostationary satellites.

  4. Implementation of 5S Method for Ergonomic Laboratory

    Science.gov (United States)

    Dila Sari, Amarria; Ilma Rahmillah, Fety; Prabowo Aji, Bagus

    2017-06-01

    This article discusses 5S implementation in Work System Design and Ergonomic Laboratory, Department of Industrial Engineering, Islamic University of Indonesia. There are some problems related to equipment settings for activity involving students such as files which is accumulated over the previous year practicum, as well as the movement of waste in the form of time due to the placement of goods that do not fit. Therefore, this study aims to apply the 5S method in DSK & E laboratory to facilitate the work processes and reduce waste. The project is performed by laboratory management using 5S methods in response to continuous improvement (Kaizen). Moreover, some strategy and suggestions are promoted to impose 5S system within the laboratory. As a result, the tidiness and cleanliness can be achieved that lead to the great performance of laboratory users. Score assessment before implementing 5S DSKE laboratory is at 64 (2.56) while the score after implementation is 32 (1.28) and shows an improvement of 50%. This has implications for better use in the laboratory area, save time when looking for tools and materials due to its location and good visual control, as well as improving the culture and spirit of ‘5S’ on staff regarding better working environment

  5. 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.

  6. MUSCLE: multiple sequence alignment with high accuracy and high throughput.

    Science.gov (United States)

    Edgar, Robert C

    2004-01-01

    We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.

  7. Semiautomated improvement of RNA alignments

    DEFF Research Database (Denmark)

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

    2007-01-01

    connects to external tools to provide a flexible semiautomatic editing environment. A new method, Pcluster, is introduced for dividing the sequences of an RNA alignment into subgroups with secondary structure differences. Pcluster was used to evaluate 574 seed alignments obtained from the Rfam database...... and we identified 71 alignments with significant prediction of inconsistent base pairs and 102 alignments with significant prediction of novel base pairs. Four RNA families were used to illustrate how SARSE can be used to manually or automatically correct the inconsistent base pairs detected by Pcluster......: the mir-399 RNA, vertebrate telomase RNA (vert-TR), bacterial transfer-messenger RNA (tmRNA), and the signal recognition particle (SRP) RNA. The general use of the method is illustrated by the ability to accommodate pseudoknots and handle even large and divergent RNA families. The open architecture...

  8. Alignment at the ESRF

    International Nuclear Information System (INIS)

    Martin, D.; Levet, N.; Gatta, G.

    1999-01-01

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

  9. Novel Method for 5G Systems NLOS Channels Parameter Estimation

    Directory of Open Access Journals (Sweden)

    Vladeta Milenkovic

    2017-01-01

    Full Text Available For the development of new 5G systems to operate in mm bands, there is a need for accurate radio propagation modelling at these bands. In this paper novel approach for NLOS channels parameter estimation will be presented. Estimation will be performed based on LCR performance measure, which will enable us to estimate propagation parameters in real time and to avoid weaknesses of ML and moment method estimation approaches.

  10. Accelerator and transport line survey and alignment

    International Nuclear Information System (INIS)

    Ruland, R.E.

    1991-10-01

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

  11. 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....

  12. Alignment Methods Developed for the Validation of the Thermal and Mechanical Behaviour of the Two Beam Test Modules for the CLIC Project

    CERN Document Server

    Mainaud Durand, Helene; Sosin, Mateusz; Rude, Vivien

    2014-01-01

    CLIC project will consist of more than 20 000 two meters long modules. A test setup made of three modules is being built at CERN to validate the assembly and integration of all components and technical systems and to validate the short range strategy of pre-alignment. The test setup has been installed in a room equipped with a sophisticated system of ventilation able to reproduce the environmental conditions of the CLIC tunnel. Some of the components have been equipped with electrical heaters to simulate the power dissipation, combined with a water cooling system integrated in the RF components. Using these installations, to have a better understanding of the thermal and mechanical behaviour of a module under different operation modes, machine cycles have been simulated; the misalignment of the components and their supports has been observed. This paper describes the measurements methods developed for such a project and the results obtained.

  13. TEXTILE INDUSTRY APPLICATION OF THE 5S METHOD

    Directory of Open Access Journals (Sweden)

    Raluca BRAD

    2015-05-01

    Full Text Available The paper presents the 5S method, developed to ensure ergonomics in the workplace, productivity growth, reducing defects and increasing cleaning. 5S is a fundamental tool to promote continuous improvement process in organizations and represents a transformation in 5 steps of a job, which is characterized by maximum efficiency at the micro level and minimum loss. The tools which can be used for implementing could be the Kaizen circles for training, analysis and implementation, as well as visual elements, posters or graphics. The 5 phases are Seiri, Seiton, Seiso, Seiketsu and Shitsuke, which can be translate as Sort, Set in order, Scrub, Standardize, and Sustain, focusing on orderliness and being applied especially in Japanese factories. The stages includes inputs objectives related to the efficiency and effectiveness of the process, but also subjective, which refers to moral values, education, training, culture. For each S stage, the most important elements which are underlying the implementation and maintain the compliance are described. Any company that applied the 5S program will have quick and visible results, reducing different types of waste. The final section presents a case study and some rules in order to sustain the designed standards and implement a continuous quality improvement. The concluding remarks could be considered as work instructions in order to implement the 5S rules.

  14. Aligning and synchronization of MIS5 proxy records from Lake Ohrid (FYROM) with independently dated Mediterranean archives: implications for DEEP core chronology

    Science.gov (United States)

    Zanchetta, Giovanni; Regattieri, Eleonora; Giaccio, Biagio; Wagner, Bernd; Sulpizio, Roberto; Francke, Alex; Vogel, Hendrik; Sadori, Laura; Masi, Alessia; Sinopoli, Gaia; Lacey, Jack H.; Leng, Melanie J.; Leicher, Niklas

    2016-05-01

    The DEEP site sediment sequence obtained during the ICDP SCOPSCO project at Lake Ohrid was dated using tephrostratigraphic information, cyclostratigraphy, and orbital tuning through the marine isotope stages (MIS) 15-1. Although this approach is suitable for the generation of a general chronological framework of the long succession, it is insufficient to resolve more detailed palaeoclimatological questions, such as leads and lags of climate events between marine and terrestrial records or between different regions. Here, we demonstrate how the use of different tie points can affect cyclostratigraphy and orbital tuning for the period between ca. 140 and 70 ka and how the results can be correlated with directly/indirectly radiometrically dated Mediterranean marine and continental proxy records. The alternative age model presented here shows consistent differences with that initially proposed by Francke et al. (2015) for the same interval, in particular at the level of the MIS6-5e transition. According to this new age model, different proxies from the DEEP site sediment record support an increase of temperatures between glacial to interglacial conditions, which is almost synchronous with a rapid increase in sea surface temperature observed in the western Mediterranean. The results show how a detailed study of independent chronological tie points is important to align different records and to highlight asynchronisms of climate events. Moreover, Francke et al. (2016) have incorporated the new chronology proposed for tephra OH-DP-0499 in the final DEEP age model. This has reduced substantially the chronological discrepancies between the DEEP site age model and the model proposed here for the last glacial-interglacial transition.

  15. 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).

  16. Highly Enhanced Gas Adsorption Properties in Vertically Aligned MoS2 Layers.

    Science.gov (United States)

    Cho, Soo-Yeon; Kim, Seon Joon; Lee, Youhan; Kim, Jong-Seon; Jung, Woo-Bin; Yoo, Hae-Wook; Kim, Jihan; Jung, Hee-Tae

    2015-09-22

    In this work, we demonstrate that gas adsorption is significantly higher in edge sites of vertically aligned MoS2 compared to that of the conventional basal plane exposed MoS2 films. To compare the effect of the alignment of MoS2 on the gas adsorption properties, we synthesized three distinct MoS2 films with different alignment directions ((1) horizontally aligned MoS2 (basal plane exposed), (2) mixture of horizontally aligned MoS2 and vertically aligned layers (basal and edge exposed), and (3) vertically aligned MoS2 (edge exposed)) by using rapid sulfurization method of CVD process. Vertically aligned MoS2 film shows about 5-fold enhanced sensitivity to NO2 gas molecules compared to horizontally aligned MoS2 film. Vertically aligned MoS2 has superior resistance variation compared to horizontally aligned MoS2 even with same surface area exposed to identical concentration of gas molecules. We found that electrical response to target gas molecules correlates directly with the density of the exposed edge sites of MoS2 due to high adsorption of gas molecules onto edge sites of vertically aligned MoS2. Density functional theory (DFT) calculations corroborate the experimental results as stronger NO2 binding energies are computed for multiple configurations near the edge sites of MoS2, which verifies that electrical response to target gas molecules (NO2) correlates directly with the density of the exposed edge sites of MoS2 due to high adsorption of gas molecules onto edge sites of vertically aligned MoS2. We believe that this observation extends to other 2D TMD materials as well as MoS2 and can be applied to significantly enhance the gas sensor performance in these materials.

  17. A New Alignment Method Based on The Wavelet Multi-Scale Cross-Correlation for Noisy High Resolution ECG Records

    National Research Council Canada - National Science Library

    Laciar, E

    2001-01-01

    ... between the wavelet transforms of the template and the detected beat, respectively. The wavelet and temporal methods were tested for several simulated records corrupted with white noise and electromyographic (EMG...

  18. 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.

  19. Paper S12 5 : Self-aligned a-IGZO TFTs : Impact of S/D contacts formation on their Negative-Bias-Illumination-Stress (NBIS) instability

    NARCIS (Netherlands)

    Nag, M.; Steudel, S.; Smout, S.; Bhoolokam, A.; Genoe, J.; Cobb, B.; Kumar, A.; Groeseneken, G.; Heremans, P.

    2015-01-01

    In this work, we present the impact of S/D contact formation, that is, by SiN plasma doping (hydrogen incorporation), metallic reduction (by calcium) and by argon plasma (compositional change) on NBIS instabilities of self-aligned a-IGZO TFTs.

  20. MOSS-5: A Fast Method of Approximating Counts of 5-Node Graphlets in Large Graphs

    KAUST Repository

    Wang, Pinghui

    2017-09-26

    Counting 3-, 4-, and 5-node graphlets in graphs is important for graph mining applications such as discovering abnormal/evolution patterns in social and biology networks. In addition, it is recently widely used for computing similarities between graphs and graph classification applications such as protein function prediction and malware detection. However, it is challenging to compute these metrics for a large graph or a large set of graphs due to the combinatorial nature of the problem. Despite recent efforts in counting triangles (a 3-node graphlet) and 4-node graphlets, little attention has been paid to characterizing 5-node graphlets. In this paper, we develop a computationally efficient sampling method to estimate 5-node graphlet counts. We not only provide fast sampling methods and unbiased estimators of graphlet counts, but also derive simple yet exact formulas for the variances of the estimators which is of great value in practice-the variances can be used to bound the estimates\\' errors and determine the smallest necessary sampling budget for a desired accuracy. We conduct experiments on a variety of real-world datasets, and the results show that our method is several orders of magnitude faster than the state-of-the-art methods with the same accuracy.

  1. Making the Right Pick: Aligning Order Picking Methods, Incentive Systems and Regulatory Focus to Increase Picking Performance

    NARCIS (Netherlands)

    J. de Vries (Jelle); M.B.M. de Koster (René); D.A. Stam (Daan)

    2015-01-01

    textabstractA unique controlled field experiment investigates order picking performance (in terms of productivity, quality, and job satisfaction). We examined three manual picker-to-parts order picking methods (parallel, zone, and dynamic zone picking) under two different incentive systems

  2. Integrating the Self and the Spirit: Strategies for Aligning Qualitative Research Teaching with Indigenous Methods, Methodologies, and Epistemology

    Directory of Open Access Journals (Sweden)

    Sarah K. Knudson

    2015-07-01

    Full Text Available Many universities internationally now make concerted efforts to promote curriculum development and classroom and campus cultures that recognize diversity in student viewpoints and life experiences. Increasingly, these efforts have involved promoting recognition and inclusion of indigenous knowledges in the university setting. If adopted in the classroom, the promotion of indigenous perspectives suggests exciting possibilities for teaching qualitative research critically. Existing educational resources, however, offer little guidance on achieving this through undergraduate qualitative methods teaching. Using examples of Canadian undergraduate teaching initiatives, I suggest that by integrating indigenous methods, perspectives, and epistemology, particularly through student opportunities for community-engaged learning and exposure to participatory action research, teaching qualitative research can promote critical recognition of multiple ways of knowing. URN: http://nbn-resolving.de/urn:nbn:de:0114-fqs150347

  3. Surface-roughness-assisted formation of large-scale vertically aligned CdS nanorod arrays via solvothermal method

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Minmin [National Laboratory of Solid State Microstructures, School of Electronic Science and Engineering, Nanjing University, Nanjing 210093 (China); Yan, Shancheng, E-mail: yansc@njupt.edu.cn [National Laboratory of Solid State Microstructures, School of Electronic Science and Engineering, Nanjing University, Nanjing 210093 (China); School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210046 (China); Shi, Yi, E-mail: yshi@nju.edu.cn [National Laboratory of Solid State Microstructures, School of Electronic Science and Engineering, Nanjing University, Nanjing 210093 (China); Yang, Meng; Sun, Huabin; Wang, Jianyu; Yin, Yao; Gao, Fan [National Laboratory of Solid State Microstructures, School of Electronic Science and Engineering, Nanjing University, Nanjing 210093 (China)

    2013-05-15

    Large-scale cadmium sulfide (CdS) nanorod arrays were successfully synthesized on several different substrates through solvothermal reaction. During the growth experiments, we observed that the adhesion strength of the CdS nanorod arrays to different substrates differed dramatically, causing some of the CdS coating being easily flushed away by deionized water (DI water). With doubts and suspicions, we seriously investigate the original morphology of all the substrates by using atomic force microscopy (AFM). The phase, morphology, crystal structure and photoelectric property of all the products were characterized by X-ray diffractometer (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), Raman spectroscopy and current–voltage (I–V) probe station. The growth mechanism of solvothermal reaction was proposed on the basis of all the characterizations. Our approach presents a universal method of liquid phase epitaxy of 1D material on a wide range of substrates of any shape.

  4. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez.

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

  5. Alignment of the TFTR bumper limiter

    International Nuclear Information System (INIS)

    Barnes, G.W.; Owens, D.K.; Loesser, G.D.; Ulrickson, M.

    1989-01-01

    The TFTR Bumper Limiter (BL) is an axisymmetric toroidal limiter mounted on the inner wall of the vacuum vessel. It subtends 120 degree poloidally and has a surface area of 22 m 2 . The plasma facing surface consists of 1,000 kg of graphite tiles mounted on watercooled Inconel backing plates. During the initial installation in the Spring of 1985, the limiter surface was aligned to the toroidal magnetic field by mechanical and magnetic measurements to an estimated accuracy of ±2 mm. During subsequent operation, especially in the 1988 run period in which 30 MW of Neutral Beam Injection routinely occurred, several tiles at points on the limiter which protruded slightly into the plasma were severely damaged. The damage, cracked and spalled tiles, is believed to be initiated by high energy disruptions and aggravated by normal high power operation. The damage pattern and temperature rise during normal operation are consistent with this interpretation. A vacuum vessel opening to replace the damaged tiles and realign the limiter was required. The bumper limiter was reshaped to be circular to ±0.5 mm at the midplane by means of mechanical measurements in order to better distribute the heat loads and eliminate hot spots. The ±0.5 mm accuracy is determined by the variation in individual tile thickness which is ±0.5 mm. This paper describes the methods used to mechanically align the limiter and presents evidence based on machine operation with plasma that the limiter is reasonably well aligned with the toroidal field. Future work dealing with the alignment of the total limiter to the toroidal field using mechanical and magnetic measurements and the replacement of a subset of the carbon tiles with carbon-carbon composite material is also discussed. 7 refs., 4 figs

  6. Automatic alignment of radionuclide images

    International Nuclear Information System (INIS)

    Barber, D.C.

    1982-01-01

    The variability of the position, dimensions and orientation of a radionuclide image within the field of view of a gamma camera hampers attempts to analyse the image numerically. This paper describes a method of using a set of training images of a particular type, in this case right lateral brain images, to define the likely variations in the position, dimensions and orientation for that type of image and to provide alignment data for a program that automatically aligns new images of the specified type to a standard position, size and orientation. Examples are given of the use of this method on three types of radionuclide image. (author)

  7. Measurements of magnetic field alignment

    International Nuclear Information System (INIS)

    Kuchnir, M.; Schmidt, E.E.

    1987-01-01

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

  8. 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.

  9. A general salt-templating method to fabricate vertically aligned graphitic carbon nanosheets and their metal carbide hybrids for superior lithium ion batteries and water splitting.

    Science.gov (United States)

    Zhu, Jixin; Sakaushi, Ken; Clavel, Guylhaine; Shalom, Menny; Antonietti, Markus; Fellinger, Tim-Patrick

    2015-04-29

    The synthesis of vertically aligned functional graphitic carbon nanosheets (CNS) is challenging. Herein, we demonstrate a general approach for the fabrication of vertically aligned CNS and metal carbide@CNS composites via a facile salt templating induced self-assembly. The resulting vertically aligned CNS and metal carbide@CNS structures possess ultrathin walls, good electrical conductivity, strong adhesion, excellent structural robustness, and small particle size. In electrochemical energy conversion and storage such unique features are favorable for providing efficient mass transport as well as a large and accessible electroactive surface. The materials were tested as electrodes in a lithium ion battery and in electrochemical water splitting. The vertically aligned nanosheets exhibit remarkable lithium ion storage properties and, concurrently, excellent properties as electrocatalysts for hydrogen evolution.

  10. Technology Alignment and Portfolio Prioritization (TAPP): Advanced Methods in Strategic Analysis, Technology Forecasting and Long Term Planning for Human Exploration and Operations, Advanced Exploration Systems and Advanced Concepts

    Science.gov (United States)

    Funaro, Gregory V.; Alexander, Reginald A.

    2015-01-01

    The Advanced Concepts Office (ACO) at NASA, Marshall Space Flight Center is expanding its current technology assessment methodologies. ACO is developing a framework called TAPP that uses a variety of methods, such as association mining and rule learning from data mining, structure development using a Technological Innovation System (TIS), and social network modeling to measure structural relationships. The role of ACO is to 1) produce a broad spectrum of ideas and alternatives for a variety of NASA's missions, 2) determine mission architecture feasibility and appropriateness to NASA's strategic plans, and 3) define a project in enough detail to establish an initial baseline capable of meeting mission objectives ACO's role supports the decision­-making process associated with the maturation of concepts for traveling through, living in, and understanding space. ACO performs concept studies and technology assessments to determine the degree of alignment between mission objectives and new technologies. The first step in technology assessment is to identify the current technology maturity in terms of a technology readiness level (TRL). The second step is to determine the difficulty associated with advancing a technology from one state to the next state. NASA has used TRLs since 1970 and ACO formalized them in 1995. The DoD, ESA, Oil & Gas, and DoE have adopted TRLs as a means to assess technology maturity. However, "with the emergence of more complex systems and system of systems, it has been increasingly recognized that TRL assessments have limitations, especially when considering [the] integration of complex systems." When performing the second step in a technology assessment, NASA requires that an Advancement Degree of Difficulty (AD2) method be utilized. NASA has used and developed or used a variety of methods to perform this step: Expert Opinion or Delphi Approach, Value Engineering or Value Stream, Analytical Hierarchy Process (AHP), Technique for the Order of

  11. 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.

  12. Solving the shrinkage-induced PDMS alignment registration issue in multilayer soft lithography

    International Nuclear Information System (INIS)

    Moraes, Christopher; Sun, Yu; Simmons, Craig A

    2009-01-01

    Shrinkage of polydimethylsiloxane (PDMS) complicates alignment registration between layers during multilayer soft lithography fabrication. This often hinders the development of large-scale microfabricated arrayed devices. Here we report a rapid method to construct large-area, multilayered devices with stringent alignment requirements. This technique, which exploits a previously unrecognized aspect of sandwich mold fabrication, improves device yield, enables highly accurate alignment over large areas of multilayered devices and does not require strict regulation of fabrication conditions or extensive calibration processes. To demonstrate this technique, a microfabricated Braille display was developed and characterized. High device yield and accurate alignment within 15 µm were achieved over three layers for an array of 108 Braille units spread over a 6.5 cm 2 area, demonstrating the fabrication of well-aligned devices with greater ease and efficiency than previously possible

  13. Methods and applications of HPLC-AMS (WBio 5)

    International Nuclear Information System (INIS)

    Bucholz, B A; Clifford, A J; Duecker, S R; Lin, Y; Vogel, J S

    1999-01-01

    Pharmacokinetics of physiologic doses of nutrients, pesticides, and herbicides can easily be traced in humans using a(sup 14)C-labelled compound. Basic kinetics can be monitored in blood or urine by measuring the elevation in the(sup 14)C content above the control predose tissue and converting to equivalents of the parent compound. High Performance Liquid Chromatography (HPLC) is an excellent method for the chemical separation of complex mixtures whose profiles afford estimation of biochemical pathways of metabolism. Compounds elute from the HPLC systems with characteristic retention times and can be collected in fractions that can then be graphitized for AMS measurement. Unknowns are identified by coelution with known standards and chemical tests that reveal functional groupings. Metabolites are quantified with the(sup 14)C signal. Thoroughly accounting for the carbon inventory in the LC solvents, ion-pairing agents, samples, and carriers adds some complexity to the analysis. In most cases the total carbon inventory is dominated by carrier. Baseline background and stability need to be carefully monitored. Limits of quantitation near 10 amol of(sup 14)C per HPLC fraction are typically achieved. Baselines are maintained by limiting injected(sup 14)C activity and lt;0.17 Bq (4.5 pCi) on the HPLC column

  14. 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...

  15. 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, ...

  16. 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

  17. 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.

  18. 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

  19. XUV ionization of aligned molecules

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-11-15

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

  20. XUV ionization of aligned molecules

    International Nuclear Information System (INIS)

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

    2011-01-01

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

  1. Aligning Assessments for COSMA Accreditation

    Science.gov (United States)

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

    2015-01-01

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

  2. 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.

  3. Method for enzyme synthesis of radioactive thymine 5'-deoxyribonucleotides

    International Nuclear Information System (INIS)

    Nejedly, Z.; Ekl, J.; Hybs, K.; Kolina, J.; Filip, J.; Votruba, I.; Skoda, J.

    1978-01-01

    The enzyme synthesis is described for thymidine-5'-monophosphate, thymidine-5'-diphosphate and thymidine-5'-triphosphate specifically or nonspecifically labelled with 14 C or 3 H. The anabolic transformation of radioactive thymine to radioactive thymine 5'-deoxyribonucleotides is catalyzed by the action of enzyme preparations separated from Escherichia coli bacteria. It is achieved by the action of nonpurified cell-free extracts on special auxotrophic mutants of the thymine-dependent Escherichia coli SPT - strain in the presence of deoxyriboso-1-phosphate and adenosine-5'-triphosphate. The radioactive thymidine-5'-monophosphate may further be phosphorylated. In reaction mixtures, radioactive thymine, deoxyriboso-1-phosphate and adenosine-5'-triphosphate are used in molar ratios of 1:1:2 to 1:10:100, the optimum molar ratio being 1:5:10. (B.S.)

  4. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.; Bonny, Talal; Salama, Khaled N.

    2012-01-01

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

  5. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.

    2012-01-26

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

  6. Grain alignment in starless cores

    International Nuclear Information System (INIS)

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

    2015-01-01

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

  7. Plasmon Modes of Vertically Aligned Superlattices

    DEFF Research Database (Denmark)

    Filonenko, Konstantin; Duggen, Lars; Willatzen, Morten

    2017-01-01

    By using the Finite Element Method we visualize the modes of vertically aligned superlattice composed of gold and dielectric nanocylinders and investigate the emitter-plasmon interaction in approximation of weak coupling. We find that truncated vertically aligned superlattice can function...

  8. 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

  9. 5th Symposium on Hybrid RANS-LES Methods

    CERN Document Server

    Haase, Werner; Peng, Shia-Hui; Schwamborn, Dieter

    2015-01-01

    This book gathers the proceedings of the Fifth Symposium on Hybrid RANS-LES Methods, which was held on March 19-21 in College Station, Texas, USA. The different chapters, written by leading experts, reports on the most recent developments in flow physics modelling, and gives a special emphasis to industrially relevant applications of hybrid RANS-LES methods and other turbulence-resolving modelling approaches. The book addresses academic researchers, graduate students, industrial engineers, as well as industrial R&D managers and consultants dealing with turbulence modelling, simulation and measurement, and with multidisciplinary applications of computational fluid dynamics (CFD), such as flow control, aero-acoustics, aero-elasticity and CFD-based multidisciplinary optimization. It discusses in particular advanced hybrid RANS-LES methods. Further topics include wall-modelled Large Eddy Simulation (WMLES) methods, embedded LES, and a comparison of the LES methods with both hybrid RANS-LES and URANS methods. ...

  10. 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.

  11. 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.

  12. 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.

  13. When the Stars Align: On the Contributions of Gilbert Gottlieb and Peter C. M. Molenaar to Developmental Science Theory and Method

    Science.gov (United States)

    Lerner, Richard M.; Batanova, Milena; Ettekal, Andrea Vest; Hunter, Cristina

    2015-01-01

    When truly spectacular events occur in the performing arts or in team sports, when the sets of artists or athletes respectively creating these events are discussed, a common phrase used in America to explain the "good fortune" that was involved in such unique occurrences is that "the stars aligned." In this commentary on:…

  14. SPA: a probabilistic algorithm for spliced alignment.

    Directory of Open Access Journals (Sweden)

    2006-04-01

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

  15. 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.

  16. Comparative SEM analysis of nine F22 aligner cleaning strategies

    Directory of Open Access Journals (Sweden)

    Luca Lombardo

    2017-09-01

    Full Text Available Abstract Background The orthodontics industry has paid great attention to the aesthetics of orthodontic appliances, seeking to make them as invisible as possible. There are several advantages to clear aligner systems, including aesthetics, comfort, chairside time reduction, and the fact that they can be removed for meals and oral hygiene procedures. Methods Five patients were each given a series of F22 aligners, each to be worn for 14 days and nights, with the exception of meal and brushing times. Patients were instructed to clean each aligner using a prescribed strategy, and sections of the used aligners were observed under SEM. One grey-scale SEM image was saved per aligner in JPEG format with an 8-bit colour depth, and a total of 45 measurements on the grey scale (“Value” variable were made. This dataset was analysed statistically via repeated measures ANOVA to determine the effect of each of the nine cleaning strategies in each of the five patients. Results A statistically significant difference in the efficacy of the cleaning strategies was detected. Specifically, rinsing with water alone was significantly less efficacious, and a combination of cationic detergent solution and ultrasonication was significantly more efficacious than the other methods (p < 0.05. Conclusions Of the nine cleaning strategies examined, only that involving 5 min of ultrasonication at 42 k Hz combined with a 0.3% germicidal cationic detergent was observed to be statistically effective at removing the bacterial biofilm from the surface of F22 aligners.

  17. 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

  18. Alignment technology and applications of liquid crystal devices

    CERN Document Server

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

    2005-01-01

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

  19. 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 ...

  20. 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...

  1. Annotation Method (AM): SE5_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available base search. Peaks with no hit to these databases are then selected to secondary se...arch using exactMassDB and Pep1000 databases. After the database search processes, each database hits are ma...SE5_AM1 PowerGet annotation A1 In annotation process, KEGG, KNApSAcK and LipidMAPS are used for primary data

  2. 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...

  3. Nanostructured Networks for Energy Storage: Vertically Aligned Carbon Nanotubes (VACNT as Current Collectors for High-Power Li4Ti5O12(LTO//LiMn2O4(LMO Lithium-Ion Batteries

    Directory of Open Access Journals (Sweden)

    Fabian Pawlitzek

    2017-11-01

    Full Text Available As a concept for electrode architecture in high power lithium ion batteries, self-supported nanoarrays enable ultra-high power densities as a result of their open pore geometry, which results in short and direct Li+-ion and electron pathways. Vertically aligned carbon nanotubes (VACNT on metallic current collectors with low interface resistance are used as current collectors for the chemical solution infiltration of electroactive oxides to produce vertically aligned carbon nanotubes decorated with in situ grown LiMn2O4 (LMO and Li4Ti5O12 (LTO nanoparticles. The production processes steps (catalyst coating, VACNT chemical vapor deposition (CVD, infiltration, and thermal transformation are all scalable, continuous, and suitable for niche market production to achieve high oxide loadings up to 70 wt %. Due to their unique transport structure, as-prepared nanoarrays achieve remarkably high power densities up to 2.58 kW kg−1, which is based on the total electrode mass at 80 C for LiMn2O4//Li4Ti5O12 full cells. The tailoring of LTO and LMO nanoparticle size (~20–100 nm and VACNT length (array height: 60–200 µm gives insights into the rate-limiting steps at high current for these kinds of nanoarray electrodes at very high C-rates of up to 200 C. The results reveal the critical structural parameters for achieving high power densities in VACNT nanoarray full cells.

  4. Some Alignment Considerations for the Next Linear Collider

    International Nuclear Information System (INIS)

    Ruland, R

    2004-01-01

    Next Linear Collider type accelerators require a new level of alignment quality. The relative alignment of these machines is to be maintained in an error envelope dimensioned in micrometers and for certain parts in nanometers. In the nanometer domain our terra firma cannot be considered monolithic but compares closer to jelly. Since conventional optical alignment methods cannot deal with the dynamics and cannot approach the level of accuracy, special alignment and monitoring techniques must be pursued

  5. 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.

  6. Optimal Nonlinear Filter for INS Alignment

    Institute of Scientific and Technical Information of China (English)

    赵瑞; 顾启泰

    2002-01-01

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

  7. 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.

  8. 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.

  9. Methods and methodology of sexual dysfunctions with males. Chapter 5

    International Nuclear Information System (INIS)

    2000-01-01

    Examination of patients (liquidators of Chernobyl accident) was carried out in Republican Hospital for Great War Invalids. Sexual function of patients was estimated with help G.V. Vasilenko's questionnaire 'Men's sexual function'. For consideration of sexual dysfunctions the scale for qualitative estimation of potention dysfunction level was used. For revealing of vegetative nervous system dysfunction with examined patients the Ashner effect was studied. The functional status of pituitary gland - gonad system was studied by content of hormones in blood (follicle stimulating and luteinizing hormones). Results of investigations of both the sexual function and hormone level in blood were processed by method of variation statistics. For determination of each factors influence from all acting factors on sexual function the multifactorial dispersion analysis was carried out

  10. Method to produce furandicarboxylic acid (FDCA) from 5-hydroxymethylfurfural (HMF)

    Science.gov (United States)

    Dumesic, James A.; Motagamwala, Ali Hussain

    2017-04-11

    A process to produce furandicarboxylic acid (FDCA). The process includes the steps of reacting a C6 sugar-containing reactant in a reaction solution comprising a first organic solvent selected from the group consisting of beta-, gamma-, and delta-lactones, hydrofurans, hydropyrans, and combinations thereof, in the presence of an acid catalyst for a time and under conditions wherein at least a portion of the C6 sugar present in the reactant is converted to 5-(hydroxymethyl)furfural (HMF); oxidizing the HMF into FDCA with or without separating the HMF from the reaction solution; and extracting the FDCA by adding an aprotic organic solvent having a dipole moment of about 1.0 D or less to the reaction solution.

  11. Twistor methods for AdS{sub 5}

    Energy Technology Data Exchange (ETDEWEB)

    Adamo, Tim; Skinner, David; Williams, Jack [Department of Applied Mathematics & Theoretical Physics, University of Cambridge,Wilberforce Road, Cambridge, CB3 0WA United Kingdom (United Kingdom)

    2016-08-30

    We consider the application of twistor theory to five-dimensional anti-de Sitter space. The twistor space of AdS{sub 5} is the same as the ambitwistor space of the four-dimensional conformal boundary; the geometry of this correspondence is reviewed for both the bulk and boundary. A Penrose transform allows us to describe free bulk fields, with or without mass, in terms of data on twistor space. Explicit representatives for the bulk-to-boundary propagators of scalars and spinors are constructed, along with twistor action functionals for the free theories. Evaluating these twistor actions on bulk-to-boundary propagators is shown to produce the correct two-point functions.

  12. MOSS-5: A Fast Method of Approximating Counts of 5-Node Graphlets in Large Graphs

    KAUST Repository

    Wang, Pinghui; Zhao, Junzhou; Zhang, Xiangliang; Li, Zhenguo; Cheng, Jiefeng; Lui, John C.S.; Towsley, Don; Tao, Jing; Guan, Xiaohong

    2017-01-01

    Counting 3-, 4-, and 5-node graphlets in graphs is important for graph mining applications such as discovering abnormal/evolution patterns in social and biology networks. In addition, it is recently widely used for computing similarities between

  13. Intraoperative panoramic image using alignment grid, is it accurate?

    Science.gov (United States)

    Apivatthakakul, T; Duanghakrung, M; Luevitoonvechkit, S; Patumasutra, S

    2013-07-01

    Minimally invasive orthopedic trauma surgery relies heavily on intraoperative fluoroscopic images to evaluate the quality of fracture reduction and fixation. However, fluoroscopic images have a narrow field of view and often cannot visualize the entire long bone axis. To compare the coronal femoral alignment between conventional X-rays to that achieved with a new method of acquiring a panoramic intraoperative image. Twenty-four cadaveric femurs with simple diaphyseal fractures were fixed with an angulated broad DCP to create coronal plane malalignment. An intraoperative alignment grid was used to help stitch different fluoroscopic images together to produce a panoramic image. A conventional X-ray of the entire femur was then performed. The coronal plane angulation in the panoramic images was then compared to the conventional X-rays using a Wilcoxon signed rank test. The mean angle measured from the panoramic view was 173.9° (range 169.3°-178.0°) with median of 173.2°. The mean angle measured from the conventional X-ray was 173.4° (range 167.7°-178.7°) with a median angle of 173.5°. There was no significant difference between both methods of measurement (P = 0.48). Panoramic images produced by stitching fluoroscopic images together with help of an alignment grid demonstrated the same accuracy at evaluating the coronal plane alignment of femur fractures as conventional X-rays.

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

    Directory of Open Access Journals (Sweden)

    Schirmer Stefanie

    2010-04-01

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

  15. 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.

  16. 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.

  17. Ni_0_,_5Zn_0_,_5Fe_2O_3 ferrite synthesized by combustion and Pechini method for use in nanomedicine: methods evaluation

    International Nuclear Information System (INIS)

    Albuquerque, I.L.T. de; Nascimento, A.L.C.; Costa, A.C.F.M.

    2016-01-01

    The objective of this work was to synthesize the Ni0.5Zn0.5Fe2O3 ferrite by combustion reaction and Pechini method, and to evaluate structural characteristics and magnetic behavior for its use in nanomedicine. The synthesized ferrite was characterized by DRX, BET, TG and magnetic properties. According to the results of XRD, the Ni_0_,_5Zn_0_,_5Fe_2O_3 ferrite synthesized by both methods presented nano crystallite sizes, high crystallinity, surface area, stable at high temperatures and with high saturation magnetization, being higher in the ferrite synthesized by combustion reaction. Both methods produced materials that could be used in nanomedicine

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

    Directory of Open Access Journals (Sweden)

    Che-Lun Hung

    2013-01-01

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

  19. 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.

  20. 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...

  1. 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

  2. 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.

  3. 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...

  4. 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...

  5. Angular momentum alignment in molecular beam scattering

    International Nuclear Information System (INIS)

    Treffers, M.A.

    1985-01-01

    It is shown how the angular momentum alignment in a molecular beam can be determined using laser-induced fluorescence in combination with precession of the angular momenta in a magnetic field. After a general analysis of the method, some results are presented to illustrate the possibilities of the method. Experimental data are presented on the alignment production for Na 2 molecules that made a collision induced angular momentum transition. Magnitude as well as direction of the alignment have been determined for scattering with several scattering partners and for a large number of scattering angles and transitions. The last chapter deals with the total alignment production in a final J-state, i.e. without state selection of the initial rotational state. (orig.)

  6. Open bite treatment using clear aligners.

    Science.gov (United States)

    Guarneri, Maria Paola; Oliverio, Teresa; Silvestre, Ivana; Lombardo, Luca; Siciliani, Giuseppe

    2013-09-01

    A 35-year-old female patient with dentoalveolar open bite of 4 mm, molar Class I malocclusion, centered midlines, moderate crowding, and labial inclination of the lower incisor was treated with clear aligners to reduce protrusion and close the anterior open bite. The result showed that clear aligners were an effective method with which to correct this malocclusion. The treatment was complete after 18 months. The patient was satisfied with her new appearance and function.

  7. Orthodontic Tooth Movement with Clear Aligners

    OpenAIRE

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

    2012-01-01

    Clear aligners provide a convenient model to measure orthodontic tooth movement (OTM). We examined the role of in vivo aligner material fatigue and subject-specific factors in tooth movement. Fifteen subjects seeking orthodontic treatment at the University of Florida were enrolled. Results were compared with data previously collected from 37 subjects enrolled in a similar protocol. Subjects were followed prospectively for eight weeks. An upper central incisor was programmed to move 0.5 mm. ev...

  8. Generation and application of Bessel beam in alignment works

    International Nuclear Information System (INIS)

    Gale, D. M.

    2009-01-01

    The divergence of a Gaussian laser beam is a limiting factor for optical alignment tasks at large distances. Bessel beams have almost zero divergence but are still not widely used. We discuss the construction of an alignment telescope based on Bessel beam generation using a commercial laser diode module. The Bessel beam is generated with conical or plano-convex lenses, and projected using a commercial CCD camera lens to extend the useful range of the beam. Our Bessel beams have diameters of between 0.5 - 1mm over beam lengths of 15m, representing a six-fold improvement compared to Gaussian beams, while the transverse beam structure (Bessel pattern) provides an excellent alignment aid for use with beam target. Another advantage of Bessel beams is their self-regeneration property, which allows the use of multiple beam targets with minimum beam degradation. We are using our crosshair targets with crosshair targets to align optical components in a large astronomical telescope, and can achieve precisions of tens of microns over distances of 20m using purely visual methods. (Author)

  9. Laser alignment of rotating equipment at PNL

    International Nuclear Information System (INIS)

    Berndt, R.H.

    1994-05-01

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

  10. 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.

  11. THE IMPACT OF PILATES EXERCISES ON THE POSTURAL ALIGNMENT OF HEALTHY ADULTS

    Directory of Open Access Journals (Sweden)

    Bruna Krawczky

    Full Text Available ABSTRACT Introduction: Exercises of Pilates method have been widely used to improve postural alignment. There is strong evidence favoring their use in improving flexibility and balance, as well as some evidence of improvement in muscle strength. However, the benefits related to posture are not well established. Objective: To investigate in healthy adults, the impact of the Pilates method in the postural alignment through some angles in the sagittal plane and the occurrence of pain before and after an exercise session, and after the completion of a 16-session program. Methods: This is a quasi-experimental study of pre and post-intervention type. Healthy adults (n = 37 interested in starting Pilates were evaluated for acute effects on posture after a Pilates session (n = 37 and after a 16-session program, for a period of 10 weeks (n = 13. Using the postural assessment software (SAPO, six angles were analyzed: head horizontal alignment (HHA, pelvis horizontal alignment (PHA, hip angle (HA, vertical alignment of the body (VAB, thoracic kyphosis (TK, and lumbar lordosis (LL. The occurrence of pain was investigated to control adverse effects. Results: Statistically significant (p<0.05 differences found after one session include increased HHA (left view, decreased VAB (left view and TK (both side views. After 16 sessions, we observed an increase of HHA, and a decrease of TK, LL (both side views and HA (right view. All the differences point to an improvement of postural alignment. A significant reduction of prevalence of pain was verified after the first session (40.5% vs. 13.5%; p=0.004 and after the full program (30.8% vs. 15.3%; p=0.02. Conclusions: Our results suggest that the Pilates method has a positive impact on postural alignment in healthy adults, besides being a safe exercise.

  12. Grain alignment in starless cores

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-01-01

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

  13. 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...

  14. 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...

  15. 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...

  16. Synthesis of homogeneous Ca0.5Sr0.5FeO2.5+δ compound using a mirror furnace method

    International Nuclear Information System (INIS)

    Mahboub, M.S.; Zeroual, S.; Boudjada, A.

    2012-01-01

    Graphical abstract: X-ray diffraction pattern indexing of Ca 0.5 Sr 0.5 FeO 2.5+δ powder sample obtained by mirror furnace method after thermal treatment. Highlights: ► A homogenous compound Ca 0.5 Sr 0.5 FeO 2.5+δ has been synthesized for the first time by a mirror furnace method. ► Ca 0.5 Sr 0.5 FeO 2.5+δ powder sample is perfectly homogenous, confirmed by X-ray diffraction, Raman spectroscopy and EDS technique. ► The thermal treatment of Ca 0.5 Sr 0.5 FeO 2.5+δ powder sample can increase their average grain sizes. -- Abstract: A new synthesis method using melting zone technique via the double mirror furnace around 1600 °C is used to obtain homogenous brownmillerite compounds Ca 1−x Sr x FeO 2.5+δ in the range 0.3 ≤ x ≤ 0.7. These compounds play important role in understanding the mystery of the oxygen diffusion in the perovskite-related oxides. We have successfully solved the miscibility gap problem by synthesizing a good quality of homogenous powder samples of Ca 0.5 Sr 0.5 FeO 2.5+δ compound. Our result was confirmed by X-rays diffraction, Raman spectroscopy and energy dispersive spectroscopy analysis. Thermal treatment was also applied until 800 °C under vacuum to confirm again the homogeneity of powder samples, improve its quality and show that no decomposition or return to form Ca- and Sr-enriched microdomains takes place as a result of phase separation.

  17. Study of the magnetic microstructure of high-coercivity sintered SmCo5 permanent magnets with the conventional Bitter pattern technique and the colloid-SEM method

    International Nuclear Information System (INIS)

    Szmaja, Witold

    2007-01-01

    The magnetic microstructure of high-coercivity sintered SmCo 5 permanent magnets was studied with the conventional Bitter pattern technique, and also for the first time with the colloid-scanning electron microscopy (colloid-SEM) method. Both techniques were supported by digital image acquisition, enhancement and analysis. Thanks to this, it was possible to obtain high-contrast and clear images of the magnetic microstructure and to analyze them in detail, and consequently also to achieve improvements over earlier results. In the thermally demagnetized state the grains were composed of magnetic domains. On the surface perpendicular to the alignment axis, the main domains forming a maze pattern and surface reverse spikes were observed. Investigations on the surface parallel to the alignment axis, especially by the colloid-SEM technique, provided a detailed insight into the orientation of grains. The alignment of grains was good, but certainly not perfect; there were also strongly misaligned grains, although generally very rare. In most cases the domain structures within grains were independent of their neighbors, but in some cases (not so rare) the domain walls were observed to continue through the grain boundaries, indicating significant magnetostatic interaction between neighboring grains. Studies of the behavior of the magnetic microstructure under the influence of an external magnetic field, performed for the first time on the surface parallel to the alignment axis (with the conventional Bitter pattern method), showed that the domain walls move easily within the grains and that the magnetization reversal mechanism is mainly related to the nucleation and growth of reverse domains, i.e. that sintered SmCo 5 magnets are nucleation-dominated systems. Groupwise magnetization reversal of adjacent magnetically coupled grains was observed, an unfavorable effect for high-coercivity magnets. Images obtained by the colloid-SEM technique and the conventional Bitter pattern

  18. Functional alignments and self-tests for tilted and decentered optics

    International Nuclear Information System (INIS)

    Bauke, W.; Cross, E.W.

    1983-01-01

    The alignment of tilted and decentered optics is ordinarily difficult, because such optics have neither simple alignment points amenable to ordinary boresight methods, nor a simple alignment theory. Several different alignment examples which provide insight into a practical universal approach to all such systems are explored. The examples detailed are segments of the Antares Laser Fusion Project's optical train

  19. The accuracy of intramedullary tibial guide of sagittal alignment of PCL-substituting total knee arthroplasty.

    Science.gov (United States)

    Han, Hyuk-Soo; Kang, Seung-Baik; Jo, Chris H; Kim, Sun-Hong; Lee, Jung-Ha

    2010-10-01

    Experimental and clinical studies on the accuracy of the intramedullary alignment method have produced different results, and few have addressed accuracy in the sagittal plane. Reported deviations are not only attributable to the alignment method but also to radiological errors. The purpose of this study was to evaluate the accuracy of the intramedullary alignment method in the sagittal plane using computed tomography (CT) and 3-dimensional imaging software. Thirty-one TKAs were performed using an intramedullary alignment method involving the insertion of a long 8-mm diameter rod into the medullary canal to the distal metaphysis of the tibia. All alignment instruments were set to achieve an ideal varus/valgus angle of 0° in the coronal plane and a tibial slope of 0° in the sagittal plane. The accuracy of the intramedullary alignment system was assessed by measuring the coronal tibial component angle and sagittal tibial slope angles, i.e., angles between the tibial anatomical axis and the tangent to the medial and lateral tibial plateau or the cut-surface. The mean coronal tibial component angle was 88.5° ± 1.2° and the mean tibial component slope in the sagittal plane was 1.6° ± 1.2° without anterior slope. Our intramedullary tibial alignment method, which involves passing an 8-mm diameter long rod through the tibial shaft isthmus, showed good accuracy (less than 3 degrees of variation and no anterior slope) in the sagittal plane in neutral or varus knees.

  20. Aligning Responsible Business Practices

    DEFF Research Database (Denmark)

    Weller, Angeli E.

    2017-01-01

    This article offers an in-depth case study of a global high tech manufacturer that aligned its ethics and compliance, corporate social responsibility, and sustainability practices. Few large companies organize their responsible business practices this way, despite conceptual relevance and calls t...... and managers interested in understanding how responsible business practices may be collectively organized.......This article offers an in-depth case study of a global high tech manufacturer that aligned its ethics and compliance, corporate social responsibility, and sustainability practices. Few large companies organize their responsible business practices this way, despite conceptual relevance and calls...... to manage them comprehensively. A communities of practice theoretical lens suggests that intentional effort would be needed to bridge meaning between the relevant managers and practices in order to achieve alignment. The findings call attention to the important role played by employees who broker...

  1. 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

  2. Alignment of whole genomes.

    Science.gov (United States)

    Delcher, A L; Kasif, S; Fleischmann, R D; Peterson, J; White, O; Salzberg, S L

    1999-01-01

    A new system for aligning whole genome sequences is described. Using an efficient data structure called a suffix tree, the system is able to rapidly align sequences containing millions of nucleotides. Its use is demonstrated on two strains of Mycoplasma tuberculosis, on two less similar species of Mycoplasma bacteria and on two syntenic sequences from human chromosome 12 and mouse chromosome 6. In each case it found an alignment of the input sequences, using between 30 s and 2 min of computation time. From the system output, information on single nucleotide changes, translocations and homologous genes can easily be extracted. Use of the algorithm should facilitate analysis of syntenic chromosomal regions, strain-to-strain comparisons, evolutionary comparisons and genomic duplications. PMID:10325427

  3. Validation of a Micrometric remotely controlled pre-alignment system for the CLIC Linear Collider using a test setup (Mock-Up) with 5 degrees of freedom

    CERN Document Server

    Mainaud Durand, H; Griffet, S; Kemppinen, J; Leuxe, R; Sosin, M

    2011-01-01

    The CLIC main beam quadrupoles need to be prealigned within 17 um rms with respect to a straight reference line along a sliding window of 200 m. A readjustment system based on eccentric cam movers, which will provide stiffness to the support assembly, is being studied. The cam movers were qualified on a 1 degree of freedom (DOF) test setup, where a repeatability of adjustment below 1um was measured along their whole range. This paper presents the 5 DOF mock-up, built for the validation of the eccentric cam movers, as well as the first results of tests carried out: resolution of displacement along the whole range, measurements of the support eigenfrequencies.

  4. Multiple network alignment on quantum computers

    Science.gov (United States)

    Daskin, Anmer; Grama, Ananth; Kais, Sabre

    2014-12-01

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

  5. Track-Based Alignment of the Inner Detector of ATLAS

    Directory of Open Access Journals (Sweden)

    Ovcharova Ana

    2012-06-01

    Full Text Available ATLAS is a multipurpose experiment at the LHC. The tracking system of ATLAS, embedded in a 2 T solenoidal field, is composed of different technologies: silicon planar sensors (pixel and microstrips and drift-tubes. The procedure used to align the ATLAS tracker and the results of the alignment using data recorded during 2010 and 2011 using LHC proton-proton collision runs at 7 TeV are presented. Validation of the alignment is performed by measuring the alignment observables as well as many other physics observables, notably resonance invariant masses in a wide mass range (KS, J/Ψ and Z. The E/p distributions for electrons from Z → ee and W → ev are also extensively used. The results indicate that, after the alignment with real data, the attained precision of the alignment constants is approximately 5 μm. The systematic errors due to the alignment that may affect physics results are under study.

  6. 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

  7. Experimental image alignment system

    Science.gov (United States)

    Moyer, A. L.; Kowel, S. T.; Kornreich, P. G.

    1980-01-01

    A microcomputer-based instrument for image alignment with respect to a reference image is described which uses the DEFT sensor (Direct Electronic Fourier Transform) for image sensing and preprocessing. The instrument alignment algorithm which uses the two-dimensional Fourier transform as input is also described. It generates signals used to steer the stage carrying the test image into the correct orientation. This algorithm has computational advantages over algorithms which use image intensity data as input and is suitable for a microcomputer-based instrument since the two-dimensional Fourier transform is provided by the DEFT sensor.

  8. Crystallographic alignment evolution and magnetic properties of anisotropic Sm{sub 0.6}Pr{sub 0.4}Co{sub 5} nanoflakes prepared by surfactant-assisted ball milling

    Energy Technology Data Exchange (ETDEWEB)

    Xu, M.L.; Wu, Q.; Li, Y.Q.; Liu, W.Q.; Lu, Q.M.; Yue, M., E-mail: yueming@bjut.edu.cn

    2015-08-01

    The microstructure, crystal structure and magnetic properties were studied for Sm{sub 0.6}Pr{sub 0.4}Co{sub 5} nanoflakes prepared by surfactant-assisted high-energy ball milling (SAHEBM). Effect of ball-milling time on the c-axis crystallographic alignment, morphology and magnetic properties of Sm{sub 0.6}Pr{sub 0.4}Co{sub 5} nanoflakes was systematically investigated. With increasing milling time from 1 h to 7 h, the intensity ratio between (002) and (111) reflection peaks indicating degree of c-axis crystal texture of the (Sm, Pr)Co{sub 5} phase increases first, peaks at 3 h, then drops again, revealing that the strongest c-axis crystal texture was obtained in the nanoflakes milled for 3 h. On the other hand, the coercivity (H{sub ci}) of the flakes increases gradually from 1.71 to 14.65 kOe with the increase of ball milling time. As a result, an optimal magnetic properties of M{sub r} of 10.23 kGs, H{sub ci} of 11.45 kOe and (BH){sub max} of 24.40 MGOe was obtained in Sm{sub 0.6}Pr{sub 0.4}Co{sub 5} nanoflakes milled for 3 h, which also displayed a high aspect ratio, small in-plane size, pronounced (001) out-of-plane texture. - Highlights: • Anisotropic Sm{sub 0.6}Pr{sub 0.4}Co{sub 5} nanoflakes with strong c-axis texture were prepared. • Effects of ball-milling time on structure and magnetic properties were studied. • (BH){sub max} value of Sm{sub 0.6}Pr{sub 0.4}Co{sub 5} nanoflakes is larger than that of SmCo{sub 5} nanoflakes.

  9. Molecular dynamics simulation based on the multi-component molecular orbital method: Application to H5O2+,D5O2+,andT5O2+

    International Nuclear Information System (INIS)

    Ishimoto, Takayoshi; Koyama, Michihisa

    2012-01-01

    Graphical abstract: Molecular dynamics method based on multi-component molecular orbital method was applied to basic hydrogen bonding systems, H 5 O 2 + , and its isotopomers (D 5 O 2 + andT 5 O 2 + ). Highlights: ► Molecular dynamics method with nuclear quantum effect was developed. ► Multi-component molecular orbital method was used as ab initio MO calculation. ► Developed method applied to basic hydrogen bonding system, H 5 O 2 + , and isotopomers. ► O ⋯ O vibrational stretching reflected to the distribution of protonic wavefunctions. ► H/D/T isotope effect was also analyzed. - Abstract: We propose a molecular dynamics (MD) method based on the multi-component molecular orbital (MC M O) method, which takes into account the quantum effect of proton directly, for the detailed analyses of proton transfer in hydrogen bonding system. The MC M O based MD (MC M O-MD) method is applied to the basic structures, H 5 O 2 + (called “Zundel ion”), and its isotopomers (D 5 O 2 + andT 5 O 2 + ). We clearly demonstrate the geometrical difference of hydrogen bonded O ⋯ O distance induced by H/D/T isotope effect because the O ⋯ O in H-compound was longer than that in D- or T-compound. We also find the strong relation between stretching vibration of O ⋯ O and the distribution of hydrogen bonded protonic wavefunction because the protonic wavefunction tends to delocalize when the O ⋯ O distance becomes short during the dynamics. Our proposed MC M O-MD simulation is expected as a powerful tool to analyze the proton dynamics in hydrogen bonding systems.

  10. 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

  11. Aligning Mental Representations

    DEFF Research Database (Denmark)

    Kano Glückstad, Fumiko

    2013-01-01

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

  12. Community Alignment ANADP

    OpenAIRE

    Halbert, Martin; Bicarregui, Juan; Anglada, Lluis; Duranti, Luciana

    2014-01-01

    Aligning National Approaches to Digital Preservation: An Action Assembly Biblioteca de Catalunya (National Library of Catalonia) November 18-20, 2013, Barcelona, Spain Auburn University Council on Library and Information Resources (CLIR) Digital Curation Centre (DCC) Digital Preservation Network (DPN) Joint Information Systems Committee (JISC) University of North Texas Virginia Tech Interuniversity Consortium for Political and Social Research (ICPSR) Innovative Inte...

  13. Resource Alignment ANADP

    OpenAIRE

    Grindley, Neil; Cramer, Tom; Schrimpf, Sabine; Wilson, Tom

    2014-01-01

    Aligning National Approaches to Digital Preservation: An Action Assembly Biblioteca de Catalunya (National Library of Catalonia) November 18-20, 2013, Barcelona, Spain Auburn University Council on Library and Information Resources (CLIR) Digital Curation Centre (DCC) Digital Preservation Network (DPN) Joint Information Systems Committee (JISC) University of North Texas Virginia Tech Interuniversity Consortium for Political and Social Research (ICPSR) Innovative Inte...

  14. Capacity Alignment ANADP

    OpenAIRE

    Davidson, Joy; Whitehead, Martha; Molloy, Laura; Molinaro, Mary

    2014-01-01

    Aligning National Approaches to Digital Preservation: An Action Assembly Biblioteca de Catalunya (National Library of Catalonia) November 18-20, 2013, Barcelona, Spain Auburn University Council on Library and Information Resources (CLIR) Digital Curation Centre (DCC) Digital Preservation Network (DPN) Joint Information Systems Committee (JISC) University of North Texas Virginia Tech Interuniversity Consortium for Political and Social Research (ICPSR) Innovative Inte...

  15. THE ATLAS INNER DETECTOR TRACK BASED ALIGNMENT

    CERN Document Server

    Marti i Garcia, Salvador; The ATLAS collaboration

    2018-01-01

    The alignment of the ATLAS Inner Detector is performed with a track-based alignment algorithm. Its goal is to provide an accurate description of the detector geometry such that track parameters are accurately determined and free from biases. Its software implementation is modular and configurable, with a clear separation of the alignment algorithm from the detector system specifics and the database handling. The alignment must cope with the rapid movements of the detector as well as with the slow drift of the different mechanical units. Prompt alignment constants are derived for every run at the calibration stage. These sets of constants are then dynamically split from the beginning of the run in many chunks, allowing to describe the tracker geometry as it evolves with time. The alignment of the Inner Detector is validated and improved by studying resonance decays (Z and J/psi to mu+mu-), as well as using information from the calorimeter system with the E/p method with electrons. A detailed study of these res...

  16. 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.

  17. Orthodontic tooth movement with clear aligners.

    Science.gov (United States)

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

    2012-01-01

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

  18. 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.

  19. 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.

  20. 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.

  1. Stochastic sampling of the RNA structural alignment space.

    Science.gov (United States)

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

    2009-07-01

    A novel method is presented for predicting the common secondary structures and alignment of two homologous RNA sequences by sampling the 'structural alignment' space, i.e. the joint space of their alignments and common secondary structures. The structural alignment space is sampled according to a pseudo-Boltzmann distribution based on a pseudo-free energy change that combines base pairing probabilities from a thermodynamic model and alignment probabilities from a hidden Markov model. By virtue of the implicit comparative analysis between the two sequences, the method offers an improvement over single sequence sampling of the Boltzmann ensemble. A cluster analysis shows that the samples obtained from joint sampling of the structural alignment space cluster more closely than samples generated by the single sequence method. On average, the representative (centroid) structure and alignment of the most populated cluster in the sample of structures and alignments generated by joint sampling are more accurate than single sequence sampling and alignment based on sequence alone, respectively. The 'best' centroid structure that is closest to the known structure among all the centroids is, on average, more accurate than structure predictions of other methods. Additionally, cluster analysis identifies, on average, a few clusters, whose centroids can be presented as alternative candidates. The source code for the proposed method can be downloaded at http://rna.urmc.rochester.edu.

  2. A Novel microCT Method for Bone and Marrow Adipose Tissue Alignment Identifies Key Differences Between Mandible and Tibia in Rats.

    Science.gov (United States)

    Coutel, Xavier; Olejnik, Cécile; Marchandise, Pierre; Delattre, Jérôme; Béhal, Hélène; Kerckhofs, Greet; Penel, Guillaume

    2018-01-30

    Bone homeostasis is influenced by the bone marrow adipose tissue (BMAT). BMAT distribution varies from one anatomical location in the skeleton to another. We developed an advanced microfocus computed tomography imaging and analysis protocol that allows accurate alignment of both the BMAT distribution and bone micro-architecture as well as calculation of the distance of the BMAT adipocytes from the bone surface. Using this protocol, we detected a different spatial BMAT distribution between the rat tibia and mandible: in the proximal metaphysis of the tibia a large amount of BMAT (~ 20% of the total BMAT) was located close to the bone surface (BMAT was located between 40 and 60 µm from the bone surface. In the alveolar ridge of rats, the trabecular bone volume was 48.3% higher compared to the proximal metaphysis of the tibia (p BMAT content with almost no contact with the bone surface. These findings are of great interest because of the importance of the fat-bone interaction and its potential relevance to several resorptive bone diseases.

  3. 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.

  4. W-curve alignments for HIV-1 genomic comparisons.

    Directory of Open Access Journals (Sweden)

    Douglas J Cork

    2010-06-01

    Full Text Available The W-curve was originally developed as a graphical visualization technique for viewing DNA and RNA sequences. Its ability to render features of DNA also makes it suitable for computational studies. Its main advantage in this area is utilizing a single-pass algorithm for comparing the sequences. Avoiding recursion during sequence alignments offers advantages for speed and in-process resources. The graphical technique also allows for multiple models of comparison to be used depending on the nucleotide patterns embedded in similar whole genomic sequences. The W-curve approach allows us to compare large numbers of samples quickly.We are currently tuning the algorithm to accommodate quirks specific to HIV-1 genomic sequences so that it can be used to aid in diagnostic and vaccine efforts. Tracking the molecular evolution of the virus has been greatly hampered by gap associated problems predominantly embedded within the envelope gene of the virus. Gaps and hypermutation of the virus slow conventional string based alignments of the whole genome. This paper describes the W-curve algorithm itself, and how we have adapted it for comparison of similar HIV-1 genomes. A treebuilding method is developed with the W-curve that utilizes a novel Cylindrical Coordinate distance method and gap analysis method. HIV-1 C2-V5 env sequence regions from a Mother/Infant cohort study are used in the comparison.The output distance matrix and neighbor results produced by the W-curve are functionally equivalent to those from Clustal for C2-V5 sequences in the mother/infant pairs infected with CRF01_AE.Significant potential exists for utilizing this method in place of conventional string based alignment of HIV-1 genomes, such as Clustal X. With W-curve heuristic alignment, it may be possible to obtain clinically useful results in a short time-short enough to affect clinical choices for acute treatment. A description of the W-curve generation process, including a comparison

  5. W-curve alignments for HIV-1 genomic comparisons.

    Science.gov (United States)

    Cork, Douglas J; Lembark, Steven; Tovanabutra, Sodsai; Robb, Merlin L; Kim, Jerome H

    2010-06-01

    The W-curve was originally developed as a graphical visualization technique for viewing DNA and RNA sequences. Its ability to render features of DNA also makes it suitable for computational studies. Its main advantage in this area is utilizing a single-pass algorithm for comparing the sequences. Avoiding recursion during sequence alignments offers advantages for speed and in-process resources. The graphical technique also allows for multiple models of comparison to be used depending on the nucleotide patterns embedded in similar whole genomic sequences. The W-curve approach allows us to compare large numbers of samples quickly. We are currently tuning the algorithm to accommodate quirks specific to HIV-1 genomic sequences so that it can be used to aid in diagnostic and vaccine efforts. Tracking the molecular evolution of the virus has been greatly hampered by gap associated problems predominantly embedded within the envelope gene of the virus. Gaps and hypermutation of the virus slow conventional string based alignments of the whole genome. This paper describes the W-curve algorithm itself, and how we have adapted it for comparison of similar HIV-1 genomes. A treebuilding method is developed with the W-curve that utilizes a novel Cylindrical Coordinate distance method and gap analysis method. HIV-1 C2-V5 env sequence regions from a Mother/Infant cohort study are used in the comparison. The output distance matrix and neighbor results produced by the W-curve are functionally equivalent to those from Clustal for C2-V5 sequences in the mother/infant pairs infected with CRF01_AE. Significant potential exists for utilizing this method in place of conventional string based alignment of HIV-1 genomes, such as Clustal X. With W-curve heuristic alignment, it may be possible to obtain clinically useful results in a short time-short enough to affect clinical choices for acute treatment. A description of the W-curve generation process, including a comparison technique of

  6. 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

  7. Poster - 48: Clinical assessment of ExacTrac stereoscopic imaging of spine alignment for lung SBRT

    International Nuclear Information System (INIS)

    Sattarivand, Mike; Summers, Clare; Robar, James

    2016-01-01

    Purpose: To evaluate the validity of using spine as a surrogate for tumor positioning with ExacTrac stereoscopic imaging in lung stereotactic body radiation therapy (SBRT). Methods: Using the Novalis ExacTrac x-ray system, 39 lung SBRT patients (182 treatments) were aligned before treatment with 6 degrees (6D) of freedom couch (3 translations, 3 rotations) based on spine matching on stereoscopic images. The couch was shifted to treatment isocenter and pre-treatment CBCT was performed based on a soft tissue match around tumor volume. The CBCT data were used to measure residual errors following ExacTrac alignment. The thresholds for re-aligning the patients based on CBCT were 3mm shift or 3° rotation (in any 6D). In order to evaluate the effect of tumor location on residual errors, correlations between tumor distance from spine and individual residual errors were calculated. Results: Residual errors were up to 0.5±2.4mm. Using 3mm/3° thresholds, 80/182 (44%) of the treatments required re-alignment based on CBCT soft tissue matching following ExacTrac spine alignment. Most mismatches were in sup-inf, ant-post, and roll directions which had larger standard deviations. No correlation was found between tumor distance from spine and individual residual errors. Conclusion: ExacTrac stereoscopic imaging offers a quick pre-treatment patient alignment. However, bone matching based on spine is not reliable for aligning lung SBRT patients who require soft tissue image registration from CBCT. Spine can be a poor surrogate for lung SBRT patient alignment even for proximal tumor volumes.

  8. Poster - 48: Clinical assessment of ExacTrac stereoscopic imaging of spine alignment for lung SBRT

    Energy Technology Data Exchange (ETDEWEB)

    Sattarivand, Mike; Summers, Clare; Robar, James [Nova Scotia Cancer Centre, Nova Scotia Cancer Centre, Nova Scotia Cancer Centre (Canada)

    2016-08-15

    Purpose: To evaluate the validity of using spine as a surrogate for tumor positioning with ExacTrac stereoscopic imaging in lung stereotactic body radiation therapy (SBRT). Methods: Using the Novalis ExacTrac x-ray system, 39 lung SBRT patients (182 treatments) were aligned before treatment with 6 degrees (6D) of freedom couch (3 translations, 3 rotations) based on spine matching on stereoscopic images. The couch was shifted to treatment isocenter and pre-treatment CBCT was performed based on a soft tissue match around tumor volume. The CBCT data were used to measure residual errors following ExacTrac alignment. The thresholds for re-aligning the patients based on CBCT were 3mm shift or 3° rotation (in any 6D). In order to evaluate the effect of tumor location on residual errors, correlations between tumor distance from spine and individual residual errors were calculated. Results: Residual errors were up to 0.5±2.4mm. Using 3mm/3° thresholds, 80/182 (44%) of the treatments required re-alignment based on CBCT soft tissue matching following ExacTrac spine alignment. Most mismatches were in sup-inf, ant-post, and roll directions which had larger standard deviations. No correlation was found between tumor distance from spine and individual residual errors. Conclusion: ExacTrac stereoscopic imaging offers a quick pre-treatment patient alignment. However, bone matching based on spine is not reliable for aligning lung SBRT patients who require soft tissue image registration from CBCT. Spine can be a poor surrogate for lung SBRT patient alignment even for proximal tumor volumes.

  9. [Sampling methods for PM2.5 from stationary sources: a review].

    Science.gov (United States)

    Jiang, Jing-Kun; Deng, Jian-Guo; Li, Zhen; Li, Xing-Hua; Duan, Lei; Hao, Ji-Ming

    2014-05-01

    The new China national ambient air quality standard has been published in 2012 and will be implemented in 2016. To meet the requirements in this new standard, monitoring and controlling PM2,,5 emission from stationary sources are very important. However, so far there is no national standard method on sampling PM2.5 from stationary sources. Different sampling methods for PM2.5 from stationary sources and relevant international standards were reviewed in this study. It includes the methods for PM2.5 sampling in flue gas and the methods for PM2.5 sampling after dilution. Both advantages and disadvantages of these sampling methods were discussed. For environmental management, the method for PM2.5 sampling in flue gas such as impactor and virtual impactor was suggested as a standard to determine filterable PM2.5. To evaluate environmental and health effects of PM2.5 from stationary sources, standard dilution method for sampling of total PM2.5 should be established.

  10. Engaging in Argument from Evidence and the Ocean Sciences Sequence for Grades 3-5: A case study in complementing professional learning experiences with instructional materials aligned to instructional goals

    Science.gov (United States)

    Schoedinger, S. E.; Weiss, E. L.

    2016-12-01

    K-5 science teachers, who often lack a science background, have been tasked with a huge challenge in implementing NGSS—to completely change their instructional approach from one that views science as a body of knowledge to be imparted to one that is epistemic in nature. We have found that providing high-quality professional learning (PL) experiences is often not enough and that teachers must have instructional materials that align with their instructional goals. We describe a case study in which the Lawrence Hall of Science (the Hall) used the Hall-developed Ocean Sciences Sequence for Grades 3-5 (OSS 3-5) to support a rigorous PL program for grade 3-5 teachers focused on the NGSS science and engineering practice, engaging in argument from evidence. Developed prior to the release of NGSS, the Ocean Literacy Framework and the NGSS precursor, A Framework for K-12 Science Education, informed the content and instructional approaches of OSS 3-5. OSS 3-5 provides a substantial focus on making evidence-based explanations (and other science practices), while building students' ocean sciences content knowledge. From 2013-2015, the Hall engaged cohorts of teachers in a rigorous PL experience focused on engaging in argument from evidence. During the summer, teachers attended a week-long institute, in which exemplar activities from OSS 3-5 were used to model instructional practices to support arguing from evidence and related practices, e.g., developing and using models and constructing explanations. Immediately afterward, teachers enacted what they'd learned during a two-week summer school practicum. Here, they team-taught the OSS 3-5 curriculum, participated in video reflection groups, and received coaching and just-in-time input from instructors. In the subsequent academic year, many teachers began by teaching OSS 3-5 so that they could practice engaging students in argumentation in curriculum they'd already used for that purpose. Throughout the year, teachers

  11. Moving State Marine SINS Initial Alignment Based on High Degree CKF

    Directory of Open Access Journals (Sweden)

    Yong-Gang Zhang

    2014-01-01

    Full Text Available A new moving state marine initial alignment method of strap-down inertial navigation system (SINS is proposed based on high-degree cubature Kalman filter (CKF, which can capture higher order Taylor expansion terms of nonlinear alignment model than the existing third-degree CKF, unscented Kalman filter and central difference Kalman filter, and improve the accuracy of initial alignment under large heading misalignment angle condition. Simulation results show the efficiency and advantage of the proposed initial alignment method as compared with existing initial alignment methods for the moving state SINS initial alignment with large heading misalignment angle.

  12. Investigation of neptunium (5), plutonium (5) and americium (5) complexing with some anions of inorganic acids by the method of coprecipitation

    International Nuclear Information System (INIS)

    Moskvin, A.I.; Poznyakov, A.N.; AN SSSR, Moscow. Inst. Geokhimii i Analiticheskoj Khimii)

    1979-01-01

    By using the method of coprecipitation with ferric hydroxide a study has been made of Np(5), Pu(5) and Am(5) ions complexing with the anions of inorganic acids SO 4 2- , SO 3 2- , HCO 3 - and HPO 4 2- . Consideration has been also given to how the process of coprecipitation is affected by such factors as collector mass, microcomponent concentration and solution pH. A composition and stability constants of actinide complexes appearing in the systems under study have been found

  13. Alignment of concerns

    DEFF Research Database (Denmark)

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

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

  14. Seeking the perfect alignment

    CERN Multimedia

    2002-01-01

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

  15. 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.)

  16. 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.)

  17. 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.)

  18. SFESA: a web server for pairwise alignment refinement by secondary structure shifts.

    Science.gov (United States)

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

    2015-09-03

    Protein sequence alignment is essential for a variety of tasks such as homology modeling and active site prediction. Alignment errors remain the main cause of low-quality structure models. A bioinformatics tool to refine alignments is needed to make protein alignments more accurate. We developed the SFESA web server to refine pairwise protein sequence alignments. Compared to the previous version of SFESA, which required a set of 3D coordinates for a protein, the new server will search a sequence database for the closest homolog with an available 3D structure to be used as a template. For each alignment block defined by secondary structure elements in the template, SFESA evaluates alignment variants generated by local shifts and selects the best-scoring alignment variant. A scoring function that combines the sequence score of profile-profile comparison and the structure score of template-derived contact energy is used for evaluation of alignments. PROMALS pairwise alignments refined by SFESA are more accurate than those produced by current advanced alignment methods such as HHpred and CNFpred. In addition, SFESA also improves alignments generated by other software. SFESA is a web-based tool for alignment refinement, designed for researchers to compute, refine, and evaluate pairwise alignments with a combined sequence and structure scoring of alignment blocks. To our knowledge, the SFESA web server is the only tool that refines alignments by evaluating local shifts of secondary structure elements. The SFESA web server is available at http://prodata.swmed.edu/sfesa.

  19. Vertically aligned carbon nanotube emitter on metal foil for medical X-ray imaging.

    Science.gov (United States)

    Ryu, Je Hwang; Kim, Wan Sun; Lee, Seung Ho; Eom, Young Ju; Park, Hun Kuk; Park, Kyu Chang

    2013-10-01

    A simple method is proposed for growing vertically aligned carbon nanotubes on metal foil using the triode direct current plasma-enhanced chemical vapor deposition (PECVD). The carbon nanotube (CNT) electron emitter was fabricated using fewer process steps with an acid treated metal substrate. The CNT emitter was used for X-ray generation, and the X-ray image of mouse's joint was obtained with an anode current of 0.5 mA at an anode bias of 60 kV. The simple fabrication of a well-aligned CNT with a protection layer on metal foil, and its X-ray application, were studied.

  20. Self-aligned periodic Ni nano dots embedded in nano-oxide layer

    International Nuclear Information System (INIS)

    Doi, M.; Izumi, M.; Kawasaki, S.; Miyake, K.; Sahashi, M.

    2007-01-01

    The Ni nano constriction dots embedded in the Ta-nano-oxide layer (NOL) was prepared by the ion beam sputtering (IBS) method. After the various conditions of the oxidations, the structural analyses of the NOL were performed by RHEED, AES and in situ STM/AFM observations. From the current image of the conductive AFM for NOL, the periodically aligned metallic dots with the size around 5-10 nm were successfully observed. The mechanism of the formation of the self-organized aligned Ni nano constriction dots is discussed from the standpoint of the grain size, the crystal orientation, the preferred oxidation of Ta at the diffused interface

  1. Assessment of hindfoot alignment using MRI and standing hindfoot alignment radiographs (Saltzman view)

    Energy Technology Data Exchange (ETDEWEB)

    Bueber, Nydia; Zanetti, Marco [Clinic Hirslanden, Department of Musculoskeletal Radiology, Zurich (Switzerland); Frigg, Arno [Clinic Hirslanden, Centre for Foot and Ankle Surgery, Zurich (Switzerland); Saupe, Nadja [Clinic Hirslanden, Department of Musculoskeletal Radiology, Zurich (Switzerland); Clinic Hirslanden Zurich, Department of Musculoskeletal Radiology, Zurich (Switzerland)

    2018-01-15

    To compare the hindfoot alignment measured on standing HAV radiographs (Saltzman view) and on non-weight-bearing coronal MR images. The apparent moment arm was measured on weight-bearing conventional radiographs (Saltzman views) and on MRIs of the ankle in 50 consecutive patients (mean age, 54 years; age range, 18-77 years). The evaluation was performed independently by three readers using analogous reference points for both methods. Positive values were assigned when the deepest point of the calcaneus was lateral to the tibial axis as valgus, negative values as varus. The intertechnique agreement and correlation for the measurements performed with HAV radiographs and MRI were assessed for each reader using the Bland-Altman method and the Pearson correlation coefficient, respectively. The interobserver agreement was assessed using the intraclass correlation coefficient. The means of apparent moment arms, with the standard deviation (SD) in parentheses, of three readers were +2.0 (±8.4) mm, +1.5 (±6.6) mm and -1.4 (±8.2) mm on HAV radiographs and +4.6 (±7.4) mm, +6.3 (±5.3) mm and +5.4 (±6.4) mm on MRI. The Bland-Altman analysis found a systematic bias for all three readers, corresponding to an overestimation of measurements with MRI (systematic bias ranging from 2.6 to 4.8 mm). The intertechnique correlation was found moderate to high. The Pearson coefficients for the three readers were 0.75, 0.64 and 0.65. The interobserver agreement among the three readers was 0.72, 0.77 and 0.68 for HAV, MRI and both modalities together, respectively. Hindfoot alignment can be estimated on MRI but the correlation between the values on HAV radiographs and MR images is only moderate with a tendency to increased positive values (valgization) on MR images. (orig.)

  2. Top-down approach in protein RDC data analysis: de novo estimation of the alignment tensor

    International Nuclear Information System (INIS)

    Chen Kang; Tjandra, Nico

    2007-01-01

    In solution NMR spectroscopy the residual dipolar coupling (RDC) is invaluable in improving both the precision and accuracy of NMR structures during their structural refinement. The RDC also provides a potential to determine protein structure de novo. These procedures are only effective when an accurate estimate of the alignment tensor has already been made. Here we present a top-down approach, starting from the secondary structure elements and finishing at the residue level, for RDC data analysis in order to obtain a better estimate of the alignment tensor. Using only the RDCs from N-H bonds of residues in α-helices and CA-CO bonds in β-strands, we are able to determine the offset and the approximate amplitude of the RDC modulation-curve for each secondary structure element, which are subsequently used as targets for global minimization. The alignment order parameters and the orientation of the major principal axis of individual helix or strand, with respect to the alignment frame, can be determined in each of the eight quadrants of a sphere. The following minimization against RDC of all residues within the helix or strand segment can be carried out with fixed alignment order parameters to improve the accuracy of the orientation. For a helical protein Bax, the three components A xx , A yy and A zz , of the alignment order can be determined with this method in average to within 2.3% deviation from the values calculated with the available atomic coordinates. Similarly for β-sheet protein Ubiquitin they agree in average to within 8.5%. The larger discrepancy in β-strand parameters comes from both the diversity of the β-sheet structure and the lower precision of CA-CO RDCs. This top-down approach is a robust method for alignment tensor estimation and also holds a promise for providing a protein topological fold using limited sets of RDCs

  3. Observation of spin alignment of resonances produced in the 3-body reactions : $\\overline{p}$p $\\rightarrow$ $\\overline{p}$p $\\omega^{\\omicron}$ and $\\overline{p}$p $\\rightarrow$ $\\overline{N}^{x++}\\pi^{\\omicron}$ at 5.7 GeV/c

    CERN Document Server

    Alles-Borelli, V; Frisk, A; Michejda, L

    1966-01-01

    Observation of spin alignment of resonances produced in the 3-body reactions : $\\overline{p}$p $\\rightarrow$ $\\overline{p}$p $\\omega^{\\omicron}$ and $\\overline{p}$p $\\rightarrow$ $\\overline{N}^{x++}\\pi^{\\omicron}$ at 5.7 GeV/c

  4. Accelerator Technology: Geodesy and Alignment for Particle Accelerators

    CERN Document Server

    Missiaen, D

    2013-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Bushnell, Brian

    2014-03-17

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

  6. Alignment of the ALICE Inner Tracking System with cosmic-ray tracks

    CERN Document Server

    Aamodt, K; Abeysekara, U; Abrahantes Quintana, A; Adamová, D; Aggarwal, M M; Aglieri Rinella, G; Agocs, A G; Aguilar Salazar, S; Ahammed, Z; Ahmad, A; Ahmad, N; Ahn, S U; Akimoto, R; Akindinov, A; Aleksandrov, D; Alessandro, B; Alfaro Molina, R; Alici, A; Almaráz Aviña, E; Alme, J; Altini, V; Altinpinar, S; Alt, T; Andrei, C; Andronic, A; Anelli, G; Angelov, V; Anson, C; Anticic, T; Antinori, F; Antinori, S; Antipin, K; Antonczyk, D; Antonioli, P; Anzo, A; Aphecetche, L; Appelshäuser, H; Arcelli, S; Arceo, R; Arend, A; Armesto, N; Arnaldi, R; Aronsson, T; Arsene, I C; Asryan, A; Augustinus, A; Averbeck, R; Awes, T C; Äystö, J; Azmi, M D; Bablok, S; Bach, M; Badalà, A; Baek, Y W; Bagnasco, S; Bailhache, R; Bala, R; Baldisseri, A; Baldit, A; Bán, J; Barbera, R; Barile, F; Barnaföldi, G G; Barnby, L; Barret, V; Bartke, J; Basile, M; Basmanov, V; Bastid, N; Bathen, B; Batigne, G; Batyunya, B; Baumann, C; Bearden, I G; Becker, B; Belikov, I; Bellwied, R; Belmont-Moreno, E; Belogianni, A; Benhabib, L; Beolé, S; Berceanu, I; Bercuci, A; Berdermann, E; Berdnikov, Y; Betev, L; Bhasin, A; Bhati, A K; Bianchi, L; Bianchin, C; Bianchi, N; Bielcík, J; Bielcíková, J; Bilandzic, A; Bimbot, L; Biolcati, E; Blanc, A; Blanco, F; Blanco, F; Blau, D; Blume, C; Boccioli, M; Bock, N; Bogdanov, A; Bøggild, H; Bogolyubsky, M; Bohm, J; Boldizsár, L; Bombara, M; Bombonati, C; Bondila, M; Borel, H; Borshchov, V; Bortolin, C; Bose, S; Bosisio, L; Bossú, F; Botje, M; Böttger, S; Bourdaud, G; Boyer, B; Braun, M; Braun-Munzinger, P; Bravina, L; Bregant, M; Breitner, T; Bruckner, G; Bruna, E; Bruno, G E; Brun, R; Budnikov, D; Buesching, H; Bugaev, K; Buncic, P; Busch, O; Buthelezi, Z; Caffarri, D; Caines, H; Cai, X; Camacho, E; Camerini, P; Campbell, M; Canoa Roman, V; Capitani, G P; Cara Romeo, G; Carena, F; Carena, W; Carminati, F; Casanova Díaz, A; Caselle, M; Castillo Castellanos, J; Castillo Hernandez, J F; Catanescu, V; Cattaruzza, E; Cavicchioli, C; Cerello, P; Chambert, V; Chang, B; Chapeland, S; Charpy, A; Charvet, J L; Chattopadhyay, S; Chattopadhyay, S; Cherney, M; Cheshkov, C; Cheynis, B; Chiavassa, E; Chibante Barroso, V; Chinellato, D D; Chochula, P; Choi, K; Chojnacki, M; Christakoglou, P; Christensen, C H; Christiansen, P; Chujo, T; Chuman, F; Cicalo, C; Cifarelli, L; Cindolo, F; Cleymans, J; Cobanoglu, O; Coffin, J P; Coli, S; Colla, A; Conesa Balbastre, G; Conesa del Valle, Z; Conner, E S; Constantin, P; Contin, G; Contreras, J G; Cormier, T M; Corrales Morales, Y; Cortese, P; Cortés Maldonado, I; Cosentino, M R; Costa, F; Cotallo, M E; Crescio, E; Crochet, P; Cuautle, E; Cunqueiro, L; Cussonneau, J; Dainese, A; Dalsgaard, H H; Danu, A; Dash, A; Dash, S; Das, I; Das, S; de Barros, G O V; De Caro, A; de Cataldo, G; de Cuveland, J; De Falco, A; De Gaspari, M; de Groot, J; De Gruttola, D; de Haas, A P; De Marco, N; De Pasquale, S; De Remigis, R; de Rooij, R; de Vaux, G; Delagrange, H; Dellacasa, G; Deloff, A; Demanov, V; Dénes, E; Deppman, A; D'Erasmo, G; Derkach, D; Devaux, A; Di Bari, D; Di Giglio, C; Di Liberto, S; Di Mauro, A; Di Nezza, P; Dialinas, M; Díaz, L; Díaz, R; Dietel, T; Ding, H; Divià, R; Djuvsland, Ø; do Amaral Valdiviesso, G; Dobretsov, V; Dobrin, A; Dobrowolski, T; Dönigus, B; Domínguez, I; Dordic, O; Dubey, A K; Dubuisson, J; Ducroux, L; Dupieux, P; Dutta Majumdar, A K; Dutta Majumdar, M R; Elia, D; Emschermann, D; Enokizono, A; Espagnon, B; Estienne, M; Evans, D; Evrard, S; Eyyubova, G; Fabjan, C W; Fabris, D; Faivre, J; Falchieri, D; Fantoni, A; Fasel, M; Fearick, R; Fedunov, A; Fehlker, D; Fekete, V; Felea, D; Fenton-Olsen, B; Feofilov, G; Fernández Téllez, A; Ferreiro, E G; Ferretti, A; Ferretti, R; Figueredo, M A S; Filchagin, S; Fini, R; Fionda, F M; Fiore, E M; Floris, M; Fodor, Z; Foertsch, S; Foka, P; Fokin, S; Formenti, F; Fragiacomo, E; Fragkiadakis, M; Frankenfeld, U; Frolov, A; Fuchs, U; Furano, F; Furget, C; Fusco Girard, M; Gaardhøje, J J; Gadrat, S; Gagliardi, M; Gago, A; Gallio, M; Ganoti, P; Ganti, M S; Garabatos, C; García Trapaga, C; Gebelein, J; Gemme, R; Germain, M; Gheata, A; Gheata, M; Ghidini, B; Ghosh, P; Giraudo, G; Giubellino, P; Gladysz-Dziadus, E; Glasow, R; Glässel, P; Glenn, A; Gomez, R; González Santos, H; González-Trueba, L H; González-Zamora, P; Gorbunov, S; Gorbunov, Y; Gotovac, S; Gottschlag, H; Grabski, V; Grajcarek, R; Grelli, A; Grigoras, A; Grigoras, C; Grigoriev, V; Grigoryan, A; Grinyov, B; Grion, N; Gros, P; Grosse-Oetringhaus, J F; Grossiord, J Y; Grosso, R; Guarnaccia, C; Guber, F; Guernane, R; Guerzoni, B; Gulbrandsen, K; Gulkanyan, H; Gunji, T; Gupta, A; Gupta, R; Gustafsson, H A; Gutbrod, H; Haaland, Ø; Hadjidakis, C; Haiduc, M; Hamagaki, H; Hamar, G; Hamblen, J; Han, B H; Harris, J W; Hartig, M; Harutyunyan, A; Hasch, D; Hasegan, D; Hatzifotiadou, D; Hayrapetyan, A; Heide, M; Heinz, M; Helstrup, H; Herghelegiu, A; Hernández, C; Herrera Corral, G; Herrmann, N; Hetland, K F; Hicks, B; Hiei, A; Hille, P T; Hippolyte, B; Horaguchi, T; Hori, Y; Hristov, P; Hrivnácová, I; Huber, S; Humanic, T J; Hu, S; Hutter, D; Hwang, D S; Ichou, R; Ilkaev, R; Ilkiv, I; Innocenti, P G; Ippolitov, M; Irfan, M; Ivan, C; Ivanov, A; Ivanov, M; Ivanov, V; Iwasaki, T; Jachokowski, A; Jacobs, P; Jancurová, L; Jangal, S; Janik, R; Jayananda, K; Jena, C; Jena, S; Jirden, L; Jones, G T; Jones, P G; Jovanovic, P; Jung, H; Jung, W; Jusko, A; Kaidalov, A B; Kalcher, S; Kalinák, P; Kalliokoski, T; Kalweit, A; Kamal, A; Kamermans, R; Kanaki, K; Kang, E; Kang, J H; Kapitan, J; Kaplin, V; Kapusta, S; Karavicheva, T; Karpechev, E; Kazantsev, A; Kebschull, U; Keidel, R; Khan, M M; Khan, S A; Khanzadeev, A; Kharlov, Y; Kikola, D; Kileng, B; Kim, D J; Kim, D S; Kim, D W; Kim, H N; Kim, J H; Kim, J; Kim, J S; Kim, M; Kim, M; Kim, S H; Kim, S; Kim, Y; Kirsch, S; Kiselev, S; Kisel, I; Kisiel, A; Klay, J L; Klein-Bösing, C; Klein, J; Kliemant, M; Klovning, A; Kluge, A; Kniege, S; Koch, K; Kolevatov, R; Kolojvari, A; Kondratiev, V; Kondratyeva, N; Konevskih, A; Kornas, E; Kour, R; Kowalski, M; Kox, S; Kozlov, K; Králik, I; Kral, J; Kramer, F; Kraus, I; Kravcáková, A; Krawutschke, T; Krivda, M; Krumbhorn, D; Krus, M; Kryshen, E; Krzewicki, M; Kucheriaev, Y; Kuhn, C; Kuijer, P G; Kumar, L; Kumar, N; Kupczak, R; Kurashvili, P; Kurepin, A; Kurepin, A N; Kuryakin, A; Kushpil, S; Kushpil, V; Kutouski, M; Kvaerno, H; Kweon, M J; Kwon, Y; Lackner, F; Ladrón de Guevara, P; Lafage, V; Lal, C; Lara, C; La Rocca, P; Larsen, D T; Laurenti, G; Lazzeroni, C; Le Bornec, Y; Le Bris, N; Lee, H; Lee, K S; Lee, S C; Lefèvre, F; Lehnert, J; Leistam, L; Lenhardt, M; Lenti, V; León, H; León Monzón, I; León Vargas, H; Lévai, P; Lietava, R; Lindal, S; Lindenstruth, V; Lippmann, C; Lisa, M A; Listratenko, O; Liu, L; Li, Y; Loginov, V; Lohn, S; López Noriega, M; López-Ramírez, R; López Torres, E; Lopez, X; Løvhøiden, G; Lozea Feijo Soares, A; Lunardon, M; Luparello, G; Luquin, L; Lu, S; Lutz, J R; Luvisetto, M; Madagodahettige-Don, D M; Maevskaya, A; Mager, M; Mahajan, A; Mahapatra, D P; Maire, A; Makhlyueva, I; Ma, K; Malaev, M; Maldonado Cervantes, I; Malek, M; Mal'Kevich, D; Malkiewicz, T; Malzacher, P; Mamonov, A; Manceau, L; Mangotra, L; Manko, V; Manso, F; Manzari, V; Mao, Y; Mares, J; Margagliotti, G V; Margotti, A; Marín, A; Martashvili, I; Martinengo, P; Martínez Davalos, A; Martínez García, G; Martínez, M I; Maruyama, Y; Ma, R; Marzari Chiesa, A; Masciocchi, S; Masera, M; Masetti, M; Masoni, A; Massacrier, L; Mastromarco, M; Mastroserio, A; Matthews, Z L; Mattos Tavares, B; Matyja, A; Mayani, D; Mazza, G; Mazzoni, M A; Meddi, F; Menchaca-Rocha, A; Mendez Lorenzo, P; Meoni, M; Mercado Pérez, J; Mereu, P; Miake, Y; Michalon, A; Miftakhov, N; Milosevic, J; Minafra, F; Mischke, A; Miskowiec, D; Mitu, C; Mizoguchi, K; Mlynarz, J; Mohanty, B; Molnar, L; Mondal, M M; Montaño Zetina, L; Monteno, M; Montes, E; Morando, M; Moretto, S; Morsch, A; Moukhanova, T; Muccifora, V; Mudnic, E; Muhuri, S; Müller, H; Munhoz, M G; Munoz, J; Musa, L; Musso, A; Nandi, B K; Nania, R; Nappi, E; Navach, F; Navin, S; Nayak, T K; Nazarenko, S; Nazarov, G; Nedosekin, A; Nendaz, F; Newby, J; Nianine, A; Nicassio, M; Nielsen, B S; Nikolaev, S; Nikolic, V; Nikulin, S; Nikulin, V; Nilsen, B S; Nilsson, M S; Noferini, F; Nomokonov, P; Nooren, G; Novitzky, N; Nyatha, A; Nygaard, C; Nyiri, A; Nystrand, J; Ochirov, A; Odyniec, G; Oeschler, H; Oinonen, M; Okada, K; Okada, Y; Oldenburg, M; Oleniacz, J; Oppedisano, C; Orsini, F; Ortíz Velázquez, A; Ortona, G; Oskamp, C; Oskarsson, A; Osmic, F; Österman, L; Ostrowski, P; Otterlund, I; Otwinowski, J; Øvrebekk, G; Oyama, K; Ozawa, K; Pachmayer, Y; Pachr, M; Padilla, F; Pagano, P; Paic, G; Painke, F; Pajares, C; Palaha, A; Palmeri, A; Pal, S K; Pal, S; Panse, R; Pappalardo, G S; Park, W J; Pastircák, B; Pastore, C; Paticchio, V; Pavlinov, A; Pawlak, T; Peitzmann, T; Pepato, A; Pereira, H; Peressounko, D; Pérez, C; Perini, D; Perrino, D; Peryt, W; Peschek, J; Pesci, A; Peskov, V; Pestov, Y; Peters, A J; Petrácek, V; Petridis, A; Petris, M; Petrovici, M; Petrov, P; Petta, C; Peyré, J; Piano, S; Piccotti, A; Pikna, M; Pillot, P; Pinsky, L; Pitz, N; Piuz, F; Platt, R; Pluta, J; Pocheptsov, T; Pochybova, S; Podesta Lerma, P L M; Poggio, F; Poghosyan, M G; Poghosyan, T; Polák, K; Polichtchouk, B; Polozov, P; Polyakov, V; Pommeresch, B; Pop, A; Posa, F; Poskon, M; Pospisil, V; Potukuchi, B; Pouthas, J; Prasad, S K; Preghenella, R; Prino, F; Pruneau, C A; Pshenichnov, I; Puddu, G; Pujahari, P; Pulvirenti, A; Punin, A; Punin, V; Putis, M; Putschke, J; Quercigh, E; Rachevski, A; Rademakers, A; Radomski, S; Räihä, T S; Rak, J; Rakotozafindrabe, A; Ramello, L; Ramírez Reyes, A; Rammler, M; Raniwala, R; Raniwala, S; Räsänen, S; Rashevskaya, I; Rath, S; Read, K F; Real, J; Redlich, K; Renfordt, R; Reolon, A R; Reshetin, A; Rettig, F; Revol, J P; Reygers, K; Ricaud, H; Riccati, L; Ricci, R A; Richter, M; Riedler, P; Riegler, W; Riggi, F; Rivetti, A; Rodriguez Cahuantzi, M; Røed, K; Röhrich, D; Román López, S; Romita, R; Ronchetti, F; Rosinský, P; Rosnet, P; Rossegger, S; Rossi, A; Roukoutakis, F; Rousseau, S; Roy, C; Roy, P; Rubio-Montero, A J; Rui, R; Rusanov, I; Russo, G; Ryabinkin, E; Rybicki, A; Sadovsky, S; Safarík, K; Sahoo, R; Saini, J; Saiz, P; Sakata, D; Salgado, C A; Salgueiro Dominques da Silva, R; Salur, S; Samanta, T; Sambyal, S; Samsonov, V; Sándor, L; Sandoval, A; Sano, M; Sano, S; Santo, R; Santoro, R; Sarkamo, J; Saturnini, P; Scapparone, E; Scarlassara, F; Scharenberg, R P; Schiaua, C; Schicker, R; Schindler, H; Schmidt, C; Schmidt, H R; Schossmaier, K; Schreiner, S; Schuchmann, S; Schukraft, J; Schutz, Y; Schwarz, K; Schweda, K; Scioli, G; Scomparin, E; Segato, G; Semenov, D; Senyukov, S; Seo, J; Serci, S; Serkin, L; Serradilla, E; Sevcenco, A; Sgura, I; Shabratova, G; Shahoyan, R; Sharkov, G; Sharma, N; Sharma, S; Shigaki, K; Shimomura, M; Shtejer, K; Sibiriak, Y; Siciliano, M; Sicking, E; Siddi, E; Siemiarczuk, T; Silenzi, A; Silvermyr, D; Simili, E; Simonetti, G; Singaraju, R; Singhal, V; Singh, R; Sinha, B C; Sinha, T; Sitar, B; Sitta, M; Skaali, T B; Skjerdal, K; Smakal, R; Smirnov, N; Snellings, R; Snow, H; Søgaard, C; Sokolov, O; Soloviev, A; Soltveit, H K; Soltz, R; Sommer, W; Son, C W; Song, M; Son, H S; Soos, C; Soramel, F; Soyk, D; Spyropoulou-Stassinaki, M; Srivastava, B K; Stachel, J; Staley, F; Stan, I; Stefanek, G; Stefanini, G; Steinbeck, T; Stenlund, E; Steyn, G; Stocco, D; Stock, R; Stolpovsky, P; Strmen, P; Suaide, A A P; Subieta Vásquez, M A; Sugitate, T; Suire, C; Sumbera, M; Susa, T; Swoboda, D; Symons, J; Szanto de Toledo, A; Szarka, I; Szostak, A; Szuba, M; Tadel, M; Tagridis, C; Takahara, A; Takahashi, J; Tanabe, R; Tapia Takaki, J D; Taureg, H; Tauro, A; Tavlet, M; Tejeda Muñoz, G; Telesca, A; Terrevoli, C; Thäder, J; Tieulent, R; Tlusty, D; Toia, A; Tolyhy, T; Torcato de Matos, C; Torii, H; Torralba, G; Toscano, L; Tosello, F; Tournaire, A; Traczyk, T; Tribedy, P; Tröger, G; Truesdale, D; Trzaska, W H; Tsiledakis, G; Tsilis, E; Tsuji, T; Tumkin, A; Turrisi, R; Turvey, A; Tveter, T S; Tydesjö, H; Tywoniuk, K; Ulery, J; Ullaland, K; Uras, A; Urbán, J; Urciuoli, G M; Usai, G L; Vacchi, A; Vala, M; Valencia Palomo, L; Vallero, S; van den Brink, A; van der Kolk, N; Vande Vyvre, P; van Leeuwen, M; Vannucci, L; Vargas, A; Varma, R; Vasiliev, A; Vassiliev, I; Vassiliou, M; Vechernin, V; Venaruzzo, M; Vercellin, E; Vergara, S; Vernet, R; Verweij, M; Vetlitskiy, I; Vickovic, L; Viesti, G; Vikhlyantsev, O; Vilakazi, Z; Villalobos Baillie, O; Vinogradov, A; Vinogradov, L; Vinogradov, Y; Virgili, T; Viyogi, Y P; Vodopianov, A; Voloshin, K; Voloshin, S; Volpe, G; von Haller, B; Vranic, D; Vrláková, J; Vulpescu, B; Wagner, B; Wagner, V; Wallet, L; Wan, R; Wang, D; Wang, Y; Watanabe, K; Wen, Q; Wessels, J; Wiechula, J; Wikne, J; Wilk, A; Wilk, G; Williams, M C S; Willis, N; Windelband, B; Xu, C; Yang, C; Yang, H; Yasnopolsky, A; Yermia, F; Yi, J; Yin, Z; Yokoyama, H; Yoo, I-K; Yuan, X; Yushmanov, I; Zabrodin, E; Zagreev, B; Zalite, A; Zampolli, C; Zanevsky, Yu; Zaporozhets, Y; Zarochentsev, A; Závada, P; Zbroszczyk, H; Zelnicek, P; Zenin, A; Zepeda, A; Zgura, I; Zhalov, M; Zhang, X; Zhou, D; Zhou, S; Zhu, J; Zichichi, A; Zinchenko, A; Zinovjev, G; Zinovjev, M; Zoccarato, Y; Zychácek, V

    2010-01-01

    ALICE (A Large Ion Collider Experiment) is the LHC (Large Hadron Collider) experiment devoted to investigating the strongly interacting matter created in nucleus-nucleus collisions at the LHC energies. The ALICE ITS, Inner Tracking System, consists of six cylindrical layers of silicon detectors with three different technologies; in the outward direction: two layers of pixel detectors, two layers each of drift, and strip detectors. The number of parameters to be determined in the spatial alignment of the 2198 sensor modules of the ITS is about 13,000. The target alignment precision is well below 10 micron in some cases (pixels). The sources of alignment information include survey measurements, and the reconstructed tracks from cosmic rays and from proton-proton collisions. The main track-based alignment method uses the Millepede global approach. An iterative local method was developed and used as well. We present the results obtained for the ITS alignment using about 10^5 charged tracks from cosmic rays that h...

  7. Energy level alignment at hybridized organic-metal interfaces from a GW projection approach

    Science.gov (United States)

    Chen, Yifeng; Tamblyn, Isaac; Quek, Su Ying

    Energy level alignments at organic-metal interfaces are of profound importance in numerous (opto)electronic applications. Standard density functional theory (DFT) calculations generally give incorrect energy level alignments and missing long-range polarization effects. Previous efforts to address this problem using the many-electron GW method have focused on physisorbed systems where hybridization effects are insignificant. Here, we use state-of-the-art GW methods to predict the level alignment at the amine-Au interface, where molecular levels do hybridize with metallic states. This non-trivial hybridization implies that DFT result is a poor approximation to the quasiparticle states. However, we find that the self-energy operator is approximately diagonal in the molecular basis, allowing us to use a projection approach to predict the level alignments. Our results indicate that the metallic substrate reduces the HOMO-LUMO gap by 3.5 4.0 eV, depending on the molecular coverage/presence of Au adatoms. Our GW results are further compared with those of a simple image charge model that describes the level alignment in physisorbed systems. Syq and YC acknowledge Grant NRF-NRFF2013-07 and the medium-sized centre program from the National Research Foundation, Singapore.

  8. 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.

  9. Tuning band alignment by CdS layers using a SILAR method to enhance TiO2/CdS/CdSe quantum-dot solar-cell performance.

    Science.gov (United States)

    Zhang, Bingkai; Zheng, Jiaxin; Li, Xiaoning; Fang, Yanyan; Wang, Lin-Wang; Lin, Yuan; Pan, Feng

    2016-04-28

    We report tuning band alignment by optimized CdS layers using a SILAR method to achieve the recorded best performance with about 6% PCE in TiO2/CdS/CdSe QDSSCs. Combining experimental and theoretical studies, we find that a better lattices match between CdS and TiO2 assists the growth of CdSe, and the combined effect of charge transfer and surface dipole moment at the TiO2/CdS/CdSe interface shifts the energy levels of TiO2 upward and increases Voc of the solar cells. More importantly, the band gap of CdS buffer layers is sensitive to the distortion induced by lattice mismatch and numbers of CdS layers. For example, the barrier for charge transfer disappears when there are more than 4 layers of CdS, facilitating the charge injection from CdSe to TiO2.

  10. Liquid crystallinity driven highly aligned large graphene oxide composites

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-04-15

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

  11. A simple method for the detection of PM2.5 air pollutions using MODIS data

    Science.gov (United States)

    Kato, Yoshinobu

    2016-05-01

    In recent years, PM2.5 air pollution is a social and transboundary environmental issue with the rapid economic growth in many countries. As PM2.5 is small and includes various ingredients, the detection of PM2.5 air pollutions by using satellite data is difficult compared with the detection of dust and sandstorms. In this paper, we examine various images (i.e., single-band images, band-difference images, RGB composite color images) to find a good method for detecting PM2.5 air pollutions by using MODIS data. A good method for the detection of PM2.5 air pollution is {R, G, B = band10, band9, T11}, where T11 is the brightness temperature of band31. In this composite color image, PM2.5 air pollutions are represented by light purple or pink color. This proposed method is simpler than the method by Nagatani et al. (2013), and is useful to grasp the distribution of PM2.5 air pollutions in the wide area (e.g., from China and India to Japan). By comparing AVI image with the image by proposed method, DSS and PM2.5 air pollutions can be classified.

  12. Evaporation and alignment of 1-undecene functionalised nanodiamonds

    Energy Technology Data Exchange (ETDEWEB)

    Astuti, Y.; Poolton, N.R.J.; Butenko, Y.V.; Šiller, L., E-mail: lidija.siller@ncl.ac.uk

    2014-12-15

    The possibility to align diamond nanoparticles has a number of potential technological applications, but there are few methods by which this can be achieved, and research in this field can be considered to be in its infancy. Hitherto, two methods which have been commonly used are lithography and chemical vapour deposition (CVD), but these methods are both complex and have poor effectiveness. In this paper, we present a new technique for particle alignment, which is simpler and avoids particle structural damage. The method works by functionalising the nanodiamonds of size 5 nm by attaching 1-undecene onto the nanodiamond surfaces; the particles are then evaporated using UHV and deposited onto TEM grids and mica surfaces at 200 °C. XPS, SERS, HRTEM, luminescence spectroscopy and luminescence micro-imaging have been applied to characterise samples both before and after evaporation. Deposition of nanodiamond onto a mica surface resulted in particle alignment with length scales of 500 µm. The XPS and Raman spectra confirmed the absence of non-diamond carbon (sp{sup 2}-hybridized carbon). Moreover, photoluminescence (emitting in the range of 2.48–1.55 eV; 500–800 nm) which is characteristic for nanodiamond with size of 5 nm was also observed, both before and after evaporation of the functionalised nanodiamonds. - Highlights: • 1-Undecene funcionalised nanodiamonds can be evaporated in vacuum. • When evaporated on mica surface the particles form line ∼500 μm in length. • Their luminescence emission is observed at 2.48–1.55 eV (500–800 nm)

  13. Evaporation and alignment of 1-undecene functionalised nanodiamonds

    International Nuclear Information System (INIS)

    Astuti, Y.; Poolton, N.R.J.; Butenko, Y.V.; Šiller, L.

    2014-01-01

    The possibility to align diamond nanoparticles has a number of potential technological applications, but there are few methods by which this can be achieved, and research in this field can be considered to be in its infancy. Hitherto, two methods which have been commonly used are lithography and chemical vapour deposition (CVD), but these methods are both complex and have poor effectiveness. In this paper, we present a new technique for particle alignment, which is simpler and avoids particle structural damage. The method works by functionalising the nanodiamonds of size 5 nm by attaching 1-undecene onto the nanodiamond surfaces; the particles are then evaporated using UHV and deposited onto TEM grids and mica surfaces at 200 °C. XPS, SERS, HRTEM, luminescence spectroscopy and luminescence micro-imaging have been applied to characterise samples both before and after evaporation. Deposition of nanodiamond onto a mica surface resulted in particle alignment with length scales of 500 µm. The XPS and Raman spectra confirmed the absence of non-diamond carbon (sp 2 -hybridized carbon). Moreover, photoluminescence (emitting in the range of 2.48–1.55 eV; 500–800 nm) which is characteristic for nanodiamond with size of 5 nm was also observed, both before and after evaporation of the functionalised nanodiamonds. - Highlights: • 1-Undecene funcionalised nanodiamonds can be evaporated in vacuum. • When evaporated on mica surface the particles form line ∼500 μm in length. • Their luminescence emission is observed at 2.48–1.55 eV (500–800 nm)

  14. Hardware Accelerated Sequence Alignment with Traceback

    Directory of Open Access Journals (Sweden)

    Scott Lloyd

    2009-01-01

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

  15. Introduction of hind foot coronal alignment view

    International Nuclear Information System (INIS)

    Moon, Il Bong; Jeon, Ju Seob; Yoon, Kang Cheol; Choi, Nam Kil; Kim, Seung Kook

    2006-01-01

    Accurate clinical evaluation of the alignment of the calcaneus relative to the tibia in the coronal plane is essential in the evaluation and treatment of hind foot pathologic condition. Previously described standard anteroposterior, lateral, and oblique radiographic methods of the foot or ankle do not demonstrate alignment of the tibia relation to the calcaneus in the coronal plane. The purpose of this study was to introduce hind foot coronal alignment view. Both feet were imaged simultaneously on an elevated, radiolucent foot stand equipment. Both feet stood on a radiolucent platform with equal weight on both feet. Both feet are located foot axis longitudinal perpendicular to the platform. Silhouette tracing around both feet are made, and line is then drawn to bisect the silhouette of the second toe and the outline of the heel. The x-ray beam is angled down approximately 15 .deg. to 20 .deg. This image described tibial axis and medial, lateral tuberosity of calcaneus. Calcaneus do not rotated. The view is showed by talotibial joint space. Although computed tomographic and magnetic resonance imaging techniques are capable of demonstrating coronal hind foot alignment, they lack usefulness in most clinical situations because the foot is imaged in a non-weight bearing position. But hind foot coronal alignment view is obtained for evaluating position changing of inversion, eversion of the hind foot and varus, valgus deformity of calcaneus

  16. Leveraging FPGAs for Accelerating Short Read Alignment.

    Science.gov (United States)

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

    2017-01-01

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

  17. Nanoscratch technique for aligning multiwalled carbon nanotubes ...

    Indian Academy of Sciences (India)

    MWCNTs) were synthesized in an open air, without the need for a controlled atmosphere, using a rotating cathode arc discharge method with the help of a metal scraper. The physical force exerted by the scraper results in in-situ alignment of MWCNTs ...

  18. Genome Update: alignment of bacterial chromosomes

    DEFF Research Database (Denmark)

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

    2004-01-01

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

  19. Linear collider accelerator physics issues regarding alignment

    International Nuclear Information System (INIS)

    Seeman, J.T.

    1990-01-01

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

  20. Image Alignment by Piecewise Planar Region Matching

    NARCIS (Netherlands)

    Lou, Z.; Gevers, T.

    2014-01-01

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

  1. Anatomically Plausible Surface Alignment and Reconstruction

    DEFF Research Database (Denmark)

    Paulsen, Rasmus R.; Larsen, Rasmus

    2010-01-01

    With the increasing clinical use of 3D surface scanners, there is a need for accurate and reliable algorithms that can produce anatomically plausible surfaces. In this paper, a combined method for surface alignment and reconstruction is proposed. It is based on an implicit surface representation...

  2. Cascaded face alignment via intimacy definition feature

    Science.gov (United States)

    Li, Hailiang; Lam, Kin-Man; Chiu, Man-Yau; Wu, Kangheng; Lei, Zhibin

    2017-09-01

    Recent years have witnessed the emerging popularity of regression-based face aligners, which directly learn mappings between facial appearance and shape-increment manifolds. We propose a random-forest based, cascaded regression model for face alignment by using a locally lightweight feature, namely intimacy definition feature. This feature is more discriminative than the pose-indexed feature, more efficient than the histogram of oriented gradients feature and the scale-invariant feature transform feature, and more compact than the local binary feature (LBF). Experimental validation of our algorithm shows that our approach achieves state-of-the-art performance when testing on some challenging datasets. Compared with the LBF-based algorithm, our method achieves about twice the speed, 20% improvement in terms of alignment accuracy and saves an order of magnitude on memory requirement.

  3. A Comparison of Soft-Tissue Implanted Markers and Bony Anatomy Alignments for Image-Guided Treatments of Head-and-Neck Cancers

    International Nuclear Information System (INIS)

    Zeidan, Omar A.; Huddleston, Adam J.; Lee, Choonik; Langen, Katja M.; Kupelian, Patrick A.; Meeks, Sanford L.; Manon, Rafael R.

    2010-01-01

    Purpose: To compare the geometric alignments of soft-tissue implanted markers to the traditional bony-based alignments in head-and-neck cancers, on the basis of daily image guidance. Dosimetric impact of the two alignment techniques on target coverage is presented. Methods and Materials: A total of 330 retrospective alignments (5 patients) were performed on daily megavoltage computed tomography (MVCT) image sets using both alignment techniques. Intermarker distances were tracked for all fractions to assess marker interfractional stability. Using a deformable image registration algorithm, target cumulative doses were calculated according to generated shifts on daily MVCT image sets. Target D95 was used as a dosimetric endpoint to evaluate each alignment technique. Results: Intermarker distances overall were stable, with a standard deviation of <1.5 mm for all fractions and no observed temporal trends. Differences in shift magnitudes between both alignment techniques were found to be statistically significant, with a maximum observed difference of 8 mm in a given direction. Evaluation of technique-specific dose coverage based on D95 of target clinical target volume and planning target volume shows small differences (within ±5%) compared with the kilovoltage CT plan. Conclusion: The use of daily MVCT imaging demonstrates that implanted markers in oral tongue and soft-palate cancers are stable localization surrogates. Alignments based on implanted markers generate shifts comparable overall to the traditional bony-based alignment, with no observed systematic difference in magnitude or direction. The cumulative dosimetric impact on target clinical target volume and planning target volume coverage was found to be similar, despite large observed differences in daily alignment shifts between the two techniques.

  4. Method of preparing tritium-labelled thymidine-5'-monophosphates of high specific activity

    International Nuclear Information System (INIS)

    Filip, J.; Vesely, J.; Cihak, A.

    1976-01-01

    A method is described of preparing thymidine-5'-monophosphates labelled with tritium of high specific activity based on enzyme synthesis in vitro. Phosphorylation was carried out using the catalytic effect of an enzyme contained in the supernatant fraction prepared from Yoshida ascites carcinoma in rats. The course of the enzyme reaction can be controlled by the concentration of the individual reaction mixture components. The method described allows obtaining thymidine-5'-monophosphate of radiochemical purity better than 95%. (J.B.)

  5. High precision optical fiber alignment using tube laser bending

    NARCIS (Netherlands)

    Folkersma, Ger; Römer, Gerardus Richardus, Bernardus, Engelina; Brouwer, Dannis Michel; Herder, Justus Laurens

    2016-01-01

    In this paper, we present a method to align optical fibers within 0.2 μm of the optimal position, using tube laser bending and in situ measuring of the coupling efficiency. For near-UV wavelengths, passive alignment of the fibers with respect to the waveguides on photonic integrated circuit chips

  6. Isotope-selective ionization using four-pulse alignment

    International Nuclear Information System (INIS)

    Akagi, Hiroshi; Kasajima, Tatsuya; Kumada, Takayuki; Itakura, Ryuji; Yokoyama, Atsushi; Hasegawa, Hirokazu; Ohshima, Yasuhiro

    2013-01-01

    We have proposed a laser isotope separation method utilizing molecular alignment and non-resonant multiphoton ionization, and demonstrated isotope-selective ionization of 14 N 2 and 15 N 2 isotopomers, using one-pulse alignment. In the present work, we used a train of four identical pulses, instead of one pulse, to obtain the higher selectivity. (author)

  7. Automated Registration of Multimodal Optic Disc Images: Clinical Assessment of Alignment Accuracy.

    Science.gov (United States)

    Ng, Wai Siene; Legg, Phil; Avadhanam, Venkat; Aye, Kyaw; Evans, Steffan H P; North, Rachel V; Marshall, Andrew D; Rosin, Paul; Morgan, James E

    2016-04-01

    To determine the accuracy of automated alignment algorithms for the registration of optic disc images obtained by 2 different modalities: fundus photography and scanning laser tomography. Images obtained with the Heidelberg Retina Tomograph II and paired photographic optic disc images of 135 eyes were analyzed. Three state-of-the-art automated registration techniques Regional Mutual Information, rigid Feature Neighbourhood Mutual Information (FNMI), and nonrigid FNMI (NRFNMI) were used to align these image pairs. Alignment of each composite picture was assessed on a 5-point grading scale: "Fail" (no alignment of vessels with no vessel contact), "Weak" (vessels have slight contact), "Good" (vessels with 50% contact), and "Excellent" (complete alignment). Custom software generated an image mosaic in which the modalities were interleaved as a series of alternate 5×5-pixel blocks. These were graded independently by 3 clinically experienced observers. A total of 810 image pairs were assessed. All 3 registration techniques achieved a score of "Good" or better in >95% of the image sets. NRFNMI had the highest percentage of "Excellent" (mean: 99.6%; range, 95.2% to 99.6%), followed by Regional Mutual Information (mean: 81.6%; range, 86.3% to 78.5%) and FNMI (mean: 73.1%; range, 85.2% to 54.4%). Automated registration of optic disc images by different modalities is a feasible option for clinical application. All 3 methods provided useful levels of alignment, but the NRFNMI technique consistently outperformed the others and is recommended as a practical approach to the automated registration of multimodal disc images.

  8. Band alignments and improved leakage properties of (La2O3)0.5(SiO2)0.5/SiO2/GaN stacks for high-temperature metal-oxide-semiconductor field-effect transistor applications

    Science.gov (United States)

    Gao, L. G.; Xu, B.; Guo, H. X.; Xia, Y. D.; Yin, J.; Liu, Z. G.

    2009-06-01

    The band alignments of (La2O3)0.5(SiO2)0.5(LSO)/GaN and LSO/SiO2/GaN gate dielectric stacks were investigated comparatively by using x-ray photoelectron spectroscopy. The valence band offsets for LSO/GaN stack and LSO/SiO2/GaN stack are 0.88 and 1.69 eV, respectively, while the corresponding conduction band offsets are found to be 1.40 and 1.83 eV, respectively. Measurements of the leakage current density as function of temperature revealed that the LSO/SiO2/GaN stack has much lower leakage current density than that of the LSO/GaN stack, especially at high temperature. It is concluded that the presence of a SiO2 buffer layer increases band offsets and reduces the leakage current density effectively.

  9. Production and characterization of polymer nanocomposite with aligned single wall carbon nanotubes

    International Nuclear Information System (INIS)

    Chen Wei; Tao Xiaoming

    2006-01-01

    We reported a simple method to fabricate polymer nanocomposites with single-walled carbon nanotubes (SWNTs) having exceptional alignment and improved mechanical properties. The composite films were fabricated by casting a suspension of single walled carbon nanotubes in a solution of thermoplastic polyurethane and tetrahydrofuran. The orientation as well as dispersion of nanotubes was determined by scanning electron microscopy, transmission electron microscopy and polarized Raman spectroscopy. The macroscopic alignment probably results from solvent-polymer interaction induced orientation of soft segment chain during swelling and moisture curing. The tensile behavior of the aligned nanotube composite film was also studied. At a 0.5 wt.% nanotube loading, a 1.9-fold increase in Young's modulus was achieved

  10. Aligning Mathematical Tasks to the Common Core Standards for Mathematical Practice

    OpenAIRE

    Johnson, Raymond

    2016-01-01

    How do algebra teachers align mathematical tasks to the CCSSM Standards of Mathematical Practice? Using methods of design-based implementation research, we identified difficulties of alignment to practices and developed strategies identifying high-quality tasks.

  11. 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.

  12. Sagittal alignment after single cervical disc arthroplasty.

    Science.gov (United States)

    Guérin, Patrick; Obeid, Ibrahim; Gille, Olivier; Bourghli, Anouar; Luc, Stéphane; Pointillart, Vincent; Vital, Jean-Marc

    2012-02-01

    Prospective study. To analyze the sagittal balance after single-level cervical disc replacement (CDR) and range of motion (ROM). To define clinical and radiologic parameters those have a significant correlation with segmental and overall cervical curvature after CDR. Clinical outcomes and ROM after CDR with Mobi-C (LDR, Troyes, France) prosthesis have been documented in few studies. No earlier report of this prosthesis has studied correlations between static and dynamic parameters or those between static parameters and clinical outcomes. Forty patients were evaluated. Clinical outcome was assessed using the Short Form-36 questionnaire, Neck Disability Index, and a Visual Analog Scale. Spineview software (Surgiview, Paris, France) was used to investigate sagittal balance parameters and ROM. The mean follow-up was 24.3 months (range: 12 to 36 mo). Clinical outcomes were satisfactory. There was a significant improvement of Short Form-36, Neck Disability Index, and Visual Analog Scale scores. Mean ROM was 8.3 degrees preoperatively and 11.0 degrees postoperatively (P=0.013). Mean preoperative C2C7 curvature was 12.8 and 16.0 degrees at last follow-up (P=0.001). Mean preoperative functional spinal unit (FSU) angle was 2.3 and 5.3 degrees postoperatively (P<0.0001). Mean postoperative shell angle was 5.5 degrees. There was a significant correlation between postoperative C2C7 alignment and preoperative C2C7 alignment, change of C2C7 alignment, preoperative and postoperative FSU angle, and prosthesis shell angle. There was also a significant correlation between postoperative FSU angle and preoperative C2C7 alignment, preoperative FSU angle, change of FSU angle, and prosthesis shell angle. Regression analysis showed that prosthesis shell angle and preoperative FSU angle contributed significantly to postoperative FSU angle. Moreover, preoperative C2C7 alignment, preoperative FSU angle, postoperative FSU angle, and prosthesis shell angle contributed significantly to

  13. Autogenous shrinkage of Ducorit S5R ASTM C 1698-09 test method

    DEFF Research Database (Denmark)

    Damkilde, Lars

    The report deals with experimental measurement of autogenous shrinkage of Ducorit S5R according to the test method ASTM C 1698-09. This test method measures the bulk strain of a sealed cementitious specimen, at constant temperature and not subjected to external forces, from the time of final...

  14. PR2ALIGN: a stand-alone software program and a web-server for protein sequence alignment using weighted biochemical properties of amino acids.

    Science.gov (United States)

    Kuznetsov, Igor B; McDuffie, Michael

    2015-05-07

    Alignment of amino acid sequences is the main sequence comparison method used in computational molecular biology. The selection of the amino acid substitution matrix best suitable for a given alignment problem is one of the most important decisions the user has to make. In a conventional amino acid substitution matrix all elements are fixed and their values cannot be easily adjusted. Moreover, most existing amino acid substitution matrices account for the average (dis)similarities between amino acid types and do not distinguish the contribution of a specific biochemical property to these (dis)similarities. PR2ALIGN is a stand-alone software program and a web-server that provide the functionality for implementing flexible user-specified alignment scoring functions and aligning pairs of amino acid sequences based on the comparison of the profiles of biochemical properties of these sequences. Unlike the conventional sequence alignment methods that use 20x20 fixed amino acid substitution matrices, PR2ALIGN uses a set of weighted biochemical properties of amino acids to measure the distance between pairs of aligned residues and to find an optimal minimal distance global alignment. The user can provide any number of amino acid properties and specify a weight for each property. The higher the weight for a given property, the more this property affects the final alignment. We show that in many cases the approach implemented in PR2ALIGN produces better quality pair-wise alignments than the conventional matrix-based approach. PR2ALIGN will be helpful for researchers who wish to align amino acid sequences by using flexible user-specified alignment scoring functions based on the biochemical properties of amino acids instead of the amino acid substitution matrix. To the best of the authors' knowledge, there are no existing stand-alone software programs or web-servers analogous to PR2ALIGN. The software is freely available from http://pr2align.rit.albany.edu.

  15. Synthesis of Al-5Ti-1B Refiner by Melt Reaction Method

    OpenAIRE

    LI He; CHAI Li-hua; MA Teng-fei; CHEN Zi-yong

    2017-01-01

    Al-5Ti-1B refiner was successfully prepared by melt reaction method. Through the thermodynamics calculation, the initial reaction temperature was determined. The influence of reaction temperature on microstructure and absorption rate of the alloy was investigated. The phase and microstructure of the alloy were observed by X-ray diffraction, scanning electron microscope and energy dispersive spectrometer. The Al-5Ti-1B refiner was extruded at high temperature to wire with the diameter of 9.5mm...

  16. NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction

    DEFF Research Database (Denmark)

    Nielsen, Morten; Lund, Ole

    2009-01-01

    this binding event. RESULTS: Here, we present a novel artificial neural network-based method, NN-align that allows for simultaneous identification of the MHC class II binding core and binding affinity. NN-align is trained using a novel training algorithm that allows for correction of bias in the training data...

  17. A modified multiscale peak alignment method combined with trilinear decomposition to study the volatile/heat-labile components in Ligusticum chuanxiong Hort - Cyperus rotundus rhizomes by HS-SPME-GC/MS.

    Science.gov (United States)

    He, Min; Yan, Pan; Yang, Zhi-Yu; Zhang, Zhi-Min; Yang, Tian-Biao; Hong, Liang

    2018-03-15

    Head Space/Solid Phase Micro-Extraction (HS-SPME) coupled with Gas Chromatography/Mass Spectrometer (GC/MS) was used to determine the volatile/heat-labile components in Ligusticum chuanxiong Hort - Cyperus rotundus rhizomes. Facing co-eluting peaks in k samples, a trilinear structure was reconstructed to obtain the second-order advantage. The retention time (RT) shift with multi-channel detection signals for different samples has been vital in maintaining the trilinear structure, thus a modified multiscale peak alignment (mMSPA) method was proposed in this paper. The peak position and peak width of representative ion profile were firstly detected by mMSPA using Continuous Wavelet Transform with Haar wavelet as the mother wavelet (Haar CWT). Then, the raw shift was confirmed by Fast Fourier Transform (FFT) cross correlation calculation. To obtain the optimal shift, Haar CWT was again used to detect the subtle deviations and be amalgamated in calculation. Here, to ensure there is no peaks shape alternation, the alignment was performed in local domains of data matrices, and all data points in the peak zone were moved via linear interpolation in non-peak parts. Finally, chemical components of interest in Ligusticum chuanxiong Hort - Cyperus rotundus rhizomes were analyzed by HS-SPME-GCMS and mMSPA-alternating trilinear decomposition (ATLD) resolution. As a result, the concentration variation between herbs and their pharmaceutical products can provide a scientific basic for the quality standard establishment of traditional Chinese medicines. Copyright © 2018 Elsevier B.V. All rights reserved.

  18. Development of a Self Aligned CMOS Process for Flash Lamp Annealed Polycrystalline Silicon TFTs

    Science.gov (United States)

    Bischoff, Paul

    The emerging active matrix liquid crystal (AMLCD) display market requires a high performing semiconductor material to meet rising standards of operation. Currently amorphous silicon (a-Si) dominates the market but it does not have the required mobility for it to be used in AMLCD manufacturing. Other materials have been developed including crystallizing a-Si into poly-silicon. A new approach to crystallization through the use of flash lamp annealing (FLA) decreases manufacturing time and greatly improves carrier mobility. Previous work on FLA silicon for the use in CMOS transistors revealed significant lateral dopant diffusion into the channel greatly increasing the minimum channel length required for a working device. This was further confounded by the gate overlap due to misalignment during lithography patterning steps. Through the use of furnace dopant activation instead of FLA dopant activation and a self aligned gate the minimum size transistor can be greatly reduced. A new lithography mask and process flow were developed for the furnace annealing and self aligned gate. Fabrication of the self aligned devices resulted in oxidation of the Molybdenum self aligned gate. Further development is needed to successfully manufacture these devices. Non-self aligned transistors were made simultaneously with self aligned devices and used the furnace activation. These devices showed an increase in sheet resistance from 250 O to 800 O and lower mobility from 380 to 40.2 V/cm2s. The lower mobility can be contributed to an increase in implanted trap density indicating furnace annealing is an inferior activation method over FLA. The minimum transistor size however was reduced from 20 to 5 mum. With improvements in the self aligned process high performing small devices can be manufactured.

  19. All about alignment

    CERN Multimedia

    2006-01-01

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

  20. Principles of alignment of multibeam lasers for thermonuclear purposes

    International Nuclear Information System (INIS)

    Basovy, N.G.; Ol'shevskii, Y.N.; Belyan, V.F.

    1980-01-01

    The concrete object of the investigation is the alignment of the high-power 12-channel ''Del'fin'' neodymium-glass laser facilaity. The objects of the alignment are the optical channel of the laser installation, the system for pointing and focusing the laser radiation on the target, the system for positioning the target in the focal volume, and the system for monitoring the optical quality of the elements of the laser installation and laser beams and also the conditions of the target irradiation in the vacuum chamber. The list of requirements that must be satisfied by the alignment beams, the possible sources of alignment beams, the makeup of the apparatus, and the methods of aligning the laser facility are considered. The principles and the actual systems of automatic alignment of the optical elements are described, as are the operating models of the automatized units. The problem of simulating the working laser beams by the alignment beams and the possibility of automatizing the control of the spatial and angular characteristics of the laser radiation are discussed. The system for controlling the alignment processes by means of a laser is considered, as it also a scheme for incorporating the automatized alignment subsystem in the overall system for the automation of the ''Del'fin'' facility

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

    Directory of Open Access Journals (Sweden)

    Emanuel Santos

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

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

    Science.gov (United States)

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

    2015-01-01

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

  3. IMPLEMENTING THE 5S METHOD IN THE PRODUCTION SYSTEM OF DACIA & RENAULT

    Directory of Open Access Journals (Sweden)

    Marin CIOBANU

    2014-11-01

    Full Text Available The aim of this paper is to demonstrate the usefulness of the 5S method in addressing the issues of continuous improvement of productivity and quality of work. There are presented the 5 steps, techniques and the adjacent tools. Solutions implemented in the production system Dacia & Renault are indicated. This article provides a practical framework. The 5S method follows the Deming PDCA cycle which constitutes the starting point of the SDCA cycle of continuous improvement of the company's activities in order to obtain excellence. The implementing time of the method depends on the resources and materials allocated. Deployment of 5S is achieved by a scheme of "3+2": the first 3S are tangible and immediate actions, the last 2S appeal to specific management actions. The efficacy of their own workplace in total autonomy creates comfort in the work environment and gives personal benefits to workers.

  4. Pulsed taut-wire measurement of the magnetic alignment of the ITS induction cells

    International Nuclear Information System (INIS)

    Melton, J.G.; Burns, M.J.; Honaberger, D.J.

    1993-01-01

    The mechanical and magnetic alignment of the first eight induction-cell, solenoid magnets of the Integrated Test Stand (ITS) for the Dual-Axis Radiographic Hydrodynamic Test (DARHT) facility were measured by observing the deflection of a fine, taut wire carrying a pulsed current. To achieve the required alignment (less than 0.25 mm offset and less than 5 mrad tilt), the magnet design uses quadrufilar windings and iron field-smoothing rings. After detailed measurements of each solenoid magnet, the cells are assembled and then mechanically aligned using a laser and an alignment target moved along the cell centerline. After the cells are in final position, the pulsed wire method is used to verify the magnetic alignment. The measurements show an average offset of the magnetic axes from the mechanical axis of 0. 15 mm, with a maximum offset of 0.3 mm. The average tilt of the magnetic axis was 0.7 mrad with a maximum tilt of 1.4 mrad. Tilts are corrected to less than 0.3 mrad, using dipole trim magnets assembled into each cell. Correction is limited noise

  5. 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)

  6. Modeling electrical conductivities of nanocomposites with aligned carbon nanotubes

    International Nuclear Information System (INIS)

    Bao, W S; Meguid, S A; Zhu, Z H; Meguid, M J

    2011-01-01

    We have developed an improved three-dimensional (3D) percolation model to investigate the effect of the alignment of carbon nanotubes (CNTs) on the electrical conductivity of nanocomposites. In this model, both intrinsic and contact resistances are considered, and a new method of resistor network recognition that employs periodically connective paths is developed. This method leads to a reduction in the size effect of the representative cuboid in our Monte Carlo simulations. With this new technique, we were able to effectively analyze the effects of the CNT alignment upon the electrical conductivity of nanocomposites. Our model predicted that the peak value of the conductivity occurs for partially aligned rather than perfectly aligned CNTs. It has also identified the value of the peak and the corresponding alignment for different volume fractions of CNTs. Our model works well for both multi-wall CNTs (MWCNTs) and single-wall CNTs (SWCNTs), and the numerical results show a quantitative agreement with existing experimental observations.

  7. The 5S lean method as a tool of industrial management performances

    Science.gov (United States)

    Filip, F. C.; Marascu-Klein, V.

    2015-11-01

    Implementing the 5S (seiri, seiton, seiso, seiketsu, and shitsuke) method is carried out through a significant study whose purpose to analyse and deployment the management performance in order to emphasize the problems and working mistakes, reducing waste (stationary and waiting times), flow transparency, storage areas by properly marking and labelling, establishing standards work (everyone knows exactly where are the necessary things), safety and ergonomic working places (the health of all employees). The study describes the impact of the 5S lean method implemented to storing, cleaning, developing and sustaining a production working place from an industrial company. In order to check and sustain the 5S process, it is needed to use an internal audit, called “5S audit”. Implementing the 5S methodology requires organization and safety of the working process, properly marking and labelling of the working place, and audits to establish the work in progress and to maintain the improved activities.

  8. 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.

  9. 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/.

  10. PhAST: pharmacophore alignment search tool.

    Science.gov (United States)

    Hähnke, Volker; Hofmann, Bettina; Grgat, Tomislav; Proschak, Ewgenij; Steinhilber, Dieter; Schneider, Gisbert

    2009-04-15

    We present a ligand-based virtual screening technique (PhAST) for rapid hit and lead structure searching in large compound databases. Molecules are represented as strings encoding the distribution of pharmacophoric features on the molecular graph. In contrast to other text-based methods using SMILES strings, we introduce a new form of text representation that describes the pharmacophore of molecules. This string representation opens the opportunity for revealing functional similarity between molecules by sequence alignment techniques in analogy to homology searching in protein or nucleic acid sequence databases. We favorably compared PhAST with other current ligand-based virtual screening methods in a retrospective analysis using the BEDROC metric. In a prospective application, PhAST identified two novel inhibitors of 5-lipoxygenase product formation with minimal experimental effort. This outcome demonstrates the applicability of PhAST to drug discovery projects and provides an innovative concept of sequence-based compound screening with substantial scaffold hopping potential. 2008 Wiley Periodicals, Inc.

  11. 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.

  12. Method matters: Understanding diagnostic reliability in DSM-IV and DSM-5.

    Science.gov (United States)

    Chmielewski, Michael; Clark, Lee Anna; Bagby, R Michael; Watson, David

    2015-08-01

    Diagnostic reliability is essential for the science and practice of psychology, in part because reliability is necessary for validity. Recently, the DSM-5 field trials documented lower diagnostic reliability than past field trials and the general research literature, resulting in substantial criticism of the DSM-5 diagnostic criteria. Rather than indicating specific problems with DSM-5, however, the field trials may have revealed long-standing diagnostic issues that have been hidden due to a reliance on audio/video recordings for estimating reliability. We estimated the reliability of DSM-IV diagnoses using both the standard audio-recording method and the test-retest method used in the DSM-5 field trials, in which different clinicians conduct separate interviews. Psychiatric patients (N = 339) were diagnosed using the SCID-I/P; 218 were diagnosed a second time by an independent interviewer. Diagnostic reliability using the audio-recording method (N = 49) was "good" to "excellent" (M κ = .80) and comparable to the DSM-IV field trials estimates. Reliability using the test-retest method (N = 218) was "poor" to "fair" (M κ = .47) and similar to DSM-5 field-trials' estimates. Despite low test-retest diagnostic reliability, self-reported symptoms were highly stable. Moreover, there was no association between change in self-report and change in diagnostic status. These results demonstrate the influence of method on estimates of diagnostic reliability. (c) 2015 APA, all rights reserved).

  13. Solving the Bateman equations in CASMO5 using implicit ode numerical methods for stiff systems

    International Nuclear Information System (INIS)

    Hykes, J. M.; Ferrer, R. M.

    2013-01-01

    The Bateman equations, which describe the transmutation of nuclides over time as a result of radioactive decay, absorption, and fission, are often numerically stiff. This is especially true if short-lived nuclides are included in the system. This paper describes the use of implicit numerical methods for o D Es applied to the stiff Bateman equations, specifically employing the Backward Differentiation Formulas (BDF) form of the linear multistep method. As is true in other domains, using an implicit method removes or lessens the (sometimes severe) step-length constraints by which explicit methods must abide. To gauge its accuracy and speed, the BDF method is compared to a variety of other solution methods, including Runge-Kutta explicit methods and matrix exponential methods such as the Chebyshev Rational Approximation Method (CRAM). A preliminary test case was chosen as representative of a PWR lattice depletion step and was solved with numerical libraries called from a Python front-end. The Figure of Merit (a combined measure of accuracy and efficiency) for the BDF method was nearly identical to that for CRAM, while explicit methods and other matrix exponential approximations trailed behind. The test case includes 319 nuclides, in which the shortest-lived nuclide is 98 Nb with a half-life of 2.86 seconds. Finally, the BDF and CRAM methods were compared within CASMO5, where CRAM had a FOM about four times better than BDF, although the BDF implementation was not fully optimized. (authors)

  14. Cell Based Meniscal Repair Using an Aligned Bioactive Nanofibrous Sheath

    Science.gov (United States)

    2017-07-01

    to subsequently guide tissue regeneration , for example, by seeded tissue progenitor cells . To achieve this objective, the first step is to develop...AWARD NUMBER: W81XWH-15-1-0104 TITLE: Cell -Based Meniscal Repair Using an Aligned Bioactive Nanofibrous Sheath PRINCIPAL INVESTIGATOR...SUBTITLE 5a. CONTRACT NUMBER Cell -Based Meniscal Repair Using an Aligned Bioactive Nanofibrous Sheath 5b. GRANT NUMBER W81XWH-15-1-0104 5c. PROGRAM

  15. 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)

  16. 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)

  17. 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...

  18. Detecting chaos, determining the dimensions of tori and predicting slow diffusion in Fermi-Pasta-Ulam lattices by the Generalized Alignment Index method

    Science.gov (United States)

    Skokos, C.; Bountis, T.; Antonopoulos, C.

    2008-12-01

    The recently introduced GALI method is used for rapidly detecting chaos, determining the dimensionality of regular motion and predicting slow diffusion in multi-dimensional Hamiltonian systems. We propose an efficient computation of the GALIk indices, which represent volume elements of k randomly chosen deviation vectors from a given orbit, based on the Singular Value Decomposition (SVD) algorithm. We obtain theoretically and verify numerically asymptotic estimates of GALIs long-time behavior in the case of regular orbits lying on low-dimensional tori. The GALIk indices are applied to rapidly detect chaotic oscillations, identify low-dimensional tori of Fermi-Pasta-Ulam (FPU) lattices at low energies and predict weak diffusion away from quasiperiodic motion, long before it is actually observed in the oscillations.

  19. DEFENSE WASTE PROCESSING FACILITY ANALYTICAL METHOD VERIFICATION FOR THE SLUDGE BATCH 5 QUALIFICATION SAMPLE

    International Nuclear Information System (INIS)

    Click, D; Tommy Edwards, T; Henry Ajo, H

    2008-01-01

    For each sludge batch that is processed in the Defense Waste Processing Facility (DWPF), the Savannah River National Laboratory (SRNL) performs confirmation of the applicability of the digestion method to be used by the DWPF lab for elemental analysis of Sludge Receipt and Adjustment Tank (SRAT) receipt samples and SRAT product process control samples. DWPF SRAT samples are typically dissolved using a room temperature HF-HNO3 acid dissolution (i.e., DWPF Cold Chem Method, see Procedure SW4-15.201) and then analyzed by inductively coupled plasma - atomic emission spectroscopy (ICP-AES). This report contains the results and comparison of data generated from performing the Aqua Regia (AR), Sodium Peroxide/Hydroxide Fusion (PF) and DWPF Cold Chem (CC) method digestion of Sludge Batch 5 (SB5) SRAT Receipt and SB5 SRAT Product samples. The SB5 SRAT Receipt and SB5 SRAT Product samples were prepared in the SRNL Shielded Cells, and the SRAT Receipt material is representative of the sludge that constitutes the SB5 Batch composition. This is the sludge in Tank 51 that is to be transferred into Tank 40, which will contain the heel of Sludge Batch 4 (SB4), to form the SB5 Blend composition. The results for any one particular element should not be used in any way to identify the form or speciation of a particular element in the sludge or used to estimate ratios of compounds in the sludge. A statistical comparison of the data validates the use of the DWPF CC method for SB5 Batch composition. However, the difficulty that was encountered in using the CC method for SB4 brings into question the adequacy of CC for the SB5 Blend. Also, it should be noted that visible solids remained in the final diluted solutions of all samples digested by this method at SRNL (8 samples total), which is typical for the DWPF CC method but not seen in the other methods. Recommendations to the DWPF for application to SB5 based on studies to date: (1) A dissolution study should be performed on the WAPS

  20. Radioimmunoelectrophoresis, a sensitive method for detecting cleavage of the fifth component of human complement (C5)

    International Nuclear Information System (INIS)

    Perez, H.D.; Ong, R.; Banda, D.; Goldstein, I.M.

    1983-01-01

    A method has been developed for detecting cleavage of human C5 in serum and whole blood as a consequence of complement activation. Standard, single-dimension immunoelectrophoresis was performed using as antibody a radioiodinated IgG fraction prepared from a commercially available antiserum to human C5. Autoradiographs developed after radioimmunoelectrophoresis of either normal human serum or functionally pure human C5 revealed only one precipitin band. In contrast, when either zymosan-treated serum or trypsin-treated human C5 were examined with this technique, two additional precipitin bands were detected. One migrated more anodally than native C5 while the other remained at the origin (cathode). Radioimmunoelectrophoresis was significantly more sensitive as an indicator of complement activation in human serum than either measurements of total hemolytic complement or a standard assay for complement (C5)-derived chemotactic activity. (Auth.)

  1. Accelerating large-scale protein structure alignments with graphics processing units

    Directory of Open Access Journals (Sweden)

    Pang Bin

    2012-02-01

    Full Text Available Abstract Background Large-scale protein structure alignment, an indispensable tool to structural bioinformatics, poses a tremendous challenge on computational resources. To ensure structure alignment accuracy and efficiency, efforts have been made to parallelize traditional alignment algorithms in grid environments. However, these solutions are costly and of limited accessibility. Others trade alignment quality for speedup by using high-level characteristics of structure fragments for structure comparisons. Findings We present ppsAlign, a parallel protein structure Alignment framework designed and optimized to exploit the parallelism of Graphics Processing Units (GPUs. As a general-purpose GPU platform, ppsAlign could take many concurrent methods, such as TM-align and Fr-TM-align, into the parallelized algorithm design. We evaluated ppsAlign on an NVIDIA Tesla C2050 GPU card, and compared it with existing software solutions running on an AMD dual-core CPU. We observed a 36-fold speedup over TM-align, a 65-fold speedup over Fr-TM-align, and a 40-fold speedup over MAMMOTH. Conclusions ppsAlign is a high-performance protein structure alignment tool designed to tackle the computational complexity issues from protein structural data. The solution presented in this paper allows large-scale structure comparisons to be performed using massive parallel computing power of GPU.

  2. A comparison of high and low degree of freedom alignment techniques in functional PET brain activation experiments)

    International Nuclear Information System (INIS)

    Sonkkila, C.P.; Egan, G.F.; Watson, J.D.G.; Wenderoth, P.

    1998-01-01

    Full text: Cognitive activation studies in PET commonly utilise intersubject alignment as a preprocessing stage before images are compared. The accepted technique included in statistical parametric mapping (SPM) an analysis package developed by Friston et al, uses a 12 'degree of freedom' (d.o.f.) affine transformation, while a more complicated non-linear approach has recently been developed by Woods et al, but it necessitates the use of higher resolution magnetic resonance images to give sufficient information to use the high degree of freedom nonlinear alignment. This study seeks to show the differences between using the low degree of freedom alignment approach in SPM compared to that of Woods. As an example, a group of 8 normal subjects are asked to perform a complex visual paradigm during a series of PET scans designed to be sensitive to changes in blood flow. Structural MR images are also acquired for each subject. The resulting scans are then analysed with two methods: One where all images are aligned using SPM and the PET images. The second method utilises Woods' algorithm (a 5th order polynomial fit with 168 d.o.f.) and the MR images. SPM is then used to assess regions of significant change in blood flow across the group for both methods, and the results compared. When using the PET images for alignment purposes, the maximal probability for rejecting the null hypothesis of no change in regional blood flow was p = 0.471 (Talairach atlas coordinate 10 -74 -8) while utilising the MR images gives p = 0.913 for the same region. Note that to reach higher statistical significance ( eg p > 0.95 ) more subjects would be included in the study. It was concluded that there is considerable evidence to show that using MR images and Woods' nonlinear alignment gives higher statistical power than using PET images only and a low degree of freedom alignment method for resolving changes in regional blood flow in cognitive activation experiments

  3. Reliability and Validity of the Footprint Assessment Method Using Photoshop CS5 Software.

    Science.gov (United States)

    Gutiérrez-Vilahú, Lourdes; Massó-Ortigosa, Núria; Costa-Tutusaus, Lluís; Guerra-Balic, Myriam

    2015-05-01

    Several sophisticated methods of footprint analysis currently exist. However, it is sometimes useful to apply standard measurement methods of recognized evidence with an easy and quick application. We sought to assess the reliability and validity of a new method of footprint assessment in a healthy population using Photoshop CS5 software (Adobe Systems Inc, San Jose, California). Forty-two footprints, corresponding to 21 healthy individuals (11 men with a mean ± SD age of 20.45 ± 2.16 years and 10 women with a mean ± SD age of 20.00 ± 1.70 years) were analyzed. Footprints were recorded in static bipedal standing position using optical podography and digital photography. Three trials for each participant were performed. The Hernández-Corvo, Chippaux-Smirak, and Staheli indices and the Clarke angle were calculated by manual method and by computerized method using Photoshop CS5 software. Test-retest was used to determine reliability. Validity was obtained by intraclass correlation coefficient (ICC). The reliability test for all of the indices showed high values (ICC, 0.98-0.99). Moreover, the validity test clearly showed no difference between techniques (ICC, 0.99-1). The reliability and validity of a method to measure, assess, and record the podometric indices using Photoshop CS5 software has been demonstrated. This provides a quick and accurate tool useful for the digital recording of morphostatic foot study parameters and their control.

  4. A Comparison of Plain Radiography with Computer Tomography in Determining Coronal and Sagittal Alignments following Total Knee Arthroplasty

    Directory of Open Access Journals (Sweden)

    Solayar GN

    2017-07-01

    Full Text Available INTRODUCTION: Optimal coronal and sagittal component positioning is important in achieving a successful outcome following total knee arthroplasty (TKA. Modalities to determine post-operative alignment include plain radiography and computer tomography (CT imaging. This study aims to determine the accuracy and reliability of plain radiographs in measuring coronal and sagittal alignment following TKA. MATERIALS AND METHODS: A prospective, consecutive study of 58 patients undergoing TKA was performed comparing alignment data from plain radiographs and CT imaging. Hip- knee-angle (HKA, sagittal femoral angle (SFA and sagittal tibial angle (STA measurements were taken by two observers from plain radiographs and compared with CT alignment. Intra- and inter-observer correlation was calculated for each measurement. RESULTS: Intra-observer correlation was excellent for HKA (r>0.89 with a mean difference of 0.95 and STA (r>0.8 compared to SFA (r=0.5. When comparing modalities (radiographs vs CT, HKA estimations for both observers showed the least maximum and mean differences while SFA observations were the least accurate. CONCLUSION: Radiographic estimation of HKA showed excellent intra- and inter-observer correlation and corresponds well with CT imaging. However, radiographic estimation of sagittal plane alignment was less reliably measured and correlated less with CT imaging. Plain radiography was found to be inferior to CT for estimation of biplanar prosthetic alignment following TKA.

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

    Science.gov (United States)

    Wang, Dahui; Zhao, Xueqing; Hua, Hengqi; Zhang, Yongsheng; Hu, Yun; Yi, Aiping; Zhao, Jun

    2013-05-01

    A kind of beam automatic alignment method used for double paths amplification in the electron pumped excimer laser system is demonstrated. In this way, the beams from the amplifiers can be transferred along the designated direction and accordingly irradiate on the target with high stabilization and accuracy. However, owing to nonexistence of natural alignment references in excimer laser amplifiers, two cross-hairs structure is used to align the beams. Here, one crosshair put into the input beam is regarded as the near-field reference while the other put into output beam is regarded as the far-field reference. The two cross-hairs are transmitted onto Charge Coupled Devices (CCD) by image-relaying structures separately. The errors between intersection points of two cross-talk images and centroid coordinates of actual beam are recorded automatically and sent to closed loop feedback control mechanism. Negative feedback keeps running until preset accuracy is reached. On the basis of above-mentioned design, the alignment optical path is built and the software is compiled, whereafter the experiment of double paths automatic alignment in electron pumped excimer laser amplifier is carried through. Meanwhile, the related influencing factors and the alignment precision are analyzed. Experimental results indicate that the alignment system can achieve the aiming direction of automatic aligning beams in short time. The analysis shows that the accuracy of alignment system is 0.63μrad and the beam maximum restoration error is 13.75μm. Furthermore, the bigger distance between the two cross-hairs, the higher precision of the system is. Therefore, the automatic alignment system has been used in angular multiplexing excimer Main Oscillation Power Amplification (MOPA) system and can satisfy the requirement of beam alignment precision on the whole.

  6. 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.

  7. Vacuum Alignment with more Flavors

    DEFF Research Database (Denmark)

    Ryttov, Thomas

    2014-01-01

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

  8. 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

  9. Measuring the distance between multiple sequence alignments.

    Science.gov (United States)

    Blackburne, Benjamin P; Whelan, Simon

    2012-02-15

    Multiple sequence alignment (MSA) is a core method in bioinformatics. The accuracy of such alignments may influence the success of downstream analyses such as phylogenetic inference, protein structure prediction, and functional prediction. The importance of MSA has lead to the proliferation of MSA methods, with different objective functions and heuristics to search for the optimal MSA. Different methods of inferring MSAs produce different results in all but the most trivial cases. By measuring the differences between inferred alignments, we may be able to develop an understanding of how these differences (i) relate to the objective functions and heuristics used in MSA methods, and (ii) affect downstream analyses. We introduce four metrics to compare MSAs, which include the position in a sequence where a gap occurs or the location on a phylogenetic tree where an insertion or deletion (indel) event occurs. We use both real and synthetic data to explore the information given by these metrics and demonstrate how the different metrics in combination can yield more information about MSA methods and the differences between them. MetAl is a free software implementation of these metrics in Haskell. Source and binaries for Windows, Linux and Mac OS X are available from http://kumiho.smith.man.ac.uk/whelan/software/metal/.

  10. Cliché fabrication method using precise roll printing process with 5 um pattern width

    Science.gov (United States)

    Shin, Yejin; Kim, Inyoung; Oh, Dong-Ho; Lee, Taik-Min

    2016-09-01

    Among the printing processes for printed electronic devices, gravure offset and reverse offset method have drawn attention for its fine pattern printing possibility. These printing methods use cliché, which has critical effect on the final product precision and quality. In this research, a novel precise cliché replica method is proposed. It consists of copper sputtering, precise mask pattern printing with 5 um width using reverse offset printing, Ni electroplating, lift-off, etching, and DLC coating. We finally compare the fabricated replica cliché with the original one and print out precise patterns using the replica cliché.

  11. A method for classification of network traffic based on C5.0 Machine Learning Algorithm

    DEFF Research Database (Denmark)

    Bujlow, Tomasz; Riaz, M. Tahir; Pedersen, Jens Myrup

    2012-01-01

    current network traffic. To overcome the drawbacks of existing methods for traffic classification, usage of C5.0 Machine Learning Algorithm (MLA) was proposed. On the basis of statistical traffic information received from volunteers and C5.0 algorithm we constructed a boosted classifier, which was shown...... and classification, an algorithm for recognizing flow direction and the C5.0 itself. Classified applications include Skype, FTP, torrent, web browser traffic, web radio, interactive gaming and SSH. We performed subsequent tries using different sets of parameters and both training and classification options...

  12. Helical coil alignment in the advanced toroidal facility

    International Nuclear Information System (INIS)

    Taylor, D.J.; Cole, M.J.; Johnson, R.L.; Nelson, B.E.; Warwick, J.E.; Whitson, J.C.

    1985-01-01

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

  13. Relevance-based evaluation of alignment approaches: The OAEI2007 food task revisited

    NARCIS (Netherlands)

    Hage, W.R. van; Kolb, H.; Schreiber, G.

    2008-01-01

    Current state-of-the-art ontology-alignment evaluation methods are based on the assumption that alignment relations come in two flavors: correct and incorrect. Some alignment systems find more correct mappings than others and hence, by this assumption, they perform better. In practical applications

  14. 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…

  15. 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.

  16. Aligning protein sequence and analysing substitution pattern using ...

    Indian Academy of Sciences (India)

    Prakash

    Aligning protein sequences using a score matrix has became a routine but valuable method in modern biological ..... the amino acids according to their substitution behaviour ...... which may cause great change (e.g. prolonging the helix) in.

  17. 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.

  18. Quasiparticle Level Alignment for Photocatalytic Interfaces.

    Science.gov (United States)

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

    2014-05-13

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

  19. Alignment of the stanford linear collider Arcs

    International Nuclear Information System (INIS)

    Pitthan, R.; Bell, B.; Friedsam, H.

    1987-01-01

    The alignment of the Arcs for the Stanford Linear Collider at SLAC has posed problems in accelerator survey and alignment not encountered before. These problems come less from the tight tolerances of 0.1 mm, although reaching such a tight statistically defined accuracy in a controlled manner is difficult enough, but from the absence of a common reference plane for the Arcs. Traditional circular accelerators, including HERA and LEP, have been designed in one plane referenced to local gravity. For the SLC Arcs no such single plane exists. Methods and concepts developed to solve these and other problems, connected with the unique design of SLC, range from the first use of satellites for accelerator alignment, use of electronic laser theodolites for placement of components, computer control of the manual adjustment process, complete automation of the data flow incorporating the most advanced concepts of geodesy, strict separation of survey and alignment, to linear principal component analysis for the final statistical smoothing of the mechanical components

  20. 40 CFR Appendix A-3 to Part 60 - Test Methods 4 through 5I

    Science.gov (United States)

    2010-07-01

    ... (see Section 2.0). 8.2.1Place exactly 5 ml water in each impinger. Leak check the sampling train as... this will cause water to back up into the filter holder. If the desired vacuum is exceeded, either leak... Note: This method does not include all the specifications (e.g., equipment and supplies) and procedures...

  1. 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...

  2. Constructive alignment of a research-informed teaching activity within an undergraduate diagnostic radiography curriculum: A reflection

    International Nuclear Information System (INIS)

    Higgins, R.; Hogg, P.; Robinson, L.

    2017-01-01

    Aim: To evaluate the learning experience of a level 5 (year 2) student cohort within a research-informed teaching (RiT) activity and to map findings against learning outcomes and level descriptors using constructive alignment. Method: An online questionnaire was used to explore the level 5 student experience of a Research-informed Teaching (RiT) activity. Responses were retrospectively mapped against Framework for Higher Education Qualifications (FHEQ) level descriptors for level 5 using constructive alignment. Results and Discussion: Thirty one out of 46 level 5 students completed the questionnaire (67% response rate). Analysis of the questionnaire supported the integration of this RiT activity within the curriculum in terms of learning and research skill development by students. However, it was identified that this activity could be revised further to better align with level 5 descriptors and incorporate additional higher level cognitive processes. Conclusion: Learning outcomes for this RiT activity were constructively aligned with FHEQ level 5 descriptors. Recommendations are provided on how these could be further refined to ensure students undertake a more critical approach to the application of theory into practice. Discussion also considers how this process could be used to develop a similar RiT activity at level 6 (year 3). - Highlights: • Constructive alignment helped to ensure that the learning outcomes were appropriately aligned with level 5 descriptors. • Reflection identified outcomes that required further improvement to focus on higher-order thinking and application skills. • This article also illustrates how this process could be used to develop a level 6 RiT activity.

  3. Accuracy Evaluation of C4.5 and Naive Bayes Classifiers Using Attribute Ranking Method

    Directory of Open Access Journals (Sweden)

    S. Sivakumari

    2009-03-01

    Full Text Available This paper intends to classify the Ljubljana Breast Cancer dataset using C4.5 Decision Tree and Nai?ve Bayes classifiers. In this work, classification is carriedout using two methods. In the first method, dataset is analysed using all the attributes in the dataset. In the second method, attributes are ranked using information gain ranking technique and only the high ranked attributes are used to build the classification model. We are evaluating the results of C4.5 Decision Tree and Nai?ve Bayes classifiers in terms of classifier accuracy for various folds of cross validation. Our results show that both the classifiers achieve good accuracy on the dataset.

  4. THE APPARATUS FOR ALIGNMENT OF THE PHOTOMETRIC LAMP FILAMENT

    Directory of Open Access Journals (Sweden)

    V. A. Dlugunovich

    2015-01-01

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

  5. 2.5-D frequency-domain viscoelastic wave modelling using finite-element method

    Science.gov (United States)

    Zhao, Jian-guo; Huang, Xing-xing; Liu, Wei-fang; Zhao, Wei-jun; Song, Jian-yong; Xiong, Bin; Wang, Shang-xu

    2017-10-01

    2-D seismic modelling has notable dynamic information discrepancies with field data because of the implicit line-source assumption, whereas 3-D modelling suffers from a huge computational burden. The 2.5-D approach is able to overcome both of the aforementioned limitations. In general, the earth model is treated as an elastic material, but the real media is viscous. In this study, we develop an accurate and efficient frequency-domain finite-element method (FEM) for modelling 2.5-D viscoelastic wave propagation. To perform the 2.5-D approach, we assume that the 2-D viscoelastic media are based on the Kelvin-Voigt rheological model and a 3-D point source. The viscoelastic wave equation is temporally and spatially Fourier transformed into the frequency-wavenumber domain. Then, we systematically derive the weak form and its spatial discretization of 2.5-D viscoelastic wave equations in the frequency-wavenumber domain through the Galerkin weighted residual method for FEM. Fixing a frequency, the 2-D problem for each wavenumber is solved by FEM. Subsequently, a composite Simpson formula is adopted to estimate the inverse Fourier integration to obtain the 3-D wavefield. We implement the stiffness reduction method (SRM) to suppress artificial boundary reflections. The results show that this absorbing boundary condition is valid and efficient in the frequency-wavenumber domain. Finally, three numerical models, an unbounded homogeneous medium, a half-space layered medium and an undulating topography medium, are established. Numerical results validate the accuracy and stability of 2.5-D solutions and present the adaptability of finite-element method to complicated geographic conditions. The proposed 2.5-D modelling strategy has the potential to address modelling studies on wave propagation in real earth media in an accurate and efficient way.

  6. A statistically harmonized alignment-classification in image space enables accurate and robust alignment of noisy images in single particle analysis.

    Science.gov (United States)

    Kawata, Masaaki; Sato, Chikara

    2007-06-01

    In determining the three-dimensional (3D) structure of macromolecular assemblies in single particle analysis, a large representative dataset of two-dimensional (2D) average images from huge number of raw images is a key for high resolution. Because alignments prior to averaging are computationally intensive, currently available multireference alignment (MRA) software does not survey every possible alignment. This leads to misaligned images, creating blurred averages and reducing the quality of the final 3D reconstruction. We present a new method, in which multireference alignment is harmonized with classification (multireference multiple alignment: MRMA). This method enables a statistical comparison of multiple alignment peaks, reflecting the similarities between each raw image and a set of reference images. Among the selected alignment candidates for each raw image, misaligned images are statistically excluded, based on the principle that aligned raw images of similar projections have a dense distribution around the correctly aligned coordinates in image space. This newly developed method was examined for accuracy and speed using model image sets with various signal-to-noise ratios, and with electron microscope images of the Transient Receptor Potential C3 and the sodium channel. In every data set, the newly developed method outperformed conventional methods in robustness against noise and in speed, creating 2D average images of higher quality. This statistically harmonized alignment-classification combination should greatly improve the quality of single particle analysis.

  7. Modified Spectral Fatigue Methods for S-N Curves With MIL-HDBK-5J Coefficients

    Science.gov (United States)

    Irvine, Tom; Larsen, Curtis

    2016-01-01

    The rainflow method is used for counting fatigue cycles from a stress response time history, where the fatigue cycles are stress-reversals. The rainflow method allows the application of Palmgren-Miner's rule in order to assess the fatigue life of a structure subject to complex loading. The fatigue damage may also be calculated from a stress response power spectral density (PSD) using the semi-empirical Dirlik, Single Moment, Zhao-Baker and other spectral methods. These methods effectively assume that the PSD has a corresponding time history which is stationary with a normal distribution. This paper shows how the probability density function for rainflow stress cycles can be extracted from each of the spectral methods. This extraction allows for the application of the MIL-HDBK-5J fatigue coefficients in the cumulative damage summation. A numerical example is given in this paper for the stress response of a beam undergoing random base excitation, where the excitation is applied separately by a time history and by its corresponding PSD. The fatigue calculation is performed in the time domain, as well as in the frequency domain via the modified spectral methods. The result comparison shows that the modified spectral methods give comparable results to the time domain rainflow counting method.

  8. Using structure to explore the sequence alignment space of remote homologs.

    Directory of Open Access Journals (Sweden)

    Andrew Kuziemko

    2011-10-01

    Full Text Available Protein structure modeling by homology requires an accurate sequence alignment between the query protein and its structural template. However, sequence alignment methods based on dynamic programming (DP are typically unable to generate accurate alignments for remote sequence homologs, thus limiting the applicability of modeling methods. A central problem is that the alignment that is "optimal" in terms of the DP score does not necessarily correspond to the alignment that produces the most accurate structural model. That is, the correct alignment based on structural superposition will generally have a lower score than the optimal alignment obtained from sequence. Variations of the DP algorithm have been developed that generate alternative alignments that are "suboptimal" in terms of the DP score, but these still encounter difficulties in detecting the correct structural alignment. We present here a new alternative sequence alignment method that relies heavily on the structure of the template. By initially aligning the query sequence to individual fragments in secondary structure elements and combining high-scoring fragments that pass basic tests for "modelability", we can generate accurate alignments within a small ensemble. Our results suggest that the set of sequences that can currently be modeled by homology can be greatly extended.

  9. Using structure to explore the sequence alignment space of remote homologs.

    Science.gov (United States)

    Kuziemko, Andrew; Honig, Barry; Petrey, Donald

    2011-10-01

    Protein structure modeling by homology requires an accurate sequence alignment between the query protein and its structural template. However, sequence alignment methods based on dynamic programming (DP) are typically unable to generate accurate alignments for remote sequence homologs, thus limiting the applicability of modeling methods. A central problem is that the alignment that is "optimal" in terms of the DP score does not necessarily correspond to the alignment that produces the most accurate structural model. That is, the correct alignment based on structural superposition will generally have a lower score than the optimal alignment obtained from sequence. Variations of the DP algorithm have been developed that generate alternative alignments that are "suboptimal" in terms of the DP score, but these still encounter difficulties in detecting the correct structural alignment. We present here a new alternative sequence alignment method that relies heavily on the structure of the template. By initially aligning the query sequence to individual fragments in secondary structure elements and combining high-scoring fragments that pass basic tests for "modelability", we can generate accurate alignments within a small ensemble. Our results suggest that the set of sequences that can currently be modeled by homology can be greatly extended.

  10. Clear aligners for orthodontic treatment?

    Science.gov (United States)

    Javidi, Hanieh; Graham, Elizabeth

    2015-12-01

    PubMed/Medline, Embase, Cochrane Central Register of Controlled Clinical trials (CENTRAL), Web of Knowledge, SCOPUS, Google Scholar and LILACS databases. Clinical prospective and retrospective studies of orthodontic treatment with clear aligners on patients over the age of 15 that included clear descriptions of the materials and applied technique were included. Selection was undertaken independently by two reviewers. Two reviewers extracted data independently with study quality being assessed using the grading system described by the Swedish Council on Technology Assessment in Health Care (SBU). A narrative summary of the findings was presented. Eleven studies involving a total of 480 patients were included consisting of two randomised controlled trials, five prospective studies and four retrospective studies. Six studies were considered to be of moderate quality, the remainder of limited quality. Most of the studies presented with methodological problems: small sample size, bias and confounding variables, lack of method error analysis, blinding in measurements, and deficient or missing statistical methods. The quality level of the studies was not sufficient to draw any evidence-based conclusions.

  11. Education Game of Multiplying Based on Horizontal Method of HTML 5 and Android

    Directory of Open Access Journals (Sweden)

    Michael Yoseph Ricky

    2015-09-01

    Full Text Available Over the years, technology is growing rapidly followed by the development of game and its variations. Now, game is easily found on a mobile device. Moreover, game on mobile device can also be used as an excellent medium for learning or often referred as educational game because the nature of educational game is practical, easy to carry anywhere, and tends to be fun. This research was to create a mobile game application for learning with Horizontal method based on HTML 5 and Phonegap and to introduce the method as a method of mathematical multiplication process. This research used the Scrum method for program development. The results obtained showed that the game in this study is considered attractive and received a positive response from the player. Player also found it helpful to know the patterns of mathematics through the multiplication ofnumbers in this game. So through this game the player can perform mathematical multiplication calculations quickly.

  12. 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.

  13. Features of tennis methods of teaching 5-6 years old children in the initial stages

    Directory of Open Access Journals (Sweden)

    E.V. Kurmaeva

    2014-06-01

    Full Text Available Purpose : theoretical and methodological justification for the existing teaching methods tennis of 5-6 years old children. Material : 17 special analysis and scientific and methodological sources. Results : the features of the existing methods of teaching children at an early stage of training. The main theses of the existing methods: 1 the training process is carried out in the form of games; 2 the level of general physical preparedness level exceeds special; 3 The first two years of the children do not participate in official competitions; 4 education of children begins with " School Ball ", with a gradual transition to employment with racket and ball; 5 training is built on two levels: theoretical - each " part" in the form of pre- formation of a mental model of rational behavior, and practical - the formation of the ability to perform motor actions. Conclusions : it was found that the existing methods of constructing the training process for children 5-6 years do not account for their physiological characteristics, therefore proposed to use computer technology and animation, that will shorten the formation of motor skills of children.

  14. Effect of grain alignment on interface trap density of thermally oxidized aligned-crystalline silicon films

    Science.gov (United States)

    Choi, Woong; Lee, Jung-Kun; Findikoglu, Alp T.

    2006-12-01

    The authors report studies of the effect of grain alignment on interface trap density of thermally oxidized aligned-crystalline silicon (ACSi) films by means of capacitance-voltage (C-V) measurements. C-V curves were measured on metal-oxide-semiconductor (MOS) capacitors fabricated on ⟨001⟩-oriented ACSi films on polycrystalline substrates. From high-frequency C-V curves, the authors calculated a decrease of interface trap density from 2×1012to1×1011cm-2eV-1 as the grain mosaic spread in ACSi films improved from 13.7° to 6.5°. These results demonstrate the effectiveness of grain alignment as a process technique to achieve significantly enhanced performance in small-grained (⩽1μm ) polycrystalline Si MOS-type devices.

  15. 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.

  16. Measurement methods and accuracy analysis of Chang'E-5 Panoramic Camera installation parameters

    Science.gov (United States)

    Yan, Wei; Ren, Xin; Liu, Jianjun; Tan, Xu; Wang, Wenrui; Chen, Wangli; Zhang, Xiaoxia; Li, Chunlai

    2016-04-01

    Chang'E-5 (CE-5) is a lunar probe for the third phase of China Lunar Exploration Project (CLEP), whose main scientific objectives are to implement lunar surface sampling and to return the samples back to the Earth. To achieve these goals, investigation of lunar surface topography and geological structure within sampling area seems to be extremely important. The Panoramic Camera (PCAM) is one of the payloads mounted on CE-5 lander. It consists of two optical systems which installed on a camera rotating platform. Optical images of sampling area can be obtained by PCAM in the form of a two-dimensional image and a stereo images pair can be formed by left and right PCAM images. Then lunar terrain can be reconstructed based on photogrammetry. Installation parameters of PCAM with respect to CE-5 lander are critical for the calculation of exterior orientation elements (EO) of PCAM images, which is used for lunar terrain reconstruction. In this paper, types of PCAM installation parameters and coordinate systems involved are defined. Measurement methods combining camera images and optical coordinate observations are studied for this work. Then research contents such as observation program and specific solution methods of installation parameters are introduced. Parametric solution accuracy is analyzed according to observations obtained by PCAM scientifically validated experiment, which is used to test the authenticity of PCAM detection process, ground data processing methods, product quality and so on. Analysis results show that the accuracy of the installation parameters affects the positional accuracy of corresponding image points of PCAM stereo images within 1 pixel. So the measurement methods and parameter accuracy studied in this paper meet the needs of engineering and scientific applications. Keywords: Chang'E-5 Mission; Panoramic Camera; Installation Parameters; Total Station; Coordinate Conversion

  17. Report on tool transfer and alignment methods

    DEFF Research Database (Denmark)

    Tosello, Guido; Gasparin, Stefania; De Grave, Arnaud

    2010-01-01

    In the last few years, research work has been carried out regarding the feature miniaturization and tooling performance achievable with specific process chains combining different micro machining processes. On the other hand, technologies, strategies and tool design rules in order to optimize the...... process chain for tooling (i.e. hybrid tooling) based on the combination of micro milling and micro electrical discharge machining (EDM) milling, both at machine tool and at machining technology levels....

  18. Fabrication and Characterization of Aligned Flexible Lead-Free Piezoelectric Nanofibers for Wearable Device Applications

    Directory of Open Access Journals (Sweden)

    Sang Hyun Ji

    2018-03-01

    Full Text Available Flexible lead-free piezoelectric nanofibers, based on BNT-ST (0.78Bi0.5Na0.5TiO3-0.22SrTiO3 ceramic and poly(vinylidene fluoride-trifluoroethylene (PVDF-TrFE copolymers, were fabricated by an electrospinning method and the effects of the degree of alignment in the nanofibers on the piezoelectric characteristics were investigated. The microstructure of the lead-free piezoelectric nanofibers was observed by field emission scanning electron microscope (FE-SEM and the orientation was analyzed by fast Fourier transform (FFT images. X-ray diffraction (XRD analysis confirmed that the phase was not changed by the electrospinning process and maintained a perovskite phase. Polarization-electric field (P-E loops and piezoresponse force microscopy (PFM were used to investigate the piezoelectric properties of the piezoelectric nanofibers, according to the degree of alignment—the well aligned piezoelectric nanofibers had higher piezoelectric properties. Furthermore, the output voltage of the aligned lead-free piezoelectric nanofibers was measured according to the vibration frequency and the bending motion and the aligned piezoelectric nanofibers with a collector rotation speed of 1500 rpm performed the best.

  19. 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.

  20. An Analysis of Periodic Components in BL Lac Object S5 0716 +714 with MUSIC Method

    Science.gov (United States)

    Tang, J.

    2012-01-01

    Multiple signal classification (MUSIC) algorithms are introduced to the estimation of the period of variation of BL Lac objects.The principle of MUSIC spectral analysis method and theoretical analysis of the resolution of frequency spectrum using analog signals are included. From a lot of literatures, we have collected a lot of effective observation data of BL Lac object S5 0716 + 714 in V, R, I bands from 1994 to 2008. The light variation periods of S5 0716 +714 are obtained by means of the MUSIC spectral analysis method and periodogram spectral analysis method. There exist two major periods: (3.33±0.08) years and (1.24±0.01) years for all bands. The estimation of the period of variation of the algorithm based on the MUSIC spectral analysis method is compared with that of the algorithm based on the periodogram spectral analysis method. It is a super-resolution algorithm with small data length, and could be used to detect the period of variation of weak signals.

  1. Alignment control of GEO 600

    International Nuclear Information System (INIS)

    Grote, H; Heinzel, G; Freise, A; Gossler, S; Willke, B; Lueck, H; Ward, H; Casey, M M; Strain, K A; Robertson, D I; Hough, J; Danzmannx, K

    2004-01-01

    We give an overview of the automatic mirror alignment system of the gravitational wave detector GEO 600. In order to achieve the required sensitivity of the Michelson interferometer, the axes of interfering beams have to be superimposed with a residual angle of the order 10 -8 rad. The beam spots have to be centred on the mirrors to minimize coupling of alignment noise into longitudinal signals. We present the actual control topology and results from the system in operation, which controls all alignment degrees of the power-recycled Michelson. With this system continuous lock stretches of more than 121 h duration were achieved

  2. Control rod housing alignment apparatus

    International Nuclear Information System (INIS)

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

    1991-01-01

    This paper discusses an alignment device for precisely locating the position of the top of a control rod drive housing from an overlying and corresponding hole and alignment pin in a core plate within a boiling water nuclear reactor. It includes a shaft, the shaft having a length sufficient to extend from the vicinity of the top of the control rod drive housing up to and through the hole in the core plate; means for registering the top of the shaft to the hole in the core plate, the registering means including means for registering with an alignment pin in the core plate adjacent the hole

  3. 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

  4. A rapid detection method for PAI-1 promoter insertion/deletion polymorphism (4G/5G

    Directory of Open Access Journals (Sweden)

    Annichino-Bizzacchi Joyce M.

    1998-01-01

    Full Text Available Plasminogen activator inhibitor-1 (PAI-1 is an important inhibitor of fibrinolysis, and increased levels of PAI-1 are associated with atheroma and myocardial infarction. A common 4G/5G insertion/deletion polymorphism located in the promoter region of PAI-1 gene has been described associated with PAI-1 activity in plasma levels. Genotyping of this polymorphism is commonly conducted with an allele-specific oligonucleotide melting technique. In the present study, we describe a quick, easy method for genotyping 4G/5G polymorphism in the promoter region of the PAI-1 gene.

  5. Two Influential Primate Classifications Logically Aligned.

    Science.gov (United States)

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

    2016-07-01

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

  6. Markov random field based automatic image alignment for electron tomography.

    Science.gov (United States)

    Amat, Fernando; Moussavi, Farshid; Comolli, Luis R; Elidan, Gal; Downing, Kenneth H; Horowitz, Mark

    2008-03-01

    We present a method for automatic full-precision alignment of the images in a tomographic tilt series. Full-precision automatic alignment of cryo electron microscopy images has remained a difficult challenge to date, due to the limited electron dose and low image contrast. These facts lead to poor signal to noise ratio (SNR) in the images, which causes automatic feature trackers to generate errors, even with high contrast gold particles as fiducial features. To enable fully automatic alignment for full-precision reconstructions, we frame the problem probabilistically as finding the most likely particle tracks given a set of noisy images, using contextual information to make the solution more robust to the noise in each image. To solve this maximum likelihood problem, we use Markov Random Fields (MRF) to establish the correspondence of features in alignment and robust optimization for projection model estimation. The resulting algorithm, called Robust Alignment and Projection Estimation for Tomographic Reconstruction, or RAPTOR, has not needed any manual intervention for the difficult datasets we have tried, and has provided sub-pixel alignment that is as good as the manual approach by an expert user. We are able to automatically map complete and partial marker trajectories and thus obtain highly accurate image alignment. Our method has been applied to challenging cryo electron tomographic datasets with low SNR from intact bacterial cells, as well as several plastic section and X-ray datasets.

  7. Finding optimal interaction interface alignments between biological complexes

    KAUST Repository

    Cui, Xuefeng

    2015-06-13

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

  8. Acceleration of step and linear discontinuous schemes for the method of characteristics in DRAGON5

    Directory of Open Access Journals (Sweden)

    Alain Hébert

    2017-09-01

    Full Text Available The applicability of the algebraic collapsing acceleration (ACA technique to the method of characteristics (MOC in cases with scattering anisotropy and/or linear sources was investigated. Previously, the ACA was proven successful in cases with isotropic scattering and uniform (step sources. A presentation is first made of the MOC implementation, available in the DRAGON5 code. Two categories of schemes are available for integrating the propagation equations: (1 the first category is based on exact integration and leads to the classical step characteristics (SC and linear discontinuous characteristics (LDC schemes and (2 the second category leads to diamond differencing schemes of various orders in space. The acceleration of these MOC schemes using a combination of the generalized minimal residual [GMRES(m] method preconditioned with the ACA technique was focused on. Numerical results are provided for a two-dimensional (2D eight-symmetry pressurized water reactor (PWR assembly mockup in the context of the DRAGON5 code.

  9. Deterministic methods in radiation transport. A compilation of papers presented February 4--5, 1992

    Energy Technology Data Exchange (ETDEWEB)

    Rice, A.F.; Roussin, R.W. [eds.

    1992-06-01

    The Seminar on Deterministic Methods in Radiation Transport was held February 4--5, 1992, in Oak Ridge, Tennessee. Eleven presentations were made and the full papers are published in this report, along with three that were submitted but not given orally. These papers represent a good overview of the state of the art in the deterministic solution of radiation transport problems for a variety of applications of current interest to the Radiation Shielding Information Center user community.

  10. Deterministic methods in radiation transport. A compilation of papers presented February 4-5, 1992

    Energy Technology Data Exchange (ETDEWEB)

    Rice, A. F.; Roussin, R. W. [eds.

    1992-06-01

    The Seminar on Deterministic Methods in Radiation Transport was held February 4--5, 1992, in Oak Ridge, Tennessee. Eleven presentations were made and the full papers are published in this report, along with three that were submitted but not given orally. These papers represent a good overview of the state of the art in the deterministic solution of radiation transport problems for a variety of applications of current interest to the Radiation Shielding Information Center user community.

  11. 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

  12. 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.

  13. 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...

  14. 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

  15. A multi-method approach toward de novo glycan characterization: a Man-5 case study.

    Science.gov (United States)

    Prien, Justin M; Prater, Bradley D; Cockrill, Steven L

    2010-05-01

    Regulatory agencies' expectations for biotherapeutic approval are becoming more stringent with regard to product characterization, where minor species as low as 0.1% of a given profile are typically identified. The mission of this manuscript is to demonstrate a multi-method approach toward de novo glycan characterization and quantitation, including minor species at or approaching the 0.1% benchmark. Recently, unexpected isomers of the Man(5)GlcNAc(2) (M(5)) were reported (Prien JM, Ashline DJ, Lapadula AJ, Zhang H, Reinhold VN. 2009. The high mannose glycans from bovine ribonuclease B isomer characterization by ion trap mass spectrometry (MS). J Am Soc Mass Spectrom. 20:539-556). In the current study, quantitative analysis of these isomers found in commercial M(5) standard demonstrated that they are in low abundance (2-aminobenzoic acid to detect and chromatographically resolve multiple M(5) isomers in bovine ribonuclease B. With this multi-method approach, we have the capabilities to comprehensively characterize a biotherapeutic's glycan array in a de novo manner, including structural isomers at >/=0.1% of the total chromatographic peak area.

  16. A three-dimensional vertically aligned functionalized multilayer graphene architecture: an approach for graphene-based thermal interfacial materials.

    Science.gov (United States)

    Liang, Qizhen; Yao, Xuxia; Wang, Wei; Liu, Yan; Wong, Ching Ping

    2011-03-22

    Thermally conductive functionalized multilayer graphene sheets (fMGs) are efficiently aligned in large-scale by a vacuum filtration method at room temperature, as evidenced by SEM images and polarized Raman spectroscopy. A remarkably strong anisotropy in properties of aligned fMGs is observed. High electrical (∼386 S cm(-1)) and thermal conductivity (∼112 W m(-1) K(-1) at 25 °C) and ultralow coefficient of thermal expansion (∼-0.71 ppm K(-1)) in the in-plane direction of A-fMGs are obtained without any reduction process. Aligned fMGs are vertically assembled between contacted silicon/silicon surfaces with pure indium as a metallic medium. Thus-constructed three-dimensional vertically aligned fMG thermal interfacial material (VA-fMG TIM) architecture has significantly higher equivalent thermal conductivity (75.5 W m(-1) K(-1)) and lower contact thermal resistance (5.1 mm2 K W(-1)), compared with their counterpart from A-fMGs that are recumbent between silicon surfaces. This finding provides a throughout approach for a graphene-based TIM assembly as well as knowledge of vertically aligned graphene architectures, which may not only facilitate graphene's application in current demanding thermal management but also promote its widespread applications in electrodes of energy storage devices, conductive polymeric composites, etc.

  17. Beam-based alignment of C-shaped quadrupole magnets

    International Nuclear Information System (INIS)

    Portmann, G.; Robin, D.

    1998-06-01

    Many storage rings have implemented a method of finding the positional offset between the electrical center of the beam position monitors (BPM) and the magnetic center of the adjacent quadrupole magnets. The algorithm for accomplishing this is usually based on modulating the current in the quadrupole magnet and finding the beam position that minimizes the orbit perturbation. When the quadrupole magnet is C-shaped, as it is for many light sources, the modulation method can produce an erroneous measurement of the magnetic center in the horizontal plane. When the current in a C-shaped quadrupole is changed, there is an additional dipole component in the vertical field. Due to nonlinearities in the hysteresis cycle of the C-magnet geometry, the beam-based alignment technique at the Advanced Light Source (ALS) deviated horizontally by .5 mm from the actual magnetic center. By modifying the technique, the offsets were measured to an accuracy of better than 50 microm

  18. The Rigors of Aligning Performance

    Science.gov (United States)

    2015-06-01

    importance of the organization’s goals. To better align the commands goals with departmental goals, setting and continuously communicating goals and goal...which is vital to highlight the importance of the organization’s goals. To better align the commands goals with departmental goals, setting and...result of the 2004 organizational restructure, and as defined in the CONOPS, NAVFAC now operates as a matrix organization with integrated “vertical

  19. 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

  20. Vertically aligned BCN nanotubes with high capacitance.

    Science.gov (United States)

    Iyyamperumal, Eswaramoorthi; Wang, Shuangyin; Dai, Liming

    2012-06-26

    Using a chemical vapor deposition method, we have synthesized vertically aligned BCN nanotubes (VA-BCNs) on a Ni-Fe-coated SiO(2)/Si substrate from a melamine diborate precursor. The effects of pyrolysis conditions on the morphology and thermal property of grown nanotubes, as well as the nanostructure and composition of an individual BCN nanotube, were systematically studied. It was found that nitrogen atoms are bonded to carbons in both graphitic and pyridinic forms and that the resultant VA-BCNs grown at 1000 °C show the highest specific capacitance (321.0 F/g) with an excellent rate capability and high durability with respect to nonaligned BCN (167.3 F/g) and undoped multiwalled carbon nanotubes (117.3 F/g) due to synergetic effects arising from the combined co-doping of B and N in CNTs and the well-aligned nanotube structure.

  1. A Practical Guide to Multi-image Alignment

    OpenAIRE

    Aguerrebere, Cecilia; Delbracio, Mauricio; Bartesaghi, Alberto; Sapiro, Guillermo

    2018-01-01

    Multi-image alignment, bringing a group of images into common register, is an ubiquitous problem and the first step of many applications in a wide variety of domains. As a result, a great amount of effort is being invested in developing efficient multi-image alignment algorithms. Little has been done, however, to answer fundamental practical questions such as: what is the comparative performance of existing methods? is there still room for improvement? under which conditions should one techni...

  2. SU-G-JeP3-02: Comparison of Magnitude and Frequency of Patient Positioning Errors in Breast Irradiation Using AlignRT 3D Optical Surface Imaging and Skin Mark Techniques

    International Nuclear Information System (INIS)

    Yao, R; Chisela, W; Dorbu, G

    2016-01-01

    Purpose: To evaluate clinical usefulness of AlignRT (Vision RT Ltd., London, UK) in reducing patient positioning errors in breast irradiation. Methods: 60 patients undergoing whole breast irradiation were selected for this study. Patients were treated to the left or right breast lying on Qfix Access breast board (Qfix, Avondale, PA) in supine position for 28 fractions using tangential fields. 30 patients were aligned using AlignRT by aligning a breast surface region of interest (ROI) to the same area from a reference surface image extracted from planning CT. When the patient’s surface image deviated from the reference by more than 3mm on one or more translational and rotational directions, a new reference was acquired using AlignRT in-room cameras. The other 30 patients were aligned to the skin marks with room lasers. On-Board MV portal images of medial field were taken daily and matched to the DRRs. The magnitude and frequency of positioning errors were determined from measured translational shifts. Kolmogorov-Smirnov test was used to evaluate statistical differences of positional accuracy and precision between AlignRT and non-AlignRT patients. Results: The percentage of port images with no shift required was 46.5% and 27.0% in vertical, 49.8% and 25.8% in longitudinal, 47.6% and 28.5% in lateral for AlignRT and non-AlignRT patients, respectively. The percentage of port images requiring more than 3mm shifts was 18.1% and 35.1% in vertical, 28.6% and 50.8% in longitudinal, 11.3% and 24.2% in lateral for AlignRT and non-AlignRT patients, respectively. Kolmogorov-Smirnov test showed that there were significant differences between the frequency distributions of AlignRT and non-AlignRT in vertical, longitudinal, and lateral shifts. Conclusion: As confirmed by port images, AlignRT-assisted patient positioning can significantly reduce the frequency and magnitude of patient setup errors in breast irradiation compared to the use of lasers and skin marks.

  3. Use artificial neural network to align biological ontologies.

    Science.gov (United States)

    Huang, Jingshan; Dang, Jiangbo; Huhns, Michael N; Zheng, W Jim

    2008-09-16

    Being formal, declarative knowledge representation models, ontologies help to address the problem of imprecise terminologies in biological and biomedical research. However, ontologies constructed under the auspices of the Open Biomedical Ontologies (OBO) group have exhibited a great deal of variety, because different parties can design ontologies according to their own conceptual views of the world. It is therefore becoming critical to align ontologies from different parties. During automated/semi-automated alignment across biological ontologies, different semantic aspects, i.e., concept name, concept properties, and concept relationships, contribute in different degrees to alignment results. Therefore, a vector of weights must be assigned to these semantic aspects. It is not trivial to determine what those weights should be, and current methodologies depend a lot on human heuristics. In this paper, we take an artificial neural network approach to learn and adjust these weights, and thereby support a new ontology alignment algorithm, customized for biological ontologies, with the purpose of avoiding some disadvantages in both rule-based and learning-based aligning algorithms. This approach has been evaluated by aligning two real-world biological ontologies, whose features include huge file size, very few instances, concept names in numerical strings, and others. The promising experiment results verify our proposed hypothesis, i.e., three weights for semantic aspects learned from a subset of concepts are representative of all concepts in the same ontology. Therefore, our method represents a large leap forward towards automating biological ontology alignment.

  4. Electric field-induced astrocyte alignment directs neurite outgrowth.

    Science.gov (United States)

    Alexander, John K; Fuss, Babette; Colello, Raymond J

    2006-05-01

    The extension and directionality of neurite outgrowth are key to achieving successful target connections during both CNS development and during the re-establishment of connections lost after neural trauma. The degree of axonal elongation depends, in large part, on the spatial arrangement of astrocytic processes rich in growth-promoting proteins. Because astrocytes in culture align their processes on exposure to an electrical field of physiological strength, we sought to determine the extent to which aligned astrocytes affect neurite outgrowth. To this end, dorsal root ganglia cells were seeded onto cultured rat astrocytes that were pre-aligned by exposure to an electric field of physiological strength (500 mV mm(-1)). Using confocal microscopy and digital image analysis, we found that neurite outgrowth at 24 hours and at 48 hours is enhanced significantly and directed consistently along the aligned astrocyte processes. Moreover, this directed neurite outgrowth is maintained when grown on fixed, aligned astrocytes. Collectively, these results indicate that endogenous electric fields present within the developing CNS might act to align astrocyte processes, which can promote and direct neurite growth. Furthermore, these results demonstrate a simple method to produce an aligned cellular substrate, which might be used to direct regenerating neurites.

  5. Residual dipolar couplings: are multiple independent alignments always possible?

    International Nuclear Information System (INIS)

    Higman, Victoria A.; Boyd, Jonathan; Smith, Lorna J.; Redfield, Christina

    2011-01-01

    RDCs for the 14 kDa protein hen egg-white lysozyme (HEWL) have been measured in eight different alignment media. The elongated shape and strongly positively charged surface of HEWL appear to limit the protein to four main alignment orientations. Furthermore, low levels of alignment and the protein’s interaction with some alignment media increases the experimental error. Together with heterogeneity across the alignment media arising from constraints on temperature, pH and ionic strength for some alignment media, these data are suitable for structure refinement, but not the extraction of dynamic parameters. For an analysis of protein dynamics the data must be obtained with very low errors in at least three or five independent alignment media (depending on the method used) and so far, such data have only been reported for three small 6–8 kDa proteins with identical folds: ubiquitin, GB1 and GB3. Our results suggest that HEWL is likely to be representative of many other medium to large sized proteins commonly studied by solution NMR. Comparisons with over 60 high-resolution crystal structures of HEWL reveal that the highest resolution structures are not necessarily always the best models for the protein structure in solution.

  6. Integration of the BSCS 5E instructional method and technology in an anatomy and physiology lab

    Science.gov (United States)

    Gopal, Tamilselvi

    This research provides an understanding of how the 5E instructional method combined with educational technology tools can be used in teaching undergraduate college level anatomy and physiology laboratory classes. The 5E instructional model is the exemplary instructional model in teaching biology for high school students. The phases in the 5E learning cycle are Engage, Explore, Explain, Elaborate, and Evaluate. In every step of the learning cycle, the researcher used appropriate technology tools to enhance the teaching and learning processes. The researcher used the Dynamic Instructional Design model to identify the appropriate technology tools for instruction. The topics selected for modification were 'The Heart' and 'The Vascular System.' The researcher chose these two topics based on results of the preliminary survey that the researcher conducted during summer 2008. The existing topics identified on the syllabus were followed but the teaching method was changed. In order to accomplish this, the researcher created a class Website and included tools including pronunciation, spelling, an Interactive Tool, and Web links. In addition, the researcher also created teacher resources for the Pronunciation Corner and Spelling Bee, so that any teacher can customize and use these tools for their classes. The results indicated that the students took advantage of the technology provided.

  7. Magnetic moment of the fragmentation-aligned F61e (9/2+) isomer

    International Nuclear Information System (INIS)

    Matea, I.; Georgiev, G.; Lewitowicz, M.; Santos, F. de Oliveira; Daugas, J.M.; Belier, G.; Goutte, H.; Meot, V.; Roig, O.; Hass, M.; Baby, L.T.; Goldring, G.; Neyens, G.; Borremans, D.; Himpe, P.; Astabatyan, R.; Lukyanov, S.; Penionzhkevich, Yu.E.; Balabanski, D.L.; Sawicka, M.

    2004-01-01

    We report on the g factor measurement of an isomer in the neutron-rich F 26 61 e (E * =861 keV and T 1/2 =239(5) ns). The isomer was produced and spin aligned via a projectile-fragmentation reaction at intermediate energy, the time dependent perturbed angular distribution method being used for the measurement of the g factor. For the first time, due to significant improvements of the experimental technique, an appreciable residual alignment of the nuclear spin ensemble has been observed, allowing a precise determination of its g factor, including the sign: g=-0.229(2). In this way we open the possibility to study moments of very neutron-rich short-lived isomers, not accessible via other production and spin-orientation methods

  8. A rank-based sequence aligner with applications in phylogenetic analysis.

    Directory of Open Access Journals (Sweden)

    Liviu P Dinu

    Full Text Available Recent tools for aligning short DNA reads have been designed to optimize the trade-off between correctness and speed. This paper introduces a method for assigning a set of short DNA reads to a reference genome, under Local Rank Distance (LRD. The rank-based aligner proposed in this work aims to improve correctness over speed. However, some indexing strategies to speed up the aligner are also investigated. The LRD aligner is improved in terms of speed by storing [Formula: see text]-mer positions in a hash table for each read. Another improvement, that produces an approximate LRD aligner, is to consider only the positions in the reference that are likely to represent a good positional match of the read. The proposed aligner is evaluated and compared to other state of the art alignment tools in several experiments. A set of experiments are conducted to determine the precision and the recall of the proposed aligner, in the presence of contaminated reads. In another set of experiments, the proposed aligner is used to find the order, the family, or the species of a new (or unknown organism, given only a set of short Next-Generation Sequencing DNA reads. The empirical results show that the aligner proposed in this work is highly accurate from a biological point of view. Compared to the other evaluated tools, the LRD aligner has the important advantage of being very accurate even for a very low base coverage. Thus, the LRD aligner can be considered as a good alternative to standard alignment tools, especially when the accuracy of the aligner is of high importance. Source code and UNIX binaries of the aligner are freely available for future development and use at http://lrd.herokuapp.com/aligners. The software is implemented in C++ and Java, being supported on UNIX and MS Windows.

  9. Survey and alignment of high energy physics accelerators and transport lines

    International Nuclear Information System (INIS)

    Ruland, R.E.

    1992-11-01

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

  10. 40 CFR Table C-4 to Subpart C of... - Test Specifications for PM10, PM2.5 and PM10-2.5 Candidate Equivalent Methods

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 5 2010-07-01 2010-07-01 false Test Specifications for PM10, PM2.5 and PM10-2.5 Candidate Equivalent Methods C Table C-4 to Subpart C of Part 53 Protection of Environment... Pt. 53, Subpt. C, Table C-4 Table C-4 to Subpart C of Part 53—Test Specifications for PM10, PM2.5 and...

  11. Galactic cosmic ray gradients, field-aligned and latitudinal, among Voyagers 1/2 and IMP-8

    Science.gov (United States)

    Roelof, E. C.; Decker, R. B.; Krimigis, S. M.; Venkatesan, D.; Lazarus, A. J.

    1982-01-01

    The present investigation represents a summary of a comprehensive analysis of the same subject conducted by Roelof et al. (1981). It is pointed out that the tandem earth-Jupiter trajectories of the Voyager 1/2 spacecraft, combined with baseline measurements from the earth-orbiting IMP 7/8 spacecraft, provide the first opportunity for unambiguously separating latitude from radial or field-aligned effects in galactic cosmic ray gradients. Attention is given to the method of data analysis, and the separation of field-aligned and latitudinal gradients. It is found that latitudinal gradients approximately equal to or greater than 1 percent per deg in the cosmic ray intensity were a common feature of the interplanetary medium between 1 and 5 AU in 1977-78. Except in the most disturbed periods, cosmic ray intensities are well-ordered in field-aligned structures.

  12. Structural re-alignment in an immunologic surface region of ricin A chain

    Energy Technology Data Exchange (ETDEWEB)

    Zemla, A T; Zhou, C E

    2007-07-24

    We compared structure alignments generated by several protein structure comparison programs to determine whether existing methods would satisfactorily align residues at a highly conserved position within an immunogenic loop in ribosome inactivating proteins (RIPs). Using default settings, structure alignments generated by several programs (CE, DaliLite, FATCAT, LGA, MAMMOTH, MATRAS, SHEBA, SSM) failed to align the respective conserved residues, although LGA reported correct residue-residue (R-R) correspondences when the beta-carbon (Cb) position was used as the point of reference in the alignment calculations. Further tests using variable points of reference indicated that points distal from the beta carbon along a vector connecting the alpha and beta carbons yielded rigid structural alignments in which residues known to be highly conserved in RIPs were reported as corresponding residues in structural comparisons between ricin A chain, abrin-A, and other RIPs. Results suggest that approaches to structure alignment employing alternate point representations corresponding to side chain position may yield structure alignments that are more consistent with observed conservation of functional surface residues than do standard alignment programs, which apply uniform criteria for alignment (i.e., alpha carbon (Ca) as point of reference) along the entirety of the peptide chain. We present the results of tests that suggest the utility of allowing user-specified points of reference in generating alternate structural alignments, and we present a web server for automatically generating such alignments.

  13. Automated whole-genome multiple alignment of rat, mouse, and human

    Energy Technology Data Exchange (ETDEWEB)

    Brudno, Michael; Poliakov, Alexander; Salamov, Asaf; Cooper, Gregory M.; Sidow, Arend; Rubin, Edward M.; Solovyev, Victor; Batzoglou, Serafim; Dubchak, Inna

    2004-07-04

    We have built a whole genome multiple alignment of the three currently available mammalian genomes using a fully automated pipeline which combines the local/global approach of the Berkeley Genome Pipeline and the LAGAN program. The strategy is based on progressive alignment, and consists of two main steps: (1) alignment of the mouse and rat genomes; and (2) alignment of human to either the mouse-rat alignments from step 1, or the remaining unaligned mouse and rat sequences. The resulting alignments demonstrate high sensitivity, with 87% of all human gene-coding areas aligned in both mouse and rat. The specificity is also high: <7% of the rat contigs are aligned to multiple places in human and 97% of all alignments with human sequence > 100kb agree with a three-way synteny map built independently using predicted exons in the three genomes. At the nucleotide level <1% of the rat nucleotides are mapped to multiple places in the human sequence in the alignment; and 96.5% of human nucleotides within all alignments agree with the synteny map. The alignments are publicly available online, with visualization through the novel Multi-VISTA browser that we also present.

  14. CORAL: aligning conserved core regions across domain families.

    Science.gov (United States)

    Fong, Jessica H; Marchler-Bauer, Aron

    2009-08-01

    Homologous protein families share highly conserved sequence and structure regions that are frequent targets for comparative analysis of related proteins and families. Many protein families, such as the curated domain families in the Conserved Domain Database (CDD), exhibit similar structural cores. To improve accuracy in aligning such protein families, we propose a profile-profile method CORAL that aligns individual core regions as gap-free units. CORAL computes optimal local alignment of two profiles with heuristics to preserve continuity within core regions. We benchmarked its performance on curated domains in CDD, which have pre-defined core regions, against COMPASS, HHalign and PSI-BLAST, using structure superpositions and comprehensive curator-optimized alignments as standards of truth. CORAL improves alignment accuracy on core regions over general profile methods, returning a balanced score of 0.57 for over 80% of all domain families in CDD, compared with the highest balanced score of 0.45 from other methods. Further, CORAL provides E-values to aid in detecting homologous protein families and, by respecting block boundaries, produces alignments with improved 'readability' that facilitate manual refinement. CORAL will be included in future versions of the NCBI Cn3D/CDTree software, which can be downloaded at http://www.ncbi.nlm.nih.gov/Structure/cdtree/cdtree.shtml. Supplementary data are available at Bioinformatics online.

  15. Experience of the irradiation method under mixed gas (95% O2 plus 5% CO2) inhalation

    International Nuclear Information System (INIS)

    Ikeda, Michio; Tazaki, Eio

    1978-01-01

    The irradiation method under mixed gas of 95% O 2 plus CO 2 inhalation at one atomosphere was discussed to improve therapeutic results, in malignant tumors which are not greatly sensitive to irradiation. Randomized study was done in each attending institute, with common protocols. As a result, no positive effect was recognized in irradiation method under mixed gas inhalation with daily dose of 200 rad and 5 fractions per week, which is widely used clinically. But when irradiation dose was increased up to 500 to 600 rad per fraction, effect of the mixed gas was remarkable. But against this, observing for years, results in irradiation under mixed gas inhalation were not always related to the improvement of the long term survival. (author)

  16. New one-flavor hybrid Monte Carlo simulation method for lattice fermions with γ5 hermiticity

    International Nuclear Information System (INIS)

    Ogawa, Kenji

    2011-01-01

    We propose a new method for Hybrid Monte Carlo (HMC) simulations with odd numbers of dynamical fermions on the lattice. It employs a different approach from polynomial or rational HMC. In this method, γ 5 hermiticity of the lattice Dirac operators is crucial and it can be applied to Wilson, domain-wall, and overlap fermions. We compare HMC simulations with two degenerate flavors and (1+1) degenerate flavors using optimal domain-wall fermions. The ratio of the efficiency, (number of accepted trajectories)/(simulation time), is about 3:2. The relation between pseudofermion action of chirally symmetric lattice fermions in four-dimensional (overlap) and five-dimensional (domain-wall) representation are also analyzed.

  17. Radioligand assays: methods and application. 5. /sup 125/I-monoidoinsulin: preparation, immunological and biological characterization

    Energy Technology Data Exchange (ETDEWEB)

    Besch, W; Woltanski, K P; Knospe, S; Ziegler, M; Keilacker, H [Zentralinstitut fuer Diabetes, Karlsburg (German Democratic Republic)

    1980-04-01

    A reproducible method for preparation of /sup 125/I-monoiodoinsulin with fully biological activity was developed. Monoiodoinsulin has been prepared from a heterogeneous /sup 125/I iodination mixture by anion exchange chromatography on DEAE-Sephadex A-25 without using any gradient elution technique. The specific radioactivity of /sup 125/I-monoiodoinsulin was calculated to 14.3 +- 0.8 TBq/g, i.e. an iodine content of 1.04 +- 0.06 atoms per molecule of insulin. Monoiodoinsulin was indistinguishable from native insulin with respect to binding to guinea pig anti-insulin serum, and to insulin receptors of isolated rat adipocytes. The biological potency (96.5 +- 7.5 per cent of the immunoreactive insulin activity) determined by the conversion of (/sup 14/C/sub 1/)-D-glucose to /sup 14/CO/sub 2/ in vitro by rat fat cells was not significantly different from that of native insulin.

  18. Synthesis of Al-5Ti-1B Refiner by Melt Reaction Method

    Directory of Open Access Journals (Sweden)

    LI He

    2017-02-01

    Full Text Available Al-5Ti-1B refiner was successfully prepared by melt reaction method. Through the thermodynamics calculation, the initial reaction temperature was determined. The influence of reaction temperature on microstructure and absorption rate of the alloy was investigated. The phase and microstructure of the alloy were observed by X-ray diffraction, scanning electron microscope and energy dispersive spectrometer. The Al-5Ti-1B refiner was extruded at high temperature to wire with the diameter of 9.5mm, and then the refinement experiment was carried out on pure aluminium. The results indicate that the refiner consists of TiB2, TiAl3 and α-Al, and the microstructure prepared at 850℃ is the optimum and the absorption rate of Ti and B matches the best. The TiAl3 and TiB2 phases distribute homogeneously in the matrix after extrusion. When adding 0.2%(mass fraction of Al-5Ti-1B refiner, the grain size of pure aluminium reduces from 3.99mm to 0.45mm.

  19. Silicon on insulator self-aligned transistors

    Science.gov (United States)

    McCarthy, Anthony M.

    2003-11-18

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

  20. Spontaneous magnetic alignment behaviour in free-living lizards

    Science.gov (United States)

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

    2017-04-01

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

  1. Understanding Interfacial Alignment in Solution Coated Conjugated Polymer Thin Films

    International Nuclear Information System (INIS)

    Qu, Ge; Zhao, Xikang; Newbloom, Gregory M.; Zhang, Fengjiao; Mohammadi, Erfan

    2017-01-01

    Domain alignment in conjugated polymer thin films can significantly enhance charge carrier mobility. However, the alignment mechanism during meniscus-guided solution coating remains unclear. Furthermore, interfacial alignment has been rarely studied despite its direct relevance and critical importance to charge transport. In this study, we uncover a significantly higher degree of alignment at the top interface of solution coated thin films, using a donor–acceptor conjugated polymer, poly(diketopyrrolopyrrole-co-thiopheneco- thieno[3,2-b]thiophene-co-thiophene) (DPP2T-TT), as the model system. At the molecular level, we observe in-plane π–π stacking anisotropy of up to 4.8 near the top interface with the polymer backbone aligned parallel to the coating direction. The bulk of the film is only weakly aligned with the backbone oriented transverse to coating. At the mesoscale, we observe a well-defined fibril-like morphology at the top interface with the fibril long axis pointing toward the coating direction. Significantly smaller fibrils with poor orientational order are found on the bottom interface, weakly aligned orthogonal to the fibrils on the top interface. The high degree of alignment at the top interface leads to a charge transport anisotropy of up to 5.4 compared to an anisotropy close to 1 on the bottom interface. We attribute the formation of distinct interfacial morphology to the skin-layer formation associated with high Peclet number, which promotes crystallization on the top interface while suppressing it in the bulk. As a result, we further infer that the interfacial fibril alignment is driven by the extensional flow on the top interface arisen from increasing solvent evaporation rate closer to the meniscus front.

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

    Directory of Open Access Journals (Sweden)

    Nils Homer

    2009-11-01

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

  3. 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...

  4. 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...

  5. 41 CFR 301-10.5 - What are the presumptions as to the most advantageous method of transportation?

    Science.gov (United States)

    2010-07-01

    ... presumptions as to the most advantageous method of transportation? 301-10.5 Section 301-10.5 Public Contracts... most advantageous method of transportation? (a) Common carrier. Travel by common carrier is presumed to be the most advantageous method of transportation and must be used when reasonably available. (b...

  6. Alignment of the upgraded CMS pixel detector

    CERN Document Server

    Schroder, Matthias

    2018-01-01

    The all-silicon tracking system of the CMS experiment provides excellent resolution for charged tracks and an efficient tagging of heavy-flavour jets. After a new pixel detector has been installed during the LHC technical stop at the beginning of 2017, the positions, orientations, and surface curvatures of the sensors needed to be determined with a precision at the order of a few micrometres to ensure the required physics performance. This is far beyond the mechanical mounting precision but can be achieved using a track-based alignment procedure that minimises the track-hit residuals of reconstructed tracks. The results are carefully validated with data-driven methods. In this article, results of the CMS tracker alignment in 2017 from the early detector-commissioning phase and the later operation are presented, that were derived using several million reconstructed tracks in pp-collision and cosmic-ray data. Special emphasis is put on the alignment of the new pixel detector.

  7. 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.

  8. 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...

  9. Precision alignment of permanent-magnet drift tubes

    International Nuclear Information System (INIS)

    Liska, D.J.; Dauelsberg, L.B.; Spalek, G.

    1986-01-01

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

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

    DEFF Research Database (Denmark)

    Li, Ruiqiang; Yu, Chang; Li, Yingrui

    2009-01-01

    SUMMARY: SOAP2 is a significantly improved version of the short oligonucleotide alignment program that both reduces computer memory usage and increases alignment speed at an unprecedented rate. We used a Burrows Wheeler Transformation (BWT) compression index to substitute the seed strategy...... for indexing the reference sequence in the main memory. We tested it on the whole human genome and found that this new algorithm reduced memory usage from 14.7 to 5.4 GB and improved alignment speed by 20-30 times. SOAP2 is compatible with both single- and paired-end reads. Additionally, this tool now supports...... multiple text and compressed file formats. A consensus builder has also been developed for consensus assembly and SNP detection from alignment of short reads on a reference genome. AVAILABILITY: http://soap.genomics.org.cn....

  11. 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.

  12. Photometrically measured continuous personal PM(2.5) exposure: levels and correlation to a gravimetric method.

    Science.gov (United States)

    Lanki, Timo; Alm, Sari; Ruuskanen, Juhani; Janssen, Nicole A H; Jantunen, Matti; Pekkanen, Juha

    2002-05-01

    There is evidence that hourly variations in exposure to airborne particulate matter (PM) may be associated with adverse health effects. Still there are only few published data on short-term levels of personal exposure to PM in community settings. The objectives of the study were to assess hourly and shorter-term variations in personal PM(2.5) exposure in Helsinki, Finland, and to compare results from portable photometers to simultaneously measured gravimetric concentrations. The effect of relative humidity on the photometric results was also evaluated. Personal PM(2.5) exposures of elderly persons were assessed for 24 h every second week, resulting in 308 successful measurements from 47 different subjects. Large changes in concentrations in minutes after cooking or changing microenvironment were seen. The median of daily 1-h maxima was over twice the median of 24-h averages. There was a strong significant association between the two means, which was not linear. Median (95th percentile) of the photometric 24-h concentrations was 12.1 (37.7) and of the 24-h gravimetric concentrations 9.2 (21.3) microg/m3. The correlation between the photometric and the gravimetric method was quite good (R2=0.86). Participants spent 94.1% of their time indoors or in a vehicle, where relative humidity is usually low and thus not likely to cause significant effects on photometric results. Even outdoors, the relative humidity had only modest effect on concentrations. Photometers are a promising method to explore the health effects of short-term variation in personal PM(2.5) exposure.

  13. Migratory birds, the H5N1 influenza virus and the scientific method

    Directory of Open Access Journals (Sweden)

    Stilianakis Nikolaos I

    2008-05-01

    Full Text Available Abstract Background The role of migratory birds and of poultry trade in the dispersal of highly pathogenic H5N1 is still the topic of intense and controversial debate. In a recent contribution to this journal, Flint argues that the strict application of the scientific method can help to resolve this issue. Discussion We argue that Flint's identification of the scientific method with null hypothesis testing is misleading and counterproductive. There is far more to science than the testing of hypotheses; not only the justification, bur also the discovery of hypotheses belong to science. We also show why null hypothesis testing is weak and that Bayesian methods are a preferable approach to statistical inference. Furthermore, we criticize the analogy put forward by Flint between involuntary transport of poultry and long-distance migration. Summary To expect ultimate answers and unequivocal policy guidance from null hypothesis testing puts unrealistic expectations on a flawed approach to statistical inference and on science in general.

  14. A validated fast difference spectrophotometric method for 5-hydroxymethyl-2-furfural (HMF) determination in corn syrups.

    Science.gov (United States)

    de Andrade, Jucimara Kulek; de Andrade, Camila Kulek; Komatsu, Emy; Perreault, Hélène; Torres, Yohandra Reyes; da Rosa, Marcos Roberto; Felsner, Maria Lurdes

    2017-08-01

    Corn syrups, important ingredients used in food and beverage industries, often contain high levels of 5-hydroxymethyl-2-furfural (HMF), a toxic contaminant. In this work, an in house validation of a difference spectrophotometric method for HMF analysis in corn syrups was developed using sophisticated statistical tools by the first time. The methodology showed excellent analytical performance with good selectivity, linearity (R 2 =99.9%, r>0.99), accuracy and low limits (LOD=0.10mgL -1 and LOQ=0.34mgL -1 ). An excellent precision was confirmed by repeatability (RSD (%)=0.30) and intermediate precision (RSD (%)=0.36) estimates and by Horrat value (0.07). A detailed study of method precision using a nested design demonstrated that variation sources such as instruments, operators and time did not interfere in the variability of results within laboratory and consequently in its intermediate precision. The developed method is environmentally friendly, fast, cheap and easy to implement resulting in an attractive alternative for corn syrups quality control in industries and official laboratories. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. On the applicability of MP2.5 method in atmospheric reactivity

    International Nuclear Information System (INIS)

    Suleiman, S.; Novotny, M.; Cernusak, I.

    2017-01-01

    Quantum chemical study has been performed on the reaction energies of the reactions of methyl iodide CH_3I and di-iodomethane CH_2I_2 with hydroxide radical. Both series of reactions were treated using the following methods: MP2, MP3, CCSD, CCSD(T) and also with the so-called MP2.5 approximation which is expected to be a good approximation to CCSD(T) within either chemical (±4 kJ/mol) or sub-chemical accuracy (±10 kJ/mol). We have used the correlation consistent cc-pvtz basis set in all calculations. In these atmospheric reactions, we considered various types of products. These reactions represent either isogyric processes or processes leading to atomic species. When comparing the MP2.5 and CCSD(T) data for reaction energies, our results indicate that there are some differences in reaction energies when the reaction contains different number of radicals and/or atoms on both sides. In addition, all the reactions including IO species do not fit into the 'MP2.5 computational philosophy'. (authors)

  16. Alignment Focus of Daily Image Guidance for Concurrent Treatment of Prostate and Pelvic Lymph Nodes

    International Nuclear Information System (INIS)

    Ferjani, Samah; Huang, Guangshun; Shang, Qingyang; Stephans, Kevin L.; Zhong, Yahua; Qi, Peng; Tendulkar, Rahul D.; Xia, Ping

    2013-01-01

    Purpose: To determine the dosimetric impact of daily imaging alignment focus on the prostate soft tissue versus the pelvic bones for the concurrent treatment of the prostate and pelvic lymph nodes (PLN) and to assess whether multileaf collimator (MLC) tracking or adaptive planning (ART) is necessary with the current clinical planning margins of 8 mm/6 mm posterior to the prostate and 5 mm to the PLN. Methods and Materials: A total of 124 kilovoltage cone-beam computed tomography (kV-CBCT) images from 6 patients were studied. For each KV-CBCT, 4 plans were retrospectively created using an isocenter shifting method with 2 different alignment focuses (prostate, PLN), an MLC shifting method, and the ART method. The selected dosimetric endpoints were compared among these plans. Results: For the isoshift contour, isoshift bone, MLC shift, and ART plans, D99 of the prostate was ≥97% of the prescription dose in 97.6%, 73.4%, 98.4%, and 96.8% of 124 fractions, respectively. Accordingly, D99 of the PLN was ≥97% of the prescription dose in 98.4%, 98.4%, 98.4%, and 100% of 124 fractions, respectively. For the rectum, D5 exceeded 105% of the planned D5 (and D5 of ART plans) in 11% (4%), 10% (2%), and 13% (5%) of 124 fractions, respectively. For the bladder, D5 exceeded 105% of the planned D5 (and D5 of ART) plans in 0% (2%), 0% (2%), and 0% (1%) of 124 fractions, respectively. Conclusion: For concurrent treatment of the prostate and PLN, with a planning margin to the prostate of 8 mm/6 mm posterior and a planning margin of 5 mm to the PLN, aligning to the prostate soft tissue can achieve adequate dose coverage to the both target volumes; aligning to the pelvic bone would result in underdosing to the prostate in one-third of fractions. With these planning margins, MLC tracking and ART methods have no dosimetric advantages

  17. Laser shaft alignment measurement model

    Science.gov (United States)

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

    2007-12-01

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

  18. Proper alignment of the microscope.

    Science.gov (United States)

    Rottenfusser, Rudi

    2013-01-01

    The light microscope is merely the first element of an imaging system in a research facility. Such a system may include high-speed and/or high-resolution image acquisition capabilities, confocal technologies, and super-resolution methods of various types. Yet more than ever, the proverb "garbage in-garbage out" remains a fact. Image manipulations may be used to conceal a suboptimal microscope setup, but an artifact-free image can only be obtained when the microscope is optimally aligned, both mechanically and optically. Something else is often overlooked in the quest to get the best image out of the microscope: Proper sample preparation! The microscope optics can only do its job when its design criteria are matched to the specimen or vice versa. The specimen itself, the mounting medium, the cover slip, and the type of immersion medium (if applicable) are all part of the total optical makeup. To get the best results out of a microscope, understanding the functions of all of its variable components is important. Only then one knows how to optimize these components for the intended application. Different approaches might be chosen to discuss all of the microscope's components. We decided to follow the light path which starts with the light source and ends at the camera or the eyepieces. To add more transparency to this sequence, the section up to the microscope stage was called the "Illuminating Section", to be followed by the "Imaging Section" which starts with the microscope objective. After understanding the various components, we can start "working with the microscope." To get the best resolution and contrast from the microscope, the practice of "Koehler Illumination" should be understood and followed by every serious microscopist. Step-by-step instructions as well as illustrations of the beam path in an upright and inverted microscope are included in this chapter. A few practical considerations are listed in Section 3. Copyright © 2013 Elsevier Inc. All rights

  19. Alignment of the HERA-B RICH optical system with data

    International Nuclear Information System (INIS)

    Gorisek, A.; Krizan, P.; Korpar, S.; Staric, M.

    1999-01-01

    We present a method for alignment of the mirror segments in the Ring Image Cherenkov Counter of the HERA-B spectrometer. The method will use recorded data, and was tested by using simulated events. The study shows that the mirrors can be aligned accurately enough to make the corresponding error in Cherenkov angle measurement negligible compared to other contributions. The mirrors are aligned relative to one mirror segment which can be chosen arbitrarily

  20. Research on localization and alignment technology for transfer cask

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jingchuan, E-mail: jchwang@sjtu.edu.cn [Department of Automation, Shanghai Jiao Tong University, Shanghai (China); Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai (China); Yang, Ming; Chen, Weidong [Department of Automation, Shanghai Jiao Tong University, Shanghai (China); Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai (China)

    2015-10-15

    Highlights: • A method for the alignment between TB and HCB based on localizability is proposed. • A localization method based on the localizability estimation is proposed to realize the cask's localization accurately and ensures the transfer cask's accurate docking in the front of the window of Tokmak Building. • The experimental results show that the proposed algorithm works well in the indoor simulation environment. This system will be test in EAST of China. - Abstract: According to the long length characteristics of transfer cask compared to the environment space between Tokmak Building (TB) and HCB (Hot Cell Building), this paper proposes an autonomous localization and alignment method for the internal components transportation and replacement. A localization method based on the localizability estimation is used to realize the cask's localization and navigation accurately. Once the cask arrives at the front of the TB window, the position and attitude measurement system is used to detect the relative alignment error between the seal door of pallet and the window of TB real-time. The alignment between seal door and TB window could be realized based on this offset. The simulation experiment based on the real model is designed according to the real TB situation. The experiment results show that the proposed localization and alignment method can be used for transfer cask.