WorldWideScience

Sample records for gene order alignment

  1. 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.

  2. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes.

    Science.gov (United States)

    Pruesse, Elmar; Peplies, Jörg; Glöckner, Frank Oliver

    2012-07-15

    In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like the ribosomal RNA (rRNA) where already millions of sequences are publicly available and individual studies can easily produce hundreds of thousands of new sequences. Methods have been developed to cope with such numbers, but further improvements are needed to meet accuracy requirements. In this study, we present the SILVA Incremental Aligner (SINA) used to align the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA uses a combination of k-mer searching and partial order alignment (POA) to maintain very high alignment accuracy while satisfying high throughput performance demands. SINA was evaluated in comparison with the commonly used high throughput MSA programs PyNAST and mothur. The three BRAliBase III benchmark MSAs could be reproduced with 99.3, 97.6 and 96.1 accuracy. A larger benchmark MSA comprising 38 772 sequences could be reproduced with 98.9 and 99.3% accuracy using reference MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy than PyNAST and mothur in all performed benchmarks. Alignment of up to 500 sequences using the latest SILVA SSU/LSU Ref datasets as reference MSA is offered at http://www.arb-silva.de/aligner. This page also links to Linux binaries, user manual and tutorial. SINA is made available under a personal use license.

  3. Operon Gene Order Is Optimized for Ordered Protein Complex Assembly

    Science.gov (United States)

    Wells, Jonathan N.; Bergendahl, L. Therese; Marsh, Joseph A.

    2016-01-01

    Summary The assembly of heteromeric protein complexes is an inherently stochastic process in which multiple genes are expressed separately into proteins, which must then somehow find each other within the cell. Here, we considered one of the ways by which prokaryotic organisms have attempted to maximize the efficiency of protein complex assembly: the organization of subunit-encoding genes into operons. Using structure-based assembly predictions, we show that operon gene order has been optimized to match the order in which protein subunits assemble. Exceptions to this are almost entirely highly expressed proteins for which assembly is less stochastic and for which precisely ordered translation offers less benefit. Overall, these results show that ordered protein complex assembly pathways are of significant biological importance and represent a major evolutionary constraint on operon gene organization. PMID:26804901

  4. Background Adjusted Alignment-Free Dissimilarity Measures Improve the Detection of Horizontal Gene Transfer

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    Kujin Tang

    2018-04-01

    Full Text Available Horizontal gene transfer (HGT plays an important role in the evolution of microbial organisms including bacteria. Alignment-free methods based on single genome compositional information have been used to detect HGT. Currently, Manhattan and Euclidean distances based on tetranucleotide frequencies are the most commonly used alignment-free dissimilarity measures to detect HGT. By testing on simulated bacterial sequences and real data sets with known horizontal transferred genomic regions, we found that more advanced alignment-free dissimilarity measures such as CVTree and d2* that take into account the background Markov sequences can solve HGT detection problems with significantly improved performance. We also studied the influence of different factors such as evolutionary distance between host and donor sequences, size of sliding window, and host genome composition on the performances of alignment-free methods to detect HGT. Our study showed that alignment-free methods can predict HGT accurately when host and donor genomes are in different order levels. Among all methods, CVTree with word length of 3, d2* with word length 3, Markov order 1 and d2* with word length 4, Markov order 1 outperform others in terms of their highest F1-score and their robustness under the influence of different factors.

  5. Inferring Phylogenetic Networks from Gene Order Data

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    Alexey Anatolievich Morozov

    2013-01-01

    Full Text Available Existing algorithms allow us to infer phylogenetic networks from sequences (DNA, protein or binary, sets of trees, and distance matrices, but there are no methods to build them using the gene order data as an input. Here we describe several methods to build split networks from the gene order data, perform simulation studies, and use our methods for analyzing and interpreting different real gene order datasets. All proposed methods are based on intermediate data, which can be generated from genome structures under study and used as an input for network construction algorithms. Three intermediates are used: set of jackknife trees, distance matrix, and binary encoding. According to simulations and case studies, the best intermediates are jackknife trees and distance matrix (when used with Neighbor-Net algorithm. Binary encoding can also be useful, but only when the methods mentioned above cannot be used.

  6. Dipolar rotors orderly aligned in mesoporous fluorinated organosilica architectures

    KAUST Repository

    Bracco, Silvia; Beretta, Mario; Cattaneo, Alice Silvia; Comotti, Angiolina; Falqui, Andrea; Zhao, Ke; Rogers, Charles T.; Sozzani, Piero

    2015-01-01

    New mesoporous covalent frameworks, based on hybrid fluorinated organosilicas, were prepared to realize a periodic architecture of fast molecular rotors containing dynamic dipoles in their structure. The mobile elements, designed on the basis of fluorinated p-divinylbenzene moieties, were integrated into the robust covalent structure through siloxane bonds, and showed not only the rapid dynamics of the aromatic rings (ca. 108 Hz at 325 K), as detected by solid-state NMR spectroscopy, but also a dielectric response typical of a fast dipole reorientation under the stimuli of an applied electric field. Furthermore, the mesochannels are open and accessible to diffusing in gas molecules, and rotor mobility could be individually regulated by I2 vapors. The iodine enters the channels of the periodic structure and reacts with the pivotal double bonds of the divinyl-fluoro-phenylene rotors, affecting their motion and the dielectric properties. Oriented molecular rotors: Fluorinated molecular rotors (see picture) were engineered in mesoporous hybrid organosilica architectures with crystalline order in their walls. The rotor dynamics was established by magic angle spinning NMR and dielectric measurements, indicating a rotational correlation time as short as 10-9 s at 325 K. The dynamics was modulated by I2 vapors entering the pores.

  7. Dipolar rotors orderly aligned in mesoporous fluorinated organosilica architectures

    KAUST Repository

    Bracco, Silvia

    2015-02-16

    New mesoporous covalent frameworks, based on hybrid fluorinated organosilicas, were prepared to realize a periodic architecture of fast molecular rotors containing dynamic dipoles in their structure. The mobile elements, designed on the basis of fluorinated p-divinylbenzene moieties, were integrated into the robust covalent structure through siloxane bonds, and showed not only the rapid dynamics of the aromatic rings (ca. 108 Hz at 325 K), as detected by solid-state NMR spectroscopy, but also a dielectric response typical of a fast dipole reorientation under the stimuli of an applied electric field. Furthermore, the mesochannels are open and accessible to diffusing in gas molecules, and rotor mobility could be individually regulated by I2 vapors. The iodine enters the channels of the periodic structure and reacts with the pivotal double bonds of the divinyl-fluoro-phenylene rotors, affecting their motion and the dielectric properties. Oriented molecular rotors: Fluorinated molecular rotors (see picture) were engineered in mesoporous hybrid organosilica architectures with crystalline order in their walls. The rotor dynamics was established by magic angle spinning NMR and dielectric measurements, indicating a rotational correlation time as short as 10-9 s at 325 K. The dynamics was modulated by I2 vapors entering the pores.

  8. eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models.

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    Michal Brylinski

    2014-09-01

    Full Text Available Detecting similarities between ligand binding sites in the absence of global homology between target proteins has been recognized as one of the critical components of modern drug discovery. Local binding site alignments can be constructed using sequence order-independent techniques, however, to achieve a high accuracy, many current algorithms for binding site comparison require high-quality experimental protein structures, preferably in the bound conformational state. This, in turn, complicates proteome scale applications, where only various quality structure models are available for the majority of gene products. To improve the state-of-the-art, we developed eMatchSite, a new method for constructing sequence order-independent alignments of ligand binding sites in protein models. Large-scale benchmarking calculations using adenine-binding pockets in crystal structures demonstrate that eMatchSite generates accurate alignments for almost three times more protein pairs than SOIPPA. More importantly, eMatchSite offers a high tolerance to structural distortions in ligand binding regions in protein models. For example, the percentage of correctly aligned pairs of adenine-binding sites in weakly homologous protein models is only 4-9% lower than those aligned using crystal structures. This represents a significant improvement over other algorithms, e.g. the performance of eMatchSite in recognizing similar binding sites is 6% and 13% higher than that of SiteEngine using high- and moderate-quality protein models, respectively. Constructing biologically correct alignments using predicted ligand binding sites in protein models opens up the possibility to investigate drug-protein interaction networks for complete proteomes with prospective systems-level applications in polypharmacology and rational drug repositioning. eMatchSite is freely available to the academic community as a web-server and a stand-alone software distribution at http://www.brylinski.org/ematchsite.

  9. Alignment of learning objectives and assessments in therapeutics courses to foster higher-order thinking.

    Science.gov (United States)

    FitzPatrick, Beverly; Hawboldt, John; Doyle, Daniel; Genge, Terri

    2015-02-17

    To determine whether national educational outcomes, course objectives, and classroom assessments for 2 therapeutics courses were aligned for curricular content and cognitive processes, and if they included higher-order thinking. Document analysis and student focus groups were used. Outcomes, objectives, and assessment tasks were matched for specific therapeutics content and cognitive processes. Anderson and Krathwohl's Taxonomy was used to define higher-order thinking. Students discussed whether assessments tested objectives and described their thinking when responding to assessments. There were 7 outcomes, 31 objectives, and 412 assessment tasks. The alignment for content and cognitive processes was not satisfactory. Twelve students participated in the focus groups. Students thought more short-answer questions than multiple choice questions matched the objectives for content and required higher-order thinking. The alignment analysis provided data that could be used to reveal and strengthen the enacted curriculum and improve student learning.

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

    International Nuclear Information System (INIS)

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

    2017-01-01

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

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

    Science.gov (United States)

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

    2017-04-01

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

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

    DEFF Research Database (Denmark)

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

    2010-01-01

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

  13. Elliptically polarized high-order harmonics from aligned molecules within the strong-field approximation

    DEFF Research Database (Denmark)

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

    A correction term is introduced in the stationary-point analysis on high-order harmonic generation (HHG) from aligned molecules. Arising from a multi-centre expansion of the electron wave function, this term brings our numerical calculations of the Lewenstein model into qualitative agreement...

  14. Pathogenicity gene variations within the order Entomophthorales

    DEFF Research Database (Denmark)

    Grell, Morten Nedergaard; Jensen, Annette Bruun; Lange, Lene

    Fungi within the order Entomophthorales (subphylum Entomophthoromycotina) are obligate biotrophic pathogens of arthropods with a remarkable narrow host range. Infection takes place through the cuticle when conidia hit a susceptible host, facilitated by enzymatic and mechanical mechanisms. In the ...... pathogenicity genes within genera Entomophthora and Pandora, using fungal genomic DNA originating from field-collected, infected insect host species of dipteran (flies, mosquitoes) or hemipteran (aphid) origin.......Fungi within the order Entomophthorales (subphylum Entomophthoromycotina) are obligate biotrophic pathogens of arthropods with a remarkable narrow host range. Infection takes place through the cuticle when conidia hit a susceptible host, facilitated by enzymatic and mechanical mechanisms......, conidia are produced and discharged when humidity gets high—usually during night. In an earlier secretome study of field-collected grain aphids (Sitobion avenae) infected with entomophthoralean fungi, a number of pathogenesis-related, secreted enzymes were discovered (Fungal Genetics and Biology 2011, vol...

  15. Environmental constraints shaping constituent order in emerging communication systems: Structural iconicity, interactive alignment and conventionalization.

    Science.gov (United States)

    Christensen, Peer; Fusaroli, Riccardo; Tylén, Kristian

    2016-01-01

    Where does linguistic structure come from? Recent gesture elicitation studies have indicated that constituent order (corresponding to for instance subject-verb-object, or SVO in English) may be heavily influenced by human cognitive biases constraining gesture production and transmission. Here we explore the alternative hypothesis that syntactic patterns are motivated by multiple environmental and social-interactional constraints that are external to the cognitive domain. In three experiments, we systematically investigate different motivations for structure in the gestural communication of simple transitive events. The first experiment indicates that, if participants communicate about different types of events, manipulation events (e.g. someone throwing a cake) and construction events (e.g. someone baking a cake), they spontaneously and systematically produce different constituent orders, SOV and SVO respectively, thus following the principle of structural iconicity. The second experiment shows that participants' choice of constituent order is also reliably influenced by social-interactional forces of interactive alignment, that is, the tendency to re-use an interlocutor's previous choice of constituent order, thus potentially overriding affordances for iconicity. Lastly, the third experiment finds that the relative frequency distribution of referent event types motivates the stabilization and conventionalization of a single constituent order for the communication of different types of events. Together, our results demonstrate that constituent order in emerging gestural communication systems is shaped and stabilized in response to multiple external environmental and social factors: structural iconicity, interactive alignment and distributional frequency. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

    Energy Technology Data Exchange (ETDEWEB)

    Haas, B J; Salzberg, S L; Zhu, W; Pertea, M; Allen, J E; Orvis, J; White, O; Buell, C R; Wortman, J R

    2007-12-10

    EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

  17. Supply chain collaboration aligns order-winning strategy with business outcomes

    Directory of Open Access Journals (Sweden)

    Pongpak Banchuen

    2017-06-01

    Full Text Available The paper aims to find out whether appropriate choice of collaboration will enable the required order-winners, leading to improved business outcomes. Structural equation modelling (SEM was employed with cross-sectional data to test the hypothesised relationships among order-winners, modes of collaboration, and business outcomes. Results indicate that firms that focus on flexibility, quality, and delivery should develop strategic collaboration with suppliers to achieve market and innovation improvement. Cost- and quality-focussed firms should develop operational collaboration to achieve resource efficiency. The model allows managers to understand the right alignment of external suppliers while working on their own order-winners being pursued to win business performance.

  18. Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads.

    Science.gov (United States)

    Huson, Daniel H; Tappu, Rewati; Bazinet, Adam L; Xie, Chao; Cummings, Michael P; Nieselt, Kay; Williams, Rohan

    2017-01-25

    Microbiome sequencing projects typically collect tens of millions of short reads per sample. Depending on the goals of the project, the short reads can either be subjected to direct sequence analysis or be assembled into longer contigs. The assembly of whole genomes from metagenomic sequencing reads is a very difficult problem. However, for some questions, only specific genes of interest need to be assembled. This is then a gene-centric assembly where the goal is to assemble reads into contigs for a family of orthologous genes. We present a new method for performing gene-centric assembly, called protein-alignment-guided assembly, and provide an implementation in our metagenome analysis tool MEGAN. Genes are assembled on the fly, based on the alignment of all reads against a protein reference database such as NCBI-nr. Specifically, the user selects a gene family based on a classification such as KEGG and all reads binned to that gene family are assembled. Using published synthetic community metagenome sequencing reads and a set of 41 gene families, we show that the performance of this approach compares favorably with that of full-featured assemblers and that of a recently published HMM-based gene-centric assembler, both in terms of the number of reference genes detected and of the percentage of reference sequence covered. Protein-alignment-guided assembly of orthologous gene families complements whole-metagenome assembly in a new and very useful way.

  19. Membranes with highly ordered straight nanopores by selective swelling of fast perpendicularly aligned block copolymers.

    Science.gov (United States)

    Yin, Jun; Yao, Xueping; Liou, Jiun-You; Sun, Wei; Sun, Ya-Sen; Wang, Yong

    2013-11-26

    Membranes with uniform, straight nanopores have important applications in diverse fields, but their application is limited by the lack of efficient producing methods with high controllability. In this work, we reported on an extremely simple and efficient strategy to produce such well-defined membranes. We demonstrated that neutral solvents were capable of annealing amphiphilic block copolymer (BCP) films of polystyrene-block-poly(2-vinylpyridine) (PS-b-P2VP) with thicknesses up to 600 nm to the perpendicular orientation within 1 min. Annealing in neutral solvents was also effective to the perpendicular alignment of block copolymers with very high molecular weights, e.g., 362 000 Da. Remarkably, simply by immersing the annealed BCP films in hot ethanol followed by drying in air, the originally dense BCP films were nondestructively converted into porous membranes containing highly ordered, straight nanopores traversing the entire thickness of the membrane (up to 1.1 μm). Grazing incident small-angle X-ray spectroscopy confirmed the hexagonal ordering of the nanopores over large areas. We found that the overflow of P2VP chains from their reservoir P2VP cylinders and the deformation of the PS matrix in the swelling process contributed to the transformation of the solid P2VP cylinders to empty straight pores. The pore diameters can be tuned by either changing the swelling temperatures or depositing thin layers of metal oxides on the preformed membranes via atomic layer deposition with a subnanometer accuracy. To demonstrate the application of the obtained porous membranes, we used them as templates and produced centimeter-scale arrays of aligned nanotubes of metal oxides with finely tunable wall thicknesses.

  20. Frequency-domain reduced order models for gravitational waves from aligned-spin compact binaries

    International Nuclear Information System (INIS)

    Pürrer, Michael

    2014-01-01

    Black-hole binary coalescences are one of the most promising sources for the first detection of gravitational waves. Fast and accurate theoretical models of the gravitational radiation emitted from these coalescences are highly important for the detection and extraction of physical parameters. Spinning effective-one-body models for binaries with aligned-spins have been shown to be highly faithful, but are slow to generate and thus have not yet been used for parameter estimation (PE) studies. I provide a frequency-domain singular value decomposition-based surrogate reduced order model that is thousands of times faster for typical system masses and has a faithfulness mismatch of better than ∼0.1% with the original SEOBNRv1 model for advanced LIGO detectors. This model enables PE studies up to signal-to-noise ratios (SNRs) of 20 and even up to 50 for total masses below 50 M ⊙ . This paper discusses various choices for approximations and interpolation over the parameter space that can be made for reduced order models of spinning compact binaries, provides a detailed discussion of errors arising in the construction and assesses the fidelity of such models. (paper)

  1. NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes.

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    Gabriel A Al-Ghalith

    2016-01-01

    Full Text Available The explosion of bioinformatics technologies in the form of next generation sequencing (NGS has facilitated a massive influx of genomics data in the form of short reads. Short read mapping is therefore a fundamental component of next generation sequencing pipelines which routinely match these short reads against reference genomes for contig assembly. However, such techniques have seldom been applied to microbial marker gene sequencing studies, which have mostly relied on novel heuristic approaches. We propose NINJA Is Not Just Another OTU-Picking Solution (NINJA-OPS, or NINJA for short, a fast and highly accurate novel method enabling reference-based marker gene matching (picking Operational Taxonomic Units, or OTUs. NINJA takes advantage of the Burrows-Wheeler (BW alignment using an artificial reference chromosome composed of concatenated reference sequences, the "concatesome," as the BW input. Other features include automatic support for paired-end reads with arbitrary insert sizes. NINJA is also free and open source and implements several pre-filtering methods that elicit substantial speedup when coupled with existing tools. We applied NINJA to several published microbiome studies, obtaining accuracy similar to or better than previous reference-based OTU-picking methods while achieving an order of magnitude or more speedup and using a fraction of the memory footprint. NINJA is a complete pipeline that takes a FASTA-formatted input file and outputs a QIIME-formatted taxonomy-annotated BIOM file for an entire MiSeq run of human gut microbiome 16S genes in under 10 minutes on a dual-core laptop.

  2. Mitochondrial Genomes of Kinorhyncha: trnM Duplication and New Gene Orders within Animals.

    Science.gov (United States)

    Popova, Olga V; Mikhailov, Kirill V; Nikitin, Mikhail A; Logacheva, Maria D; Penin, Aleksey A; Muntyan, Maria S; Kedrova, Olga S; Petrov, Nikolai B; Panchin, Yuri V; Aleoshin, Vladimir V

    2016-01-01

    Many features of mitochondrial genomes of animals, such as patterns of gene arrangement, nucleotide content and substitution rate variation are extensively used in evolutionary and phylogenetic studies. Nearly 6,000 mitochondrial genomes of animals have already been sequenced, covering the majority of animal phyla. One of the groups that escaped mitogenome sequencing is phylum Kinorhyncha-an isolated taxon of microscopic worm-like ecdysozoans. The kinorhynchs are thought to be one of the early-branching lineages of Ecdysozoa, and their mitochondrial genomes may be important for resolving evolutionary relations between major animal taxa. Here we present the results of sequencing and analysis of mitochondrial genomes from two members of Kinorhyncha, Echinoderes svetlanae (Cyclorhagida) and Pycnophyes kielensis (Allomalorhagida). Their mitochondrial genomes are circular molecules approximately 15 Kbp in size. The kinorhynch mitochondrial gene sequences are highly divergent, which precludes accurate phylogenetic inference. The mitogenomes of both species encode a typical metazoan complement of 37 genes, which are all positioned on the major strand, but the gene order is distinct and unique among Ecdysozoa or animals as a whole. We predict four types of start codons for protein-coding genes in E. svetlanae and five in P. kielensis with a consensus DTD in single letter code. The mitochondrial genomes of E. svetlanae and P. kielensis encode duplicated methionine tRNA genes that display compensatory nucleotide substitutions. Two distant species of Kinorhyncha demonstrate similar patterns of gene arrangements in their mitogenomes. Both genomes have duplicated methionine tRNA genes; the duplication predates the divergence of two species. The kinorhynchs share a few features pertaining to gene order that align them with Priapulida. Gene order analysis reveals that gene arrangement specific of Priapulida may be ancestral for Scalidophora, Ecdysozoa, and even Protostomia.

  3. Mitochondrial Genomes of Kinorhyncha: trnM Duplication and New Gene Orders within Animals.

    Directory of Open Access Journals (Sweden)

    Olga V Popova

    Full Text Available Many features of mitochondrial genomes of animals, such as patterns of gene arrangement, nucleotide content and substitution rate variation are extensively used in evolutionary and phylogenetic studies. Nearly 6,000 mitochondrial genomes of animals have already been sequenced, covering the majority of animal phyla. One of the groups that escaped mitogenome sequencing is phylum Kinorhyncha-an isolated taxon of microscopic worm-like ecdysozoans. The kinorhynchs are thought to be one of the early-branching lineages of Ecdysozoa, and their mitochondrial genomes may be important for resolving evolutionary relations between major animal taxa. Here we present the results of sequencing and analysis of mitochondrial genomes from two members of Kinorhyncha, Echinoderes svetlanae (Cyclorhagida and Pycnophyes kielensis (Allomalorhagida. Their mitochondrial genomes are circular molecules approximately 15 Kbp in size. The kinorhynch mitochondrial gene sequences are highly divergent, which precludes accurate phylogenetic inference. The mitogenomes of both species encode a typical metazoan complement of 37 genes, which are all positioned on the major strand, but the gene order is distinct and unique among Ecdysozoa or animals as a whole. We predict four types of start codons for protein-coding genes in E. svetlanae and five in P. kielensis with a consensus DTD in single letter code. The mitochondrial genomes of E. svetlanae and P. kielensis encode duplicated methionine tRNA genes that display compensatory nucleotide substitutions. Two distant species of Kinorhyncha demonstrate similar patterns of gene arrangements in their mitogenomes. Both genomes have duplicated methionine tRNA genes; the duplication predates the divergence of two species. The kinorhynchs share a few features pertaining to gene order that align them with Priapulida. Gene order analysis reveals that gene arrangement specific of Priapulida may be ancestral for Scalidophora, Ecdysozoa, and even

  4. 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).

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

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    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.

  6. 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

  7. Scaffold filling, contig fusion and comparative gene order inference

    Directory of Open Access Journals (Sweden)

    Rounsley Steve

    2010-06-01

    Full Text Available Abstract Background There has been a trend in increasing the phylogenetic scope of genome sequencing without finishing the sequence of the genome. Increasing numbers of genomes are being published in scaffold or contig form. Rearrangement algorithms, however, including gene order-based phylogenetic tools, require whole genome data on gene order or syntenic block order. How then can we use rearrangement algorithms to compare genomes available in scaffold form only? Can the comparative evidence predict the location of unsequenced genes? Results Our method involves optimally filling in genes missing from the scaffolds, while incorporating the augmented scaffolds directly into the rearrangement algorithms as if they were chromosomes. This is accomplished by an exact, polynomial-time algorithm. We then correct for the number of extra fusion/fission operations required to make scaffolds comparable to full assemblies. We model the relationship between the ratio of missing genes actually absent from the genome versus merely unsequenced ones, on one hand, and the increase of genomic distance after scaffold filling, on the other. We estimate the parameters of this model through simulations and by comparing the angiosperm genomes Ricinus communis and Vitis vinifera. Conclusions The algorithm solves the comparison of genomes with 18,300 genes, including 4500 missing from one genome, in less than a minute on a MacBook, putting virtually all genomes within range of the method.

  8. Scaffold filling, contig fusion and comparative gene order inference.

    Science.gov (United States)

    Muñoz, Adriana; Zheng, Chunfang; Zhu, Qian; Albert, Victor A; Rounsley, Steve; Sankoff, David

    2010-06-04

    There has been a trend in increasing the phylogenetic scope of genome sequencing without finishing the sequence of the genome. Increasing numbers of genomes are being published in scaffold or contig form. Rearrangement algorithms, however, including gene order-based phylogenetic tools, require whole genome data on gene order or syntenic block order. How then can we use rearrangement algorithms to compare genomes available in scaffold form only? Can the comparative evidence predict the location of unsequenced genes? Our method involves optimally filling in genes missing from the scaffolds, while incorporating the augmented scaffolds directly into the rearrangement algorithms as if they were chromosomes. This is accomplished by an exact, polynomial-time algorithm. We then correct for the number of extra fusion/fission operations required to make scaffolds comparable to full assemblies. We model the relationship between the ratio of missing genes actually absent from the genome versus merely unsequenced ones, on one hand, and the increase of genomic distance after scaffold filling, on the other. We estimate the parameters of this model through simulations and by comparing the angiosperm genomes Ricinus communis and Vitis vinifera. The algorithm solves the comparison of genomes with 18,300 genes, including 4500 missing from one genome, in less than a minute on a MacBook, putting virtually all genomes within range of the method.

  9. Importance of the alignment of polar π conjugated molecules inside carbon nanotubes in determining second-order non-linear optical properties.

    Science.gov (United States)

    Yumura, Takashi; Yamamoto, Wataru

    2017-09-20

    We employed density functional theory (DFT) calculations with dispersion corrections to investigate energetically preferred alignments of certain p,p'-dimethylaminonitrostilbene (DANS) molecules inside an armchair (m,m) carbon nanotube (n × DANS@(m,m)), where the number of inner molecules (n) is no greater than 3. Here, three types of alignments of DANS are considered: a linear alignment in a parallel fashion and stacking alignments in parallel and antiparallel fashions. According to DFT calculations, a threshold tube diameter for containing DANS molecules in linear or stacking alignments was found to be approximately 1.0 nm. Nanotubes with diameters smaller than 1.0 nm result in the selective formation of linearly aligned DANS molecules due to strong confinement effects within the nanotubes. By contrast, larger diameter nanotubes allow DANS molecules to align in a stacking and linear fashion. The type of alignment adopted by the DANS molecules inside a nanotube is responsible for their second-order non-linear optical properties represented by their static hyperpolarizability (β 0 values). In fact, we computed β 0 values of DANS assemblies taken from optimized n × DANS@(m,m) structures, and their values were compared with those of a single DANS molecule. DFT calculations showed that β 0 values of DANS molecules depend on their alignment, which decrease in the following order: linear alignment > parallel stacking alignment > antiparallel stacking alignment. In particular, a linear alignment has a β 0 value more significant than that of the same number of isolated molecules. Therefore, the linear alignment of DANS molecules, which is only allowed inside smaller diameter nanotubes, can strongly enhance their second-order non-linear optical properties. Since the nanotube confinement determines the alignment of DANS molecules, a restricted nanospace can be utilized to control their second-order non-linear optical properties. These DFT findings can assist in the

  10. Wafer-Scale High-Throughput Ordered Growth of Vertically Aligned ZnO Nanowire Arrays

    KAUST Repository

    Wei, Yaguang; Wu, Wenzhuo; Guo, Rui; Yuan, Dajun; Das, Suman; Wang, Zhong Lin

    2010-01-01

    -synthesized morphology. The development of textured ZnO seed layers for replacing single crystalline GaN and ZnO substrates extends the large-scale fabrication of vertically aligned ZnO NW arrays on substrates of other materials, such as polymers, Si, and glass

  11. Massive ordering and alignment of cylindrical micro-objects by photovoltaic optoelectronic tweezers.

    Science.gov (United States)

    Elvira, Iris; Muñoz-Martínez, Juan F; Barroso, Álvaro; Denz, Cornelia; Ramiro, José B; García-Cabañes, Angel; Agulló-López, Fernando; Carrascosa, Mercedes

    2018-01-01

    Optical tools for manipulation and trapping of micro- and nano-objects are a fundamental issue for many applications in nano- and biotechnology. This work reports on the use of one such method, known as photovoltaic optoelectronics tweezers, to orientate and organize cylindrical microcrystals, specifically elongated zeolite L, on the surface of Fe-doped LiNbO 3 crystal plates. Patterns of aligned zeolites have been achieved through the forces and torques generated by the bulk photovoltaic effect. The alignment patterns with zeolites parallel or perpendicular to the substrate surface are highly dependent on the features of light distribution and crystal configuration. Moreover, dielectrophoretic chains of zeolites with lengths up to 100 μm have often been observed. The experimental results of zeolite trapping and alignment have been discussed and compared together with theoretical simulations of the evanescent photovoltaic electric field and the dielectrophoretic potential. They demonstrate the remarkable capabilities of the optoelectronic photovoltaic method to orientate and pattern anisotropic microcrystals. The combined action of patterning and alignment offers a unique tool to prepare functional nanostructures with potential applications in a variety of fields such as nonlinear optics or plasmonics.

  12. Inversions and the dynamics of eukaryotic gene order.

    NARCIS (Netherlands)

    Huynen, M.A.; Snel, B.; Bork, P.

    2001-01-01

    Comparisons of the gene order in closely related genomes reveal a major role for inversions in the genome shuffling process. In contrast to prokaryotes, where the inversions are predominantly large, half of the inversions between Saccharomyces cerevisiae and Candida albicans appear to be small,

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

    International Nuclear Information System (INIS)

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

    2006-01-01

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

  14. Wafer-Scale High-Throughput Ordered Growth of Vertically Aligned ZnO Nanowire Arrays

    KAUST Repository

    Wei, Yaguang

    2010-09-08

    This article presents an effective approach for patterned growth of vertically aligned ZnO nanowire (NW) arrays with high throughput and low cost at wafer scale without using cleanroom technology. Periodic hole patterns are generated using laser interference lithography on substrates coated with the photoresist SU-8. ZnO NWs are selectively grown through the holes via a low-temperature hydrothermal method without using a catalyst and with a superior control over orientation, location/density, and as-synthesized morphology. The development of textured ZnO seed layers for replacing single crystalline GaN and ZnO substrates extends the large-scale fabrication of vertically aligned ZnO NW arrays on substrates of other materials, such as polymers, Si, and glass. This combined approach demonstrates a novel method of manufacturing large-scale patterned one-dimensional nanostructures on various substrates for applications in energy harvesting, sensing, optoelectronics, and electronic devices. © 2010 American Chemical Society.

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

    International Nuclear Information System (INIS)

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

    2010-01-01

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

  16. Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs.

    Science.gov (United States)

    Moriya, Yuki; Yamada, Takuji; Okuda, Shujiro; Nakagawa, Zenichi; Kotera, Masaaki; Tokimatsu, Toshiaki; Kanehisa, Minoru; Goto, Susumu

    2016-03-28

    Although there are several databases that contain data on many metabolites and reactions in biochemical pathways, there is still a big gap in the numbers between experimentally identified enzymes and metabolites. It is supposed that many catalytic enzyme genes are still unknown. Although there are previous studies that estimate the number of candidate enzyme genes, these studies required some additional information aside from the structures of metabolites such as gene expression and order in the genome. In this study, we developed a novel method to identify a candidate enzyme gene of a reaction using the chemical structures of the substrate-product pair (reactant pair). The proposed method is based on a search for similar reactant pairs in a reference database and offers ortholog groups that possibly mediate the given reaction. We applied the proposed method to two experimentally validated reactions. As a result, we confirmed that the histidine transaminase was correctly identified. Although our method could not directly identify the asparagine oxo-acid transaminase, we successfully found the paralog gene most similar to the correct enzyme gene. We also applied our method to infer candidate enzyme genes in the mesaconate pathway. The advantage of our method lies in the prediction of possible genes for orphan enzyme reactions where any associated gene sequences are not determined yet. We believe that this approach will facilitate experimental identification of genes for orphan enzymes.

  17. 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

  18. 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

  19. Quantifying the Hierarchical Order in Self-Aligned Carbon Nanotubes from Atomic to Micrometer Scale.

    Science.gov (United States)

    Meshot, Eric R; Zwissler, Darwin W; Bui, Ngoc; Kuykendall, Tevye R; Wang, Cheng; Hexemer, Alexander; Wu, Kuang Jen J; Fornasiero, Francesco

    2017-06-27

    Fundamental understanding of structure-property relationships in hierarchically organized nanostructures is crucial for the development of new functionality, yet quantifying structure across multiple length scales is challenging. In this work, we used nondestructive X-ray scattering to quantitatively map the multiscale structure of hierarchically self-organized carbon nanotube (CNT) "forests" across 4 orders of magnitude in length scale, from 2.0 Å to 1.5 μm. Fully resolved structural features include the graphitic honeycomb lattice and interlayer walls (atomic), CNT diameter (nano), as well as the greater CNT ensemble (meso) and large corrugations (micro). Correlating orientational order across hierarchical levels revealed a cascading decrease as we probed finer structural feature sizes with enhanced sensitivity to small-scale disorder. Furthermore, we established qualitative relationships for single-, few-, and multiwall CNT forest characteristics, showing that multiscale orientational order is directly correlated with number density spanning 10 9 -10 12 cm -2 , yet order is inversely proportional to CNT diameter, number of walls, and atomic defects. Lastly, we captured and quantified ultralow-q meridional scattering features and built a phenomenological model of the large-scale CNT forest morphology, which predicted and confirmed that these features arise due to microscale corrugations along the vertical forest direction. Providing detailed structural information at multiple length scales is important for design and synthesis of CNT materials as well as other hierarchically organized nanostructures.

  20. The constancy of gene conservation across divergent bacterial orders

    Directory of Open Access Journals (Sweden)

    Ackermann Martin

    2009-01-01

    Full Text Available Abstract Background Orthologous genes are frequently presumed to perform similar functions. However, outside of model organisms, this is rarely tested. One means of inferring changes in function is if there are changes in the level of gene conservation and selective constraint. Here we compare levels of gene conservation across three bacterial groups to test for changes in gene functionality. Findings The level of gene conservation for different orthologous genes is highly correlated across clades, even for highly divergent groups of bacteria. These correlations do not arise from broad differences in gene functionality (e.g. informational genes vs. metabolic genes, but instead seem to result from very specific differences in gene function. Furthermore, these functional differences appear to be maintained over very long periods of time. Conclusion These results suggest that even over broad time scales, most bacterial genes are under a nearly constant level of purifying selection, and that bacterial evolution is thus dominated by selective and functional stasis.

  1. Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser

    LENUS (Irish Health Repository)

    Fitzpatrick, David A

    2010-05-10

    Abstract Background Candida species are the most common cause of opportunistic fungal infection worldwide. Recent sequencing efforts have provided a wealth of Candida genomic data. We have developed the Candida Gene Order Browser (CGOB), an online tool that aids comparative syntenic analyses of Candida species. CGOB incorporates all available Candida clade genome sequences including two Candida albicans isolates (SC5314 and WO-1) and 8 closely related species (Candida dubliniensis, Candida tropicalis, Candida parapsilosis, Lodderomyces elongisporus, Debaryomyces hansenii, Pichia stipitis, Candida guilliermondii and Candida lusitaniae). Saccharomyces cerevisiae is also included as a reference genome. Results CGOB assignments of homology were manually curated based on sequence similarity and synteny. In total CGOB includes 65617 genes arranged into 13625 homology columns. We have also generated improved Candida gene sets by merging\\/removing partial genes in each genome. Interrogation of CGOB revealed that the majority of tandemly duplicated genes are under strong purifying selection in all Candida species. We identified clusters of adjacent genes involved in the same metabolic pathways (such as catabolism of biotin, galactose and N-acetyl glucosamine) and we showed that some clusters are species or lineage-specific. We also identified one example of intron gain in C. albicans. Conclusions Our analysis provides an important resource that is now available for the Candida community. CGOB is available at http:\\/\\/cgob.ucd.ie.

  2. Importance of globin gene order for correct developmental expression.

    NARCIS (Netherlands)

    O. Hanscombe (Olivia); D. Whyatt (David); P.J. Fraser (Peter); N. Yannoutsos (Nikos); D.R. Greaves (David); N.O. Dillon (Niall); F.G. Grosveld (Frank)

    1991-01-01

    textabstractWe have used transgenic mice to study the influence of position of the human globin genes relative to the locus control region (LCR) on their expression pattern during development. The LCR, which is located 5' of the globin gene cluster, is normally required for the activation of all the

  3. Extensive paraphylies within sharks of the order Carcharhiniformes inferred from nuclear and mitochondrial genes.

    Science.gov (United States)

    Iglésias, Samuel P; Lecointre, Guillaume; Sellos, Daniel Y

    2005-03-01

    Using nuclear coding and mitochondrial ribosomal genes we try to clarify relationships within Carcharhiniformes with special focus on the two most problematic groups: scyliorhinids and triakids. The mitochondrial aligned sequences are 1542 bp long, and include principally portion of 16S rRNA gene. They are obtained for two outgroup species and 43 Carcharhiniformes species, covering 5 of the 8 families and 15 of the 48 genera of the order. The nuclear RAG1 sequences are 1454 bp long, and are obtained for 17 species representative of the diversity of all species sampled. We used Maximum Parsimony and Maximum Likelihood criteria for tree reconstruction. Paraphylies within the family Scyliorhinidae was proposed for the first time by Maisey [Zool. J. Linn. Soc. 82, 33, 1984] in a morphological cladistic analysis. This result has never been proposed again until recently from molecular phylogenies [Mol. Phylogenet. Evol. 31, 214, 2004]. Here, independent and simultaneous analyses of nuclear and mitochondrial data are congruent in supporting the paraphyly of scyliorhinids. Two groups of scyliorhinids are obtained, thoroughly in line with discrimination proposed by previous authors, based on presence/absence of supraorbital crests on the chondrocranium. The first group (Scyliorhinus+Cephaloscyllium) is basal within carcharhiniforms and the second group (Apristurus+Asymbolus+Cephalurus+Galeus+Parmaturus) is sister group of all the other families investigated (Carcharhinidae, Proscyllidae, Pseudotriakidae, and Triakidae). The paraphyly of triakids appeared probable but more investigations are needed. In conclusion several independent morphological and molecular phylogenetic studies support paraphyly within scyliorhinids. So we propose a new classification for the group, with the redefinition of the family Scyliorhinidae sensu stricto and the resurrection of the family Pentanchidae with a new definition.

  4. A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria.

    Science.gov (United States)

    Gaby, John Christian; Buckley, Daniel H

    2014-01-01

    We describe a nitrogenase gene sequence database that facilitates analysis of the evolution and ecology of nitrogen-fixing organisms. The database contains 32 954 aligned nitrogenase nifH sequences linked to phylogenetic trees and associated sequence metadata. The database includes 185 linked multigene entries including full-length nifH, nifD, nifK and 16S ribosomal RNA (rRNA) gene sequences. Evolutionary analyses enabled by the multigene entries support an ancient horizontal transfer of nitrogenase genes between Archaea and Bacteria and provide evidence that nifH has a different history of horizontal gene transfer from the nifDK enzyme core. Further analyses show that lineages in nitrogenase cluster I and cluster III have different rates of substitution within nifD, suggesting that nifD is under different selection pressure in these two lineages. Finally, we find that that the genetic divergence of nifH and 16S rRNA genes does not correlate well at sequence dissimilarity values used commonly to define microbial species, as stains having <3% sequence dissimilarity in their 16S rRNA genes can have up to 23% dissimilarity in nifH. The nifH database has a number of uses including phylogenetic and evolutionary analyses, the design and assessment of primers/probes and the evaluation of nitrogenase sequence diversity. Database URL: http://www.css.cornell.edu/faculty/buckley/nifh.htm.

  5. Unusual Gene Order and Organization of the Sea Urchin HoxCluster

    Energy Technology Data Exchange (ETDEWEB)

    Richardson, Paul M.; Lucas, Susan; Cameron, R. Andrew; Rowen,Lee; Nesbitt, Ryan; Bloom, Scott; Rast, Jonathan P.; Berney, Kevin; Arenas-Mena, Cesar; Martinez, Pedro; Davidson, Eric H.; Peterson, KevinJ.; Hood, Leroy

    2005-05-10

    The highly consistent gene order and axial colinear expression patterns found in vertebrate hox gene clusters are less well conserved across the rest of bilaterians. We report the first deuterostome instance of an intact hox cluster with a unique gene order where the paralog groups are not expressed in a sequential manner. The finished sequence from BAC clones from the genome of the sea urchin, Strongylocentrotus purpuratus, reveals a gene order wherein the anterior genes (Hox1, Hox2 and Hox3) lie nearest the posterior genes in the cluster such that the most 3' gene is Hox5. (The gene order is : 5'-Hox1,2, 3, 11/13c, 11/13b, '11/13a, 9/10, 8, 7, 6, 5 - 3)'. The finished sequence result is corroborated by restriction mapping evidence and BAC-end scaffold analyses. Comparisons with a putative ancestral deuterostome Hox gene cluster suggest that the rearrangements leading to the sea urchin gene order were many and complex.

  6. Computational fitness landscape for all gene-order permutations of an RNA virus.

    Directory of Open Access Journals (Sweden)

    Kwang-il Lim

    2009-02-01

    Full Text Available How does the growth of a virus depend on the linear arrangement of genes in its genome? Answering this question may enhance our basic understanding of virus evolution and advance applications of viruses as live attenuated vaccines, gene-therapy vectors, or anti-tumor therapeutics. We used a mathematical model for vesicular stomatitis virus (VSV, a prototype RNA virus that encodes five genes (N-P-M-G-L, to simulate the intracellular growth of all 120 possible gene-order variants. Simulated yields of virus infection varied by 6,000-fold and were found to be most sensitive to gene-order permutations that increased levels of the L gene transcript or reduced levels of the N gene transcript, the lowest and highest expressed genes of the wild-type virus, respectively. Effects of gene order on virus growth also depended upon the host-cell environment, reflecting different resources for protein synthesis and different cell susceptibilities to infection. Moreover, by computationally deleting intergenic attenuations, which define a key mechanism of transcriptional regulation in VSV, the variation in growth associated with the 120 gene-order variants was drastically narrowed from 6,000- to 20-fold, and many variants produced higher progeny yields than wild-type. These results suggest that regulation by intergenic attenuation preceded or co-evolved with the fixation of the wild type gene order in the evolution of VSV. In summary, our models have begun to reveal how gene functions, gene regulation, and genomic organization of viruses interact with their host environments to define processes of viral growth and evolution.

  7. Computer Vision Evidence Supporting Craniometric Alignment of Rat Brain Atlases to Streamline Expert-Guided, First-Order Migration of Hypothalamic Spatial Datasets Related to Behavioral Control

    Science.gov (United States)

    Khan, Arshad M.; Perez, Jose G.; Wells, Claire E.; Fuentes, Olac

    2018-01-01

    The rat has arguably the most widely studied brain among all animals, with numerous reference atlases for rat brain having been published since 1946. For example, many neuroscientists have used the atlases of Paxinos and Watson (PW, first published in 1982) or Swanson (S, first published in 1992) as guides to probe or map specific rat brain structures and their connections. Despite nearly three decades of contemporaneous publication, no independent attempt has been made to establish a basic framework that allows data mapped in PW to be placed in register with S, or vice versa. Such data migration would allow scientists to accurately contextualize neuroanatomical data mapped exclusively in only one atlas with data mapped in the other. Here, we provide a tool that allows levels from any of the seven published editions of atlases comprising three distinct PW reference spaces to be aligned to atlas levels from any of the four published editions representing S reference space. This alignment is based on registration of the anteroposterior stereotaxic coordinate (z) measured from the skull landmark, Bregma (β). Atlas level alignments performed along the z axis using one-dimensional Cleveland dot plots were in general agreement with alignments obtained independently using a custom-made computer vision application that utilized the scale-invariant feature transform (SIFT) and Random Sample Consensus (RANSAC) operation to compare regions of interest in photomicrographs of Nissl-stained tissue sections from the PW and S reference spaces. We show that z-aligned point source data (unpublished hypothalamic microinjection sites) can be migrated from PW to S space to a first-order approximation in the mediolateral and dorsoventral dimensions using anisotropic scaling of the vector-formatted atlas templates, together with expert-guided relocation of obvious outliers in the migrated datasets. The migrated data can be contextualized with other datasets mapped in S space, including

  8. Computer Vision Evidence Supporting Craniometric Alignment of Rat Brain Atlases to Streamline Expert-Guided, First-Order Migration of Hypothalamic Spatial Datasets Related to Behavioral Control

    Directory of Open Access Journals (Sweden)

    Arshad M. Khan

    2018-05-01

    Full Text Available The rat has arguably the most widely studied brain among all animals, with numerous reference atlases for rat brain having been published since 1946. For example, many neuroscientists have used the atlases of Paxinos and Watson (PW, first published in 1982 or Swanson (S, first published in 1992 as guides to probe or map specific rat brain structures and their connections. Despite nearly three decades of contemporaneous publication, no independent attempt has been made to establish a basic framework that allows data mapped in PW to be placed in register with S, or vice versa. Such data migration would allow scientists to accurately contextualize neuroanatomical data mapped exclusively in only one atlas with data mapped in the other. Here, we provide a tool that allows levels from any of the seven published editions of atlases comprising three distinct PW reference spaces to be aligned to atlas levels from any of the four published editions representing S reference space. This alignment is based on registration of the anteroposterior stereotaxic coordinate (z measured from the skull landmark, Bregma (β. Atlas level alignments performed along the z axis using one-dimensional Cleveland dot plots were in general agreement with alignments obtained independently using a custom-made computer vision application that utilized the scale-invariant feature transform (SIFT and Random Sample Consensus (RANSAC operation to compare regions of interest in photomicrographs of Nissl-stained tissue sections from the PW and S reference spaces. We show that z-aligned point source data (unpublished hypothalamic microinjection sites can be migrated from PW to S space to a first-order approximation in the mediolateral and dorsoventral dimensions using anisotropic scaling of the vector-formatted atlas templates, together with expert-guided relocation of obvious outliers in the migrated datasets. The migrated data can be contextualized with other datasets mapped in S

  9. An evaluation of chondrocyte morphology and gene expression on superhydrophilic vertically-aligned multi-walled carbon nanotube films

    International Nuclear Information System (INIS)

    Antonioli, Eliane; Lobo, Anderson O.; Ferretti, Mario; Cohen, Moisés; Marciano, Fernanda R.; Corat, Evaldo J.; Trava-Airoldi, Vladimir J.

    2013-01-01

    Cartilage serves as a low-friction and wear-resistant articulating surface in diarthrodial joints and is also important during early stages of bone remodeling. Recently, regenerative cartilage research has focused on combinations of cells paired with scaffolds. Superhydrophilic vertically aligned carbon nanotubes (VACNTs) are of particular interest in regenerative medicine. The aim of this study is to evaluate cell expansion of human articular chondrocytes on superhydrophilic VACNTs, as well as their morphology and gene expression. VACNT films were produced using a microwave plasma chamber on Ti substrates and submitted to an O 2 plasma treatment to make them superhydrophilic. Human chondrocytes were cultivated on superhydrophilic VACNTs up to five days. Quantitative RT-PCR was performed to measure type I and type II Collagen, Sox9, and Aggrecan mRNA expression levels. The morphology was analyzed by scanning electron microscopy (SEM) and confocal microscopy. SEM images demonstrated that superhydrophilic VACNTs permit cell growth and adhesion of human chondrocytes. The chondrocytes had an elongated morphology with some prolongations. Chondrocytes cultivated on superhydrophilic VACNTs maintain the level expression of Aggrecan, Sox9, and Collagen II determined by qPCR. This study was the first to indicate that superhydrophilic VACNTs may be used as an efficient scaffold for cartilage or bone repair. Highlights: ► Chondrocytes were cultivated on Superhydrophilic Vertically Aligned Multiwall Carbon Nanotubes (VACNT). ► We have shown a correlation between gene expression and thermodynamics aspects. ► Superhydrhophilic VACNT will be an excellent substrate for cartilage and bone tissue regeneration.

  10. An evaluation of chondrocyte morphology and gene expression on superhydrophilic vertically-aligned multi-walled carbon nanotube films

    Energy Technology Data Exchange (ETDEWEB)

    Antonioli, Eliane, E-mail: eliane.antonioli@einstein.br [Research and Education Institute, Hospital Israelita Albert Einstein, Sao Paulo, SP (Brazil); Lobo, Anderson O., E-mail: aolobo@univap.br [Laboratory of Biomedical Nanotechnology, Universidade do Vale do Paraiba, Sao Jose dos Campos, Sao Paulo (Brazil); Ferretti, Mario, E-mail: ferretti@einstein.br [Research and Education Institute, Hospital Israelita Albert Einstein, Sao Paulo, SP (Brazil); Ortophedic Division, Federal University of Sao Paulo, SP (Brazil); Cohen, Moises, E-mail: m.cohen@uol.com.br [Research and Education Institute, Hospital Israelita Albert Einstein, Sao Paulo, SP (Brazil); Ortophedic Division, Federal University of Sao Paulo, SP (Brazil); Marciano, Fernanda R., E-mail: femarciano@uol.com.br [Laboratory of Biomedical Nanotechnology, Universidade do Vale do Paraiba, Sao Jose dos Campos, Sao Paulo (Brazil); Corat, Evaldo J., E-mail: corat@las.inpe.br [Laboratorio Associado de Sensores e Materiais, Instituto Nacional de Pesquisas Espaciais, Sao Jose dos Campos, Sao Paulo (Brazil); Trava-Airoldi, Vladimir J., E-mail: vladimir@las.inpe.br [Laboratorio Associado de Sensores e Materiais, Instituto Nacional de Pesquisas Espaciais, Sao Jose dos Campos, Sao Paulo (Brazil)

    2013-03-01

    Cartilage serves as a low-friction and wear-resistant articulating surface in diarthrodial joints and is also important during early stages of bone remodeling. Recently, regenerative cartilage research has focused on combinations of cells paired with scaffolds. Superhydrophilic vertically aligned carbon nanotubes (VACNTs) are of particular interest in regenerative medicine. The aim of this study is to evaluate cell expansion of human articular chondrocytes on superhydrophilic VACNTs, as well as their morphology and gene expression. VACNT films were produced using a microwave plasma chamber on Ti substrates and submitted to an O{sub 2} plasma treatment to make them superhydrophilic. Human chondrocytes were cultivated on superhydrophilic VACNTs up to five days. Quantitative RT-PCR was performed to measure type I and type II Collagen, Sox9, and Aggrecan mRNA expression levels. The morphology was analyzed by scanning electron microscopy (SEM) and confocal microscopy. SEM images demonstrated that superhydrophilic VACNTs permit cell growth and adhesion of human chondrocytes. The chondrocytes had an elongated morphology with some prolongations. Chondrocytes cultivated on superhydrophilic VACNTs maintain the level expression of Aggrecan, Sox9, and Collagen II determined by qPCR. This study was the first to indicate that superhydrophilic VACNTs may be used as an efficient scaffold for cartilage or bone repair. Highlights: Black-Right-Pointing-Pointer Chondrocytes were cultivated on Superhydrophilic Vertically Aligned Multiwall Carbon Nanotubes (VACNT). Black-Right-Pointing-Pointer We have shown a correlation between gene expression and thermodynamics aspects. Black-Right-Pointing-Pointer Superhydrhophilic VACNT will be an excellent substrate for cartilage and bone tissue regeneration.

  11. 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

  12. ORF Alignment: ch_oct10_gene_aa_db [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ch_oct10_gene_aa_db Chro.60303 >1wicA 11 152 1 150 4e-26 ... gb|EAL37012.1| conserverd MSP-domain transme...mbrane protein [Cryptosporidium ... hominis] ... Length = 150 ... Query: 1 ... MSME...GAKLVRVHPEKALEFPLVLYSSVTTPLILENITSSTVAFKIKTTAPRGYLVRPSSG 60 ... MSMEGAKLVRVHPEKALEFPLVLYSSVTTPLIL...ENITSSTVAFKIKTTAPRGYLVRPSSG Sbjct: 1 ... MSMEGAKLVRVHPEKALEFPLVLYSSVTTPLILENITSSTVA

  13. Outgroup, alignment and modelling improvements indicate that two TNFSF13-like genes existed in the vertebrate ancestor.

    Science.gov (United States)

    Redmond, Anthony K; Pettinello, Rita; Dooley, Helen

    2017-03-01

    The molecular machinery required for lymphocyte development and differentiation appears to have emerged concomitantly with distinct B- and T-like lymphocyte subsets in the ancestor of all vertebrates. The TNFSF superfamily (TNFSF) members BAFF (TNFSF13/Blys) and APRIL (TNFSF13) are key regulators of B cell development survival, and activation in mammals, but the temporal emergence of these molecules, and their precise relationship to the newly identified TNFSF gene BALM (BAFF and APRIL-like molecule), have not yet been elucidated. Here, to resolve the early evolutionary history of this family, we improved outgroup sampling and alignment quality, and applied better fitting substitution models compared to past studies. Our analyses reveal that BALM is a definitive TNFSF13 family member, which split from BAFF in the gnathostome (jawed vertebrate) ancestor. Most importantly, however, we show that both the APRIL and BAFF lineages existed in the ancestors of all extant vertebrates. This implies that APRIL has been lost, or is yet to be found, in cyclostomes (jawless vertebrates). Our results suggest that lineage-specific gene duplication and loss events have caused lymphocyte regulation, despite shared origins, to become secondarily distinct between gnathostomes and cyclostomes. Finally, the structure of lamprey BAFF-like, and its phylogenetic placement as sister to BAFF and BALM, but not the more slowly evolving APRIL, indicates that the primordial lymphocyte regulator was more APRIL-like than BAFF-like.

  14. larvalign: Aligning Gene Expression Patterns from the Larval Brain of Drosophila melanogaster.

    Science.gov (United States)

    Muenzing, Sascha E A; Strauch, Martin; Truman, James W; Bühler, Katja; Thum, Andreas S; Merhof, Dorit

    2018-01-01

    The larval brain of the fruit fly Drosophila melanogaster is a small, tractable model system for neuroscience. Genes for fluorescent marker proteins can be expressed in defined, spatially restricted neuron populations. Here, we introduce the methods for 1) generating a standard template of the larval central nervous system (CNS), 2) spatial mapping of expression patterns from different larvae into a reference space defined by the standard template. We provide a manually annotated gold standard that serves for evaluation of the registration framework involved in template generation and mapping. A method for registration quality assessment enables the automatic detection of registration errors, and a semi-automatic registration method allows one to correct registrations, which is a prerequisite for a high-quality, curated database of expression patterns. All computational methods are available within the larvalign software package: https://github.com/larvalign/larvalign/releases/tag/v1.0.

  15. An evaluation of chondrocyte morphology and gene expression on superhydrophilic vertically-aligned multi-walled carbon nanotube films.

    Science.gov (United States)

    Antonioli, Eliane; Lobo, Anderson O; Ferretti, Mario; Cohen, Moisés; Marciano, Fernanda R; Corat, Evaldo J; Trava-Airoldi, Vladimir J

    2013-03-01

    Cartilage serves as a low-friction and wear-resistant articulating surface in diarthrodial joints and is also important during early stages of bone remodeling. Recently, regenerative cartilage research has focused on combinations of cells paired with scaffolds. Superhydrophilic vertically aligned carbon nanotubes (VACNTs) are of particular interest in regenerative medicine. The aim of this study is to evaluate cell expansion of human articular chondrocytes on superhydrophilic VACNTs, as well as their morphology and gene expression. VACNT films were produced using a microwave plasma chamber on Ti substrates and submitted to an O2 plasma treatment to make them superhydrophilic. Human chondrocytes were cultivated on superhydrophilic VACNTs up to five days. Quantitative RT-PCR was performed to measure type I and type II Collagen, Sox9, and Aggrecan mRNA expression levels. The morphology was analyzed by scanning electron microscopy (SEM) and confocal microscopy. SEM images demonstrated that superhydrophilic VACNTs permit cell growth and adhesion of human chondrocytes. The chondrocytes had an elongated morphology with some prolongations. Chondrocytes cultivated on superhydrophilic VACNTs maintain the level expression of Aggrecan, Sox9, and Collagen II determined by qPCR. This study was the first to indicate that superhydrophilic VACNTs may be used as an efficient scaffold for cartilage or bone repair. Copyright © 2012 Elsevier B.V. All rights reserved.

  16. Unusual conservation of mitochondrial gene order in Crassostrea oysters: evidence for recent speciation in Asia

    Science.gov (United States)

    2010-01-01

    Background Oysters are morphologically plastic and hence difficult subjects for taxonomic and evolutionary studies. It is long been suspected, based on the extraordinary species diversity observed, that Asia Pacific is the epicenter of oyster speciation. To understand the species diversity and its evolutionary history, we collected five Crassostrea species from Asia and sequenced their complete mitochondrial (mt) genomes in addition to two newly released Asian oysters (C. iredalei and Saccostrea mordax) for a comprehensive analysis. Results The six Asian Crassostrea mt genomes ranged from 18,226 to 22,446 bp in size, and all coded for 39 genes (12 proteins, 2 rRNAs and 25 tRNAs) on the same strand. Their genomes contained a split of the rrnL gene and duplication of trnM, trnK and trnQ genes. They shared the same gene order that differed from an Atlantic sister species by as many as nine tRNA changes (6 transpositions and 3 duplications) and even differed significantly from S. mordax in protein-coding genes. Phylogenetic analysis indicates that the six Asian Crassostrea species emerged between 3 and 43 Myr ago, while the Atlantic species evolved 83 Myr ago. Conclusions The complete conservation of gene order in the six Asian Crassostrea species over 43 Myr is highly unusual given the remarkable rate of rearrangements in their sister species and other bivalves. It provides strong evidence for the recent speciation of the six Crassostrea species in Asia. It further indicates that changes in mt gene order may not be strictly a function of time but subject to other constraints that are presently not well understood. PMID:21189147

  17. A highly order-structured membrane electrode assembly with vertically aligned carbon nanotubes for ultra-low Pt loading PEM fuel cells

    Energy Technology Data Exchange (ETDEWEB)

    Tian, Zhi Qun; Lim, San Hua; Poh, Chee Kok; Lin, Jianyi [Institute of Chemical and Engineering Sciences, 1 Pesek Road, Jurong Island, Singapore 627833 (Singapore); Tang, Zhe; Chua, Daniel [Department of Materials Science and Engineering, National University of Singapore, Singapore 117542 (Singapore); Xia, Zetao [Institute of Materials Research and Engineering, 3 Research Link, Singapore 117602 (Singapore); Luo, Zhiqiang; Shen, Zexiang [Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore (Singapore); Shen, Pei Kang [State Key Laboratory of Optoelectronic Materials and Technologies, and Key Laboratory of Low-carbon Chemistry and Energy Conservation of Guangdong Province, School of Physics and Engineering, Sun Yat-sen University, Guangzhou, 510275 (China); Feng, Yuan Ping [Department of Physics, National University of Singapore, Singapore 117542 (Singapore)

    2011-11-15

    A simple method was developed to prepare ultra-low Pt loading membrane electrode assembly (MEA) using vertically aligned carbon nanotubes (VACNTs) as highly ordered catalyst support for PEM fuel cells application. In the method, VACNTs were directly grown on the cheap household aluminum foil by plasma enhanced chemical vapor deposition (PECVD), using Fe/Co bimetallic catalyst. By depositing a Pt thin layer on VACNTs/Al and subsequent hot pressing, Pt/VACNTs can be 100% transferred from Al foil onto polymer electrolyte membrane for the fabrication of MEA. The whole transfer process does not need any chemical removal and destroy membrane. The PEM fuel cell with the MEA fabricated using this method showed an excellent performance with ultra-low Pt loading down to 35 {mu}g cm{sup -2} which was comparable to that of the commercial Pt catalyst on carbon powder with 400 {mu}g cm{sup -2}. To the best of our knowledge, for the first time, we identified that it is possible to substantially reduce the Pt loading one order by application of order-structured electrode based on VACNTs as Pt catalysts support, compared with the traditional random electrode at a comparable performance through experimental and mathematical methods. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  18. 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

  19. Tumor Classification Using High-Order Gene Expression Profiles Based on Multilinear ICA

    Directory of Open Access Journals (Sweden)

    Ming-gang Du

    2009-01-01

    Full Text Available Motivation. Independent Components Analysis (ICA maximizes the statistical independence of the representational components of a training gene expression profiles (GEP ensemble, but it cannot distinguish relations between the different factors, or different modes, and it is not available to high-order GEP Data Mining. In order to generalize ICA, we introduce Multilinear-ICA and apply it to tumor classification using high order GEP. Firstly, we introduce the basis conceptions and operations of tensor and recommend Support Vector Machine (SVM classifier and Multilinear-ICA. Secondly, the higher score genes of original high order GEP are selected by using t-statistics and tabulate tensors. Thirdly, the tensors are performed by Multilinear-ICA. Finally, the SVM is used to classify the tumor subtypes. Results. To show the validity of the proposed method, we apply it to tumor classification using high order GEP. Though we only use three datasets, the experimental results show that the method is effective and feasible. Through this survey, we hope to gain some insight into the problem of high order GEP tumor classification, in aid of further developing more effective tumor classification algorithms.

  20. DNA impedance biosensor for detection of cancer, TP53 gene mutation, based on gold nanoparticles/aligned carbon nanotubes modified electrode.

    Science.gov (United States)

    Fayazfar, H; Afshar, A; Dolati, M; Dolati, A

    2014-07-11

    For the first time, a new platform based on electrochemical growth of Au nanoparticles on aligned multi-walled carbon nanotubes (A-MWCNT) was developed for sensitive lable-free DNA detection of the TP53 gene mutation, one of the most popular genes in cancer research. Electrochemical impedance spectroscopy (EIS) was used to monitor the sequence-specific DNA hybridization events related to TP53 gene. Compared to the bare Ta or MWCNT/Ta electrodes, the synergistic interactions of vertically aligned MWCNT array and gold nanoparticles at modified electrode could improve the density of the probe DNA attachment and resulting the sensitivity of the DNA sensor greatly. Using EIS, over the extended DNA concentration range, the change of charge transfer resistance was found to have a linear relationship in respect to the logarithm of the complementary oligonucleotides sequence concentrations in the wide range of 1.0×10(-15)-1.0×10(-7)M, with a detection limit of 1.0×10(-17)M (S/N=3). The prepared sensor also showed good stability (14 days), reproducibility (RSD=2.1%) and could be conveniently regenerated via dehybridization in hot water. The significant improvement in sensitivity illustrates that combining gold nanoparticles with the on-site fabricated aligned MWCNT array represents a promising platform for achieving sensitive biosensor for fast mutation screening related to most human cancer types. Copyright © 2014. Published by Elsevier B.V.

  1. Evolution of multicopper oxidase genes in coprophilous and non-coprophilous members of the order sordariales.

    Science.gov (United States)

    Pöggeler, Stefanie

    2011-04-01

    Multicopper oxidases (MCO) catalyze the biological oxidation of various aromatic substrates and have been identified in plants, insects, bacteria, and wood rotting fungi. In nature, they are involved in biodegradation of biopolymers such as lignin and humic compounds, but have also been tested for various industrial applications. In fungi, MCOs have been shown to play important roles during their life cycles, such as in fruiting body formation, pigment formation and pathogenicity. Coprophilous fungi, which grow on the dung of herbivores, appear to encode an unexpectedly high number of enzymes capable of at least partly degrading lignin. This study compared the MCO-coding capacity of the coprophilous filamentous ascomycetes Podospora anserina and Sordaria macrospora with closely related non-coprophilous members of the order Sordariales. An increase of MCO genes in coprophilic members of the Sordariales most probably occurred by gene duplication and horizontal gene transfer events.

  2. Gene order data from a model amphibian (Ambystoma: new perspectives on vertebrate genome structure and evolution

    Directory of Open Access Journals (Sweden)

    Voss S Randal

    2006-08-01

    Full Text Available Abstract Background Because amphibians arise from a branch of the vertebrate evolutionary tree that is juxtaposed between fishes and amniotes, they provide important comparative perspective for reconstructing character changes that have occurred during vertebrate evolution. Here, we report the first comparative study of vertebrate genome structure that includes a representative amphibian. We used 491 transcribed sequences from a salamander (Ambystoma genetic map and whole genome assemblies for human, mouse, rat, dog, chicken, zebrafish, and the freshwater pufferfish Tetraodon nigroviridis to compare gene orders and rearrangement rates. Results Ambystoma has experienced a rate of genome rearrangement that is substantially lower than mammalian species but similar to that of chicken and fish. Overall, we found greater conservation of genome structure between Ambystoma and tetrapod vertebrates, nevertheless, 57% of Ambystoma-fish orthologs are found in conserved syntenies of four or more genes. Comparisons between Ambystoma and amniotes reveal extensive conservation of segmental homology for 57% of the presumptive Ambystoma-amniote orthologs. Conclusion Our analyses suggest relatively constant interchromosomal rearrangement rates from the euteleost ancestor to the origin of mammals and illustrate the utility of amphibian mapping data in establishing ancestral amniote and tetrapod gene orders. Comparisons between Ambystoma and amniotes reveal some of the key events that have structured the human genome since diversification of the ancestral amniote lineage.

  3. Output ordering and prioritisation system (OOPS): ranking biosynthetic gene clusters to enhance bioactive metabolite discovery.

    Science.gov (United States)

    Peña, Alejandro; Del Carratore, Francesco; Cummings, Matthew; Takano, Eriko; Breitling, Rainer

    2017-12-18

    The rapid increase of publicly available microbial genome sequences has highlighted the presence of hundreds of thousands of biosynthetic gene clusters (BGCs) encoding valuable secondary metabolites. The experimental characterization of new BGCs is extremely laborious and struggles to keep pace with the in silico identification of potential BGCs. Therefore, the prioritisation of promising candidates among computationally predicted BGCs represents a pressing need. Here, we propose an output ordering and prioritisation system (OOPS) which helps sorting identified BGCs by a wide variety of custom-weighted biological and biochemical criteria in a flexible and user-friendly interface. OOPS facilitates a judicious prioritisation of BGCs using G+C content, coding sequence length, gene number, cluster self-similarity and codon bias parameters, as well as enabling the user to rank BGCs based upon BGC type, novelty, and taxonomic distribution. Effective prioritisation of BGCs will help to reduce experimental attrition rates and improve the breadth of bioactive metabolites characterized.

  4. 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.

  5. 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 ...

  6. TIR-NBS-LRR genes are rare in monocots: evidence from diverse monocot orders

    Directory of Open Access Journals (Sweden)

    Tarr D Ellen K

    2009-09-01

    Full Text Available Abstract Background Plant resistance (R gene products recognize pathogen effector molecules. Many R genes code for proteins containing nucleotide binding site (NBS and C-terminal leucine-rich repeat (LRR domains. NBS-LRR proteins can be divided into two groups, TIR-NBS-LRR and non-TIR-NBS-LRR, based on the structure of the N-terminal domain. Although both classes are clearly present in gymnosperms and eudicots, only non-TIR sequences have been found consistently in monocots. Since most studies in monocots have been limited to agriculturally important grasses, it is difficult to draw conclusions. The purpose of our study was to look for evidence of these sequences in additional monocot orders. Findings Using degenerate PCR, we amplified NBS sequences from four monocot species (C. blanda, D. marginata, S. trifasciata, and Spathiphyllum sp., a gymnosperm (C. revoluta and a eudicot (C. canephora. We successfully amplified TIR-NBS-LRR sequences from dicot and gymnosperm DNA, but not from monocot DNA. Using databases, we obtained NBS sequences from additional monocots, magnoliids and basal angiosperms. TIR-type sequences were not present in monocot or magnoliid sequences, but were present in the basal angiosperms. Phylogenetic analysis supported a single TIR clade and multiple non-TIR clades. Conclusion We were unable to find monocot TIR-NBS-LRR sequences by PCR amplification or database searches. In contrast to previous studies, our results represent five monocot orders (Poales, Zingiberales, Arecales, Asparagales, and Alismatales. Our results establish the presence of TIR-NBS-LRR sequences in basal angiosperms and suggest that although these sequences were present in early land plants, they have been reduced significantly in monocots and magnoliids.

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

    Directory of Open Access Journals (Sweden)

    Pereira Luísa

    2009-07-01

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

  8. Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phylogenetic and population studies

    Science.gov (United States)

    2011-01-01

    Background Copepods are highly diverse and abundant, resulting in extensive ecological radiation in marine ecosystems. Calanus sinicus dominates continental shelf waters in the northwest Pacific Ocean and plays an important role in the local ecosystem by linking primary production to higher trophic levels. A lack of effective molecular markers has hindered phylogenetic and population genetic studies concerning copepods. As they are genome-level informative, mitochondrial DNA sequences can be used as markers for population genetic studies and phylogenetic studies. Results The mitochondrial genome of C. sinicus is distinct from other arthropods owing to the concurrence of multiple non-coding regions and a reshuffled gene arrangement. Further particularities in the mitogenome of C. sinicus include low A + T-content, symmetrical nucleotide composition between strands, abbreviated stop codons for several PCGs and extended lengths of the genes atp6 and atp8 relative to other copepods. The monophyletic Copepoda should be placed within the Vericrustacea. The close affinity between Cyclopoida and Poecilostomatoida suggests reassigning the latter as subordinate to the former. Monophyly of Maxillopoda is rejected. Within the alignment of 11 C. sinicus mitogenomes, there are 397 variable sites harbouring three 'hotspot' variable sites and three microsatellite loci. Conclusion The occurrence of the circular subgenomic fragment during laboratory assays suggests that special caution should be taken when sequencing mitogenomes using long PCR. Such a phenomenon may provide additional evidence of mitochondrial DNA recombination, which appears to have been a prerequisite for shaping the present mitochondrial profile of C. sinicus during its evolution. The lack of synapomorphic gene arrangements among copepods has cast doubt on the utility of gene order as a useful molecular marker for deep phylogenetic analysis. However, mitochondrial genomic sequences have been valuable markers for

  9. Phylogeny and mitochondrial gene order variation in Lophotrochozoa in the light of new mitogenomic data from Nemertea

    Directory of Open Access Journals (Sweden)

    von Döhren Jörn

    2009-08-01

    Full Text Available Abstract Background The new animal phylogeny established several taxa which were not identified by morphological analyses, most prominently the Ecdysozoa (arthropods, roundworms, priapulids and others and Lophotrochozoa (molluscs, annelids, brachiopods and others. Lophotrochozoan interrelationships are under discussion, e.g. regarding the position of Nemertea (ribbon worms, which were discussed to be sister group to e.g. Mollusca, Brachiozoa or Platyhelminthes. Mitochondrial genomes contributed well with sequence data and gene order characters to the deep metazoan phylogeny debate. Results In this study we present the first complete mitochondrial genome record for a member of the Nemertea, Lineus viridis. Except two trnP and trnT, all genes are located on the same strand. While gene order is most similar to that of the brachiopod Terebratulina retusa, sequence based analyses of mitochondrial genes place nemerteans close to molluscs, phoronids and entoprocts without clear preference for one of these taxa as sister group. Conclusion Almost all recent analyses with large datasets show good support for a taxon comprising Annelida, Mollusca, Brachiopoda, Phoronida and Nemertea. But the relationships among these taxa vary between different studies. The analysis of gene order differences gives evidence for a multiple independent occurrence of a large inversion in the mitochondrial genome of Lophotrochozoa and a re-inversion of the same part in gastropods. We hypothesize that some regions of the genome have a higher chance for intramolecular recombination than others and gene order data have to be analysed carefully to detect convergent rearrangement events.

  10. Single-copy genes define a conserved order between rice and wheat for understanding differences caused by duplication, deletion, and transposition of genes.

    Science.gov (United States)

    Singh, Nagendra K; Dalal, Vivek; Batra, Kamlesh; Singh, Binay K; Chitra, G; Singh, Archana; Ghazi, Irfan A; Yadav, Mahavir; Pandit, Awadhesh; Dixit, Rekha; Singh, Pradeep K; Singh, Harvinder; Koundal, Kirpa R; Gaikwad, Kishor; Mohapatra, Trilochan; Sharma, Tilak R

    2007-01-01

    The high-quality rice genome sequence is serving as a reference for comparative genome analysis in crop plants, especially cereals. However, early comparisons with bread wheat showed complex patterns of conserved synteny (gene content) and colinearity (gene order). Here, we show the presence of ancient duplicated segments in the progenitor of wheat, which were first identified in the rice genome. We also show that single-copy (SC) rice genes, those representing unique matches with wheat expressed sequence tag (EST) unigene contigs in the whole rice genome, show more than twice the proportion of genes mapping to syntenic wheat chromosome as compared to the multicopy (MC) or duplicated rice genes. While 58.7% of the 1,244 mapped SC rice genes were located in single syntenic wheat chromosome groups, the remaining 41.3% were distributed randomly to the other six non-syntenic wheat groups. This could only be explained by a background dispersal of genes in the genome through transposition or other unknown mechanism. The breakdown of rice-wheat synteny due to such transpositions was much greater near the wheat centromeres. Furthermore, the SC rice genes revealed a conserved primordial gene order that gives clues to the origin of rice and wheat chromosomes from a common ancestor through polyploidy, aneuploidy, centromeric fusions, and translocations. Apart from the bin-mapped wheat EST contigs, we also compared 56,298 predicted rice genes with 39,813 wheat EST contigs assembled from 409,765 EST sequences and identified 7,241 SC rice gene homologs of wheat. Based on the conserved colinearity of 1,063 mapped SC rice genes across the bins of individual wheat chromosomes, we predicted the wheat bin location of 6,178 unmapped SC rice gene homologs and validated the location of 213 of these in the telomeric bins of 21 wheat chromosomes with 35.4% initial success. This opens up the possibility of directed mapping of a large number of conserved SC rice gene homologs in wheat

  11. Species-specific evolution of class I MHC genes in iguanas (order: Squamata; subfamily: Iguaninae).

    Science.gov (United States)

    Glaberman, Scott; Caccone, Adalgisa

    2008-07-01

    Over the last few decades, the major histocompatibility complex (MHC) has emerged as a model for understanding the influence of natural selection on genetic diversity in populations as well as for investigating the genetic basis of host resistance to pathogens. However, many vertebrate taxa remain underrepresented in the field of MHC research, preventing its application to studies of disease, evolution, and conservation genetics in these groups. This is particularly true for squamates, which are by far the most diversified order of non-avian reptiles but have not been the subject of any recent MHC studies. In this paper, we present MHC class I complementary DNA data from three squamate species in the subfamily Iguaninae (iguanas): the Galápagos marine iguana (Amblyrhynchus cristatus), the Galápagos land iguana (Conolophus subcristatus), and the green iguana (Iguana iguana). All sequences obtained are related to the few published class I genes from other squamates. There is evidence for multiple loci in each species, and the conserved alpha-3 domain appears to be evolving in a species-specific manner. Conversely, there is some indication of shared polymorphism between species in the peptide-binding alpha-1 and alpha-2 domains, suggesting that these two regions have different phylogenetic histories. The great similarity between alpha-3 sequences in marine iguanas in particular suggests that concerted evolution is acting to homogenize class I loci within species. However, while less likely, the data are also compatible with a birth and death model of evolution.

  12. Evolutionary novelty in gravity sensing through horizontal gene transfer and high-order protein assembly.

    Directory of Open Access Journals (Sweden)

    Tu Anh Nguyen

    2018-04-01

    Full Text Available Horizontal gene transfer (HGT can promote evolutionary adaptation by transforming a species' relationship to the environment. In most well-understood cases of HGT, acquired and donor functions appear to remain closely related. Thus, the degree to which HGT can lead to evolutionary novelties remains unclear. Mucorales fungi sense gravity through the sedimentation of vacuolar protein crystals. Here, we identify the octahedral crystal matrix protein (OCTIN. Phylogenetic analysis strongly supports acquisition of octin by HGT from bacteria. A bacterial OCTIN forms high-order periplasmic oligomers, and inter-molecular disulphide bonds are formed by both fungal and bacterial OCTINs, suggesting that they share elements of a conserved assembly mechanism. However, estimated sedimentation velocities preclude a gravity-sensing function for the bacterial structures. Together, our data suggest that HGT from bacteria into the Mucorales allowed a dramatic increase in assembly scale and emergence of the gravity-sensing function. We conclude that HGT can lead to evolutionary novelties that emerge depending on the physiological and cellular context of protein assembly.

  13. 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...

  14. 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...

  15. An Approximation to the Temporal Order in Endogenous Circadian Rhythms of Genes Implicated in Human Adipose Tissue Metabolism

    Science.gov (United States)

    GARAULET, MARTA; ORDOVÁS, JOSÉ M.; GÓMEZ-ABELLÁN, PURIFICACIÓN; MARTÍNEZ, JOSE A.; MADRID, JUAN A.

    2015-01-01

    Although it is well established that human adipose tissue (AT) shows circadian rhythmicity, published studies have been discussed as if tissues or systems showed only one or few circadian rhythms at a time. To provide an overall view of the internal temporal order of circadian rhythms in human AT including genes implicated in metabolic processes such as energy intake and expenditure, insulin resistance, adipocyte differentiation, dyslipidemia, and body fat distribution. Visceral and subcutaneous abdominal AT biopsies (n = 6) were obtained from morbid obese women (BMI ≥ 40 kg/m2). To investigate rhythmic expression pattern, AT explants were cultured during 24-h and gene expression was analyzed at the following times: 08:00, 14:00, 20:00, 02:00 h using quantitative real-time PCR. Clock genes, glucocorticoid metabolism-related genes, leptin, adiponectin and their receptors were studied. Significant differences were found both in achrophases and relative-amplitude among genes (P 30%). When interpreting the phase map of gene expression in both depots, data indicated that circadian rhythmicity of the genes studied followed a predictable physiological pattern, particularly for subcutaneous AT. Interesting are the relationships between adiponectin, leptin, and glucocorticoid metabolism-related genes circadian profiles. Their metabolic significance is discussed. Visceral AT behaved in a different way than subcutaneous for most of the genes studied. For every gene, protein mRNA levels fluctuated during the day in synchrony with its receptors. We have provided an overall view of the internal temporal order of circadian rhythms in human adipose tissue. PMID:21520059

  16. Mitochondrial genomes of Meloidogyne chitwoodi and M. incognita (Nematoda: Tylenchina): comparative analysis, gene order and phylogenetic relationships with other nematodes.

    Science.gov (United States)

    Humphreys-Pereira, Danny A; Elling, Axel A

    2014-01-01

    Root-knot nematodes (Meloidogyne spp.) are among the most important plant pathogens. In this study, the mitochondrial (mt) genomes of the root-knot nematodes, M. chitwoodi and M. incognita were sequenced. PCR analyses suggest that both mt genomes are circular, with an estimated size of 19.7 and 18.6-19.1kb, respectively. The mt genomes each contain a large non-coding region with tandem repeats and the control region. The mt gene arrangement of M. chitwoodi and M. incognita is unlike that of other nematodes. Sequence alignments of the two Meloidogyne mt genomes showed three translocations; two in transfer RNAs and one in cox2. Compared with other nematode mt genomes, the gene arrangement of M. chitwoodi and M. incognita was most similar to Pratylenchus vulnus. Phylogenetic analyses (Maximum Likelihood and Bayesian inference) were conducted using 78 complete mt genomes of diverse nematode species. Analyses based on nucleotides and amino acids of the 12 protein-coding mt genes showed strong support for the monophyly of class Chromadorea, but only amino acid-based analyses supported the monophyly of class Enoplea. The suborder Spirurina was not monophyletic in any of the phylogenetic analyses, contradicting the Clade III model, which groups Ascaridomorpha, Spiruromorpha and Oxyuridomorpha based on the small subunit ribosomal RNA gene. Importantly, comparisons of mt gene arrangement and tree-based methods placed Meloidogyne as sister taxa of Pratylenchus, a migratory plant endoparasitic nematode, and not with the sedentary endoparasitic Heterodera. Thus, comparative analyses of mt genomes suggest that sedentary endoparasitism in Meloidogyne and Heterodera is based on convergent evolution. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Revisiting the phylogeny of Zoanthidea (Cnidaria: Anthozoa): Staggered alignment of hypervariable sequences improves species tree inference.

    Science.gov (United States)

    Swain, Timothy D

    2018-01-01

    The recent rapid proliferation of novel taxon identification in the Zoanthidea has been accompanied by a parallel propagation of gene trees as a tool of species discovery, but not a corresponding increase in our understanding of phylogeny. This disparity is caused by the trade-off between the capabilities of automated DNA sequence alignment and data content of genes applied to phylogenetic inference in this group. Conserved genes or segments are easily aligned across the order, but produce poorly resolved trees; hypervariable genes or segments contain the evolutionary signal necessary for resolution and robust support, but sequence alignment is daunting. Staggered alignments are a form of phylogeny-informed sequence alignment composed of a mosaic of local and universal regions that allow phylogenetic inference to be applied to all nucleotides from both hypervariable and conserved gene segments. Comparisons between species tree phylogenies inferred from all data (staggered alignment) and hypervariable-excluded data (standard alignment) demonstrate improved confidence and greater topological agreement with other sources of data for the complete-data tree. This novel phylogeny is the most comprehensive to date (in terms of taxa and data) and can serve as an expandable tool for evolutionary hypothesis testing in the Zoanthidea. Spanish language abstract available in Text S1. Translation by L. O. Swain, DePaul University, Chicago, Illinois, 60604, USA. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. 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

  19. 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...

  20. The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations

    Directory of Open Access Journals (Sweden)

    Parmigiani Giovanni

    2009-08-01

    Full Text Available Abstract Background A major challenge in computational biology is to extract knowledge about the genetic nature of disease from high-throughput data. However, an important obstacle to both biological understanding and clinical applications is the "black box" nature of the decision rules provided by most machine learning approaches, which usually involve many genes combined in a highly complex fashion. Achieving biologically relevant results argues for a different strategy. A promising alternative is to base prediction entirely upon the relative expression ordering of a small number of genes. Results We present a three-gene version of "relative expression analysis" (RXA, a rigorous and systematic comparison with earlier approaches in a variety of cancer studies, a clinically relevant application to predicting germline BRCA1 mutations in breast cancer and a cross-study validation for predicting ER status. In the BRCA1 study, RXA yields high accuracy with a simple decision rule: in tumors carrying mutations, the expression of a "reference gene" falls between the expression of two differentially expressed genes, PPP1CB and RNF14. An analysis of the protein-protein interactions among the triplet of genes and BRCA1 suggests that the classifier has a biological foundation. Conclusion RXA has the potential to identify genomic "marker interactions" with plausible biological interpretation and direct clinical applicability. It provides a general framework for understanding the roles of the genes involved in decision rules, as illustrated for the difficult and clinically relevant problem of identifying BRCA1 mutation carriers.

  1. Analysis of an ordered, comprehensive STM mutant library in infectious Borrelia burgdorferi: insights into the genes required for mouse infectivity.

    Directory of Open Access Journals (Sweden)

    Tao Lin

    Full Text Available The identification of genes important in the pathogenesis of Lyme disease Borrelia has been hampered by exceedingly low transformation rates in low-passage, infectious organisms. Using the infectious, moderately transformable B. burgdorferi derivative 5A18NP1 and signature-tagged versions of the Himar1 transposon vector pGKT, we have constructed a defined transposon library for the efficient genome-wide investigation of genes required for wild-type pathogenesis, in vitro growth, physiology, morphology, and plasmid replication. To facilitate analysis, the insertion sites of 4,479 transposon mutants were determined by sequencing. The transposon insertions were widely distributed across the entire B. burgdorferi genome, with an average of 2.68 unique insertion sites per kb DNA. The 10 linear plasmids and 9 circular plasmids had insertions in 33 to 100 percent of their predicted genes. In contrast, only 35% of genes in the 910 kb linear chromosome had incapacitating insertions; therefore, the remaining 601 chromosomal genes may represent essential gene candidates. In initial signature-tagged mutagenesis (STM analyses, 434 mutants were examined at multiple tissue sites for infectivity in mice using a semi-quantitative, Luminex-based DNA detection method. Examples of genes found to be important in mouse infectivity included those involved in motility, chemotaxis, the phosphoenolpyruvate phosphotransferase system, and other transporters, as well as putative plasmid maintenance genes. Availability of this ordered STM library and a high-throughput screening method is expected to lead to efficient assessment of the roles of B. burgdorferi genes in the infectious cycle and pathogenesis of Lyme disease.

  2. Independent losses of visual perception genes Gja10 and Rbp3 in echolocating bats (Order: Chiroptera.

    Directory of Open Access Journals (Sweden)

    Bin Shen

    Full Text Available A trade-off between the sensory modalities of vision and hearing is likely to have occurred in echolocating bats as the sophisticated mechanism of laryngeal echolocation requires considerable neural processing and has reduced the reliance of echolocating bats on vision for perceiving the environment. If such a trade-off exists, it is reasonable to hypothesize that some genes involved in visual function may have undergone relaxed selection or even functional loss in echolocating bats. The Gap junction protein, alpha 10 (Gja10, encoded by Gja10 gene is expressed abundantly in mammal retinal horizontal cells and plays an important role in horizontal cell coupling. The interphotoreceptor retinoid-binding protein (Irbp, encoded by the Rbp3 gene is mainly expressed in interphotoreceptor matrix and is known to be critical for normal functioning of the visual cycle. We sequenced Gja10 and Rbp3 genes in a taxonomically wide range of bats with divergent auditory characteristics (35 and 18 species for Gja10 and Rbp3, respectively. Both genes have became pseudogenes in species from the families Hipposideridae and Rhinolophidae that emit constant frequency echolocation calls with Doppler shift compensation at high-duty-cycles (the most sophisticated form of biosonar known, and in some bat species that emit echolocation calls at low-duty-cycles. Our study thus provides further evidence for the hypothesis that a trade-off occurs at the genetic level between vision and echolocation in bats.

  3. Independent losses of visual perception genes Gja10 and Rbp3 in echolocating bats (Order: Chiroptera).

    Science.gov (United States)

    Shen, Bin; Fang, Tao; Dai, Mengyao; Jones, Gareth; Zhang, Shuyi

    2013-01-01

    A trade-off between the sensory modalities of vision and hearing is likely to have occurred in echolocating bats as the sophisticated mechanism of laryngeal echolocation requires considerable neural processing and has reduced the reliance of echolocating bats on vision for perceiving the environment. If such a trade-off exists, it is reasonable to hypothesize that some genes involved in visual function may have undergone relaxed selection or even functional loss in echolocating bats. The Gap junction protein, alpha 10 (Gja10, encoded by Gja10 gene) is expressed abundantly in mammal retinal horizontal cells and plays an important role in horizontal cell coupling. The interphotoreceptor retinoid-binding protein (Irbp, encoded by the Rbp3 gene) is mainly expressed in interphotoreceptor matrix and is known to be critical for normal functioning of the visual cycle. We sequenced Gja10 and Rbp3 genes in a taxonomically wide range of bats with divergent auditory characteristics (35 and 18 species for Gja10 and Rbp3, respectively). Both genes have became pseudogenes in species from the families Hipposideridae and Rhinolophidae that emit constant frequency echolocation calls with Doppler shift compensation at high-duty-cycles (the most sophisticated form of biosonar known), and in some bat species that emit echolocation calls at low-duty-cycles. Our study thus provides further evidence for the hypothesis that a trade-off occurs at the genetic level between vision and echolocation in bats.

  4. The Order Bacillales Hosts Functional Homologs of the Worrisome cfr Antibiotic Resistance Gene

    DEFF Research Database (Denmark)

    Hansen, Lykke H.; Planellas, Mercè H.; Long, Katherine S.

    2012-01-01

    The cfr gene encodes the Cfr methyltransferase that methylates a single adenine in the peptidyl transferase region of bacterial ribosomes. The methylation provides resistance to several classes of antibiotics that include drugs of clinical and veterinary importance. This paper describes a first...

  5. 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...

  6. 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...

  7. 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.

  8. Mitochondrial Genomes of Kinorhyncha: trnM Duplication and New Gene Orders within Animals

    OpenAIRE

    Popova, Olga V.; Mikhailov, Kirill V.; Nikitin, Mikhail A.; Logacheva, Maria D.; Penin, Aleksey A.; Muntyan, Maria S.; Kedrova, Olga S.; Petrov, Nikolai B.; Panchin, Yuri V.; Aleoshin, Vladimir V.

    2016-01-01

    Many features of mitochondrial genomes of animals, such as patterns of gene arrangement, nucleotide content and substitution rate variation are extensively used in evolutionary and phylogenetic studies. Nearly 6,000 mitochondrial genomes of animals have already been sequenced, covering the majority of animal phyla. One of the groups that escaped mitogenome sequencing is phylum Kinorhyncha-an isolated taxon of microscopic worm-like ecdysozoans. The kinorhynchs are thought to be one of the earl...

  9. A damped oscillator imposes temporal order on posterior gap gene expression in Drosophila

    Science.gov (United States)

    Verd, Berta; Clark, Erik; Wotton, Karl R.; Janssens, Hilde; Jiménez-Guri, Eva; Crombach, Anton

    2018-01-01

    Insects determine their body segments in two different ways. Short-germband insects, such as the flour beetle Tribolium castaneum, use a molecular clock to establish segments sequentially. In contrast, long-germband insects, such as the vinegar fly Drosophila melanogaster, determine all segments simultaneously through a hierarchical cascade of gene regulation. Gap genes constitute the first layer of the Drosophila segmentation gene hierarchy, downstream of maternal gradients such as that of Caudal (Cad). We use data-driven mathematical modelling and phase space analysis to show that shifting gap domains in the posterior half of the Drosophila embryo are an emergent property of a robust damped oscillator mechanism, suggesting that the regulatory dynamics underlying long- and short-germband segmentation are much more similar than previously thought. In Tribolium, Cad has been proposed to modulate the frequency of the segmentation oscillator. Surprisingly, our simulations and experiments show that the shift rate of posterior gap domains is independent of maternal Cad levels in Drosophila. Our results suggest a novel evolutionary scenario for the short- to long-germband transition and help explain why this transition occurred convergently multiple times during the radiation of the holometabolan insects. PMID:29451884

  10. Aligned Layers of Silver Nano-Fibers

    Directory of Open Access Journals (Sweden)

    Andrii B. Golovin

    2012-02-01

    Full Text Available We describe a new dichroic polarizers made by ordering silver nano-fibers to aligned layers. The aligned layers consist of nano-fibers and self-assembled molecular aggregates of lyotropic liquid crystals. Unidirectional alignment of the layers is achieved by means of mechanical shearing. Aligned layers of silver nano-fibers are partially transparent to a linearly polarized electromagnetic radiation. The unidirectional alignment and density of the silver nano-fibers determine degree of polarization of transmitted light. The aligned layers of silver nano-fibers might be used in optics, microwave applications, and organic electronics.

  11. 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

  12. Using ESTs for phylogenomics: Can one accurately infer a phylogenetic tree from a gappy alignment?

    Directory of Open Access Journals (Sweden)

    Hartmann Stefanie

    2008-03-01

    Full Text Available Abstract Background While full genome sequences are still only available for a handful of taxa, large collections of partial gene sequences are available for many more. The alignment of partial gene sequences results in a multiple sequence alignment containing large gaps that are arranged in a staggered pattern. The consequences of this pattern of missing data on the accuracy of phylogenetic analysis are not well understood. We conducted a simulation study to determine the accuracy of phylogenetic trees obtained from gappy alignments using three commonly used phylogenetic reconstruction methods (Neighbor Joining, Maximum Parsimony, and Maximum Likelihood and studied ways to improve the accuracy of trees obtained from such datasets. Results We found that the pattern of gappiness in multiple sequence alignments derived from partial gene sequences substantially compromised phylogenetic accuracy even in the absence of alignment error. The decline in accuracy was beyond what would be expected based on the amount of missing data. The decline was particularly dramatic for Neighbor Joining and Maximum Parsimony, where the majority of gappy alignments contained 25% to 40% incorrect quartets. To improve the accuracy of the trees obtained from a gappy multiple sequence alignment, we examined two approaches. In the first approach, alignment masking, potentially problematic columns and input sequences are excluded from from the dataset. Even in the absence of alignment error, masking improved phylogenetic accuracy up to 100-fold. However, masking retained, on average, only 83% of the input sequences. In the second approach, alignment subdivision, the missing data is statistically modelled in order to retain as many sequences as possible in the phylogenetic analysis. Subdivision resulted in more modest improvements to alignment accuracy, but succeeded in including almost all of the input sequences. Conclusion These results demonstrate that partial gene

  13. Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?

    Science.gov (United States)

    Hartmann, Stefanie; Vision, Todd J

    2008-03-26

    While full genome sequences are still only available for a handful of taxa, large collections of partial gene sequences are available for many more. The alignment of partial gene sequences results in a multiple sequence alignment containing large gaps that are arranged in a staggered pattern. The consequences of this pattern of missing data on the accuracy of phylogenetic analysis are not well understood. We conducted a simulation study to determine the accuracy of phylogenetic trees obtained from gappy alignments using three commonly used phylogenetic reconstruction methods (Neighbor Joining, Maximum Parsimony, and Maximum Likelihood) and studied ways to improve the accuracy of trees obtained from such datasets. We found that the pattern of gappiness in multiple sequence alignments derived from partial gene sequences substantially compromised phylogenetic accuracy even in the absence of alignment error. The decline in accuracy was beyond what would be expected based on the amount of missing data. The decline was particularly dramatic for Neighbor Joining and Maximum Parsimony, where the majority of gappy alignments contained 25% to 40% incorrect quartets. To improve the accuracy of the trees obtained from a gappy multiple sequence alignment, we examined two approaches. In the first approach, alignment masking, potentially problematic columns and input sequences are excluded from from the dataset. Even in the absence of alignment error, masking improved phylogenetic accuracy up to 100-fold. However, masking retained, on average, only 83% of the input sequences. In the second approach, alignment subdivision, the missing data is statistically modelled in order to retain as many sequences as possible in the phylogenetic analysis. Subdivision resulted in more modest improvements to alignment accuracy, but succeeded in including almost all of the input sequences. These results demonstrate that partial gene sequences and gappy multiple sequence alignments can pose a

  14. Progressive multiple sequence alignments from triplets

    Directory of Open Access Journals (Sweden)

    Stadler Peter F

    2007-07-01

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

  15. 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.

  16. The complete mitochondrial genomes of three parasitic nematodes of birds: a unique gene order and insights into nematode phylogeny

    Science.gov (United States)

    2013-01-01

    Background Analyses of mitochondrial (mt) genome sequences in recent years challenge the current working hypothesis of Nematoda phylogeny proposed from morphology, ecology and nuclear small subunit rRNA gene sequences, and raise the need to sequence additional mt genomes for a broad range of nematode lineages. Results We sequenced the complete mt genomes of three Ascaridia species (family Ascaridiidae) that infest chickens, pigeons and parrots, respectively. These three Ascaridia species have an identical arrangement of mt genes to each other but differ substantially from other nematodes. Phylogenetic analyses of the mt genome sequences of the Ascaridia species, together with 62 other nematode species, support the monophylies of seven high-level taxa of the phylum Nematoda: 1) the subclass Dorylaimia; 2) the orders Rhabditida, Trichinellida and Mermithida; 3) the suborder Rhabditina; and 4) the infraorders Spiruromorpha and Oxyuridomorpha. Analyses of mt genome sequences, however, reject the monophylies of the suborders Spirurina and Tylenchina, and the infraorders Rhabditomorpha, Panagrolaimomorpha and Tylenchomorpha. Monophyly of the infraorder Ascaridomorpha varies depending on the methods of phylogenetic analysis. The Ascaridomorpha was more closely related to the infraorders Rhabditomorpha and Diplogasteromorpha (suborder Rhabditina) than they were to the other two infraorders of the Spirurina: Oxyuridorpha and Spiruromorpha. The closer relationship among Ascaridomorpha, Rhabditomorpha and Diplogasteromorpha was also supported by a shared common pattern of mitochondrial gene arrangement. Conclusions Analyses of mitochondrial genome sequences and gene arrangement has provided novel insights into the phylogenetic relationships among several major lineages of nematodes. Many lineages of nematodes, however, are underrepresented or not represented in these analyses. Expanding taxon sampling is necessary for future phylogenetic studies of nematodes with mt genome

  17. Deducing the temporal order of cofactor function in ligand-regulated gene transcription: theory and experimental verification.

    Science.gov (United States)

    Dougherty, Edward J; Guo, Chunhua; Simons, S Stoney; Chow, Carson C

    2012-01-01

    Cofactors are intimately involved in steroid-regulated gene expression. Two critical questions are (1) the steps at which cofactors exert their biological activities and (2) the nature of that activity. Here we show that a new mathematical theory of steroid hormone action can be used to deduce the kinetic properties and reaction sequence position for the functioning of any two cofactors relative to a concentration limiting step (CLS) and to each other. The predictions of the theory, which can be applied using graphical methods similar to those of enzyme kinetics, are validated by obtaining internally consistent data for pair-wise analyses of three cofactors (TIF2, sSMRT, and NCoR) in U2OS cells. The analysis of TIF2 and sSMRT actions on GR-induction of an endogenous gene gave results identical to those with an exogenous reporter. Thus new tools to determine previously unobtainable information about the nature and position of cofactor action in any process displaying first-order Hill plot kinetics are now available.

  18. 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...

  19. Evaluating hepatocellular carcinoma cell lines for tumour samples using within-sample relative expression orderings of genes.

    Science.gov (United States)

    Ao, Lu; Guo, You; Song, Xuekun; Guan, Qingzhou; Zheng, Weicheng; Zhang, Jiahui; Huang, Haiyan; Zou, Yi; Guo, Zheng; Wang, Xianlong

    2017-11-01

    Concerns are raised about the representativeness of cell lines for tumours due to the culture environment and misidentification. Liver is a major metastatic destination of many cancers, which might further confuse the origin of hepatocellular carcinoma cell lines. Therefore, it is of crucial importance to understand how well they can represent hepatocellular carcinoma. The HCC-specific gene pairs with highly stable relative expression orderings in more than 99% of hepatocellular carcinoma but with reversed relative expression orderings in at least 99% of one of the six types of cancer, colorectal carcinoma, breast carcinoma, non-small-cell lung cancer, gastric carcinoma, pancreatic carcinoma and ovarian carcinoma, were identified. With the simple majority rule, the HCC-specific relative expression orderings from comparisons with colorectal carcinoma and breast carcinoma could exactly discriminate primary hepatocellular carcinoma samples from both primary colorectal carcinoma and breast carcinoma samples. Especially, they correctly classified more than 90% of liver metastatic samples from colorectal carcinoma and breast carcinoma to their original tumours. Finally, using these HCC-specific relative expression orderings from comparisons with six cancer types, we identified eight of 24 hepatocellular carcinoma cell lines in the Cancer Cell Line Encyclopedia (Huh-7, Huh-1, HepG2, Hep3B, JHH-5, JHH-7, C3A and Alexander cells) that are highly representative of hepatocellular carcinoma. Evaluated with a REOs-based prognostic signature for hepatocellular carcinoma, all these eight cell lines showed the same metastatic properties of the high-risk metastatic hepatocellular carcinoma tissues. Caution should be taken for using hepatocellular carcinoma cell lines. Our results should be helpful to select proper hepatocellular carcinoma cell lines for biological experiments. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  20. 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)

  1. Chromatic bifocus alignment system for SR stepper

    International Nuclear Information System (INIS)

    Miyatake, Tsutomu

    1991-01-01

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

  2. 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...

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. Noisy: Identification of problematic columns in multiple sequence alignments

    Directory of Open Access Journals (Sweden)

    Grünewald Stefan

    2008-06-01

    Full Text Available Abstract Motivation Sequence-based methods for phylogenetic reconstruction from (nucleic acid sequence data are notoriously plagued by two effects: homoplasies and alignment errors. Large evolutionary distances imply a large number of homoplastic sites. As most protein-coding genes show dramatic variations in substitution rates that are not uncorrelated across the sequence, this often leads to a patchwork pattern of (i phylogenetically informative and (ii effectively randomized regions. In highly variable regions, furthermore, alignment errors accumulate resulting in sometimes misleading signals in phylogenetic reconstruction. Results We present here a method that, based on assessing the distribution of character states along a cyclic ordering of the taxa, allows the identification of phylogenetically uninformative homoplastic sites in a multiple sequence alignment. Removal of these sites appears to improve the performance of phylogenetic reconstruction algorithms as measured by various indices of "tree quality". In particular, we obtain more stable trees due to the exclusion of phylogenetically incompatible sites that most likely represent strongly randomized characters. Software The computer program noisy implements this approach. It can be employed to improving phylogenetic reconstruction capability with quite a considerable success rate whenever (1 the average bootstrap support obtained from the original alignment is low, and (2 there are sufficiently many taxa in the data set – at least, say, 12 to 15 taxa. The software can be obtained under the GNU Public License from http://www.bioinf.uni-leipzig.de/Software/noisy/.

  8. 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...

  9. 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 ...

  10. New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing

    Czech Academy of Sciences Publication Activity Database

    Helguera, M.; Rivarola, M.; Clavijo, B.; Martis, M.M.; Vanzetti, L.S.; Gonzalez, S.; Garbus, I.; LeRoy, P.; Šimková, Hana; Valárik, Miroslav; Caccamo, M.; Doležel, Jaroslav; Mayer, K. F. X.; Feuillet, C.; Tranquilli, G.; Paniego, N.; Echenique, V.

    2015-01-01

    Roč. 233, APR 2015 (2015), s. 200-212 ISSN 0168-9452 R&D Projects: GA ČR GBP501/12/G090; GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : Chromosome 4D survey sequence * Gene annotation * Gene content Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.362, year: 2015

  11. 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.

  12. The distribution, diversity, and importance of 16S rRNA gene introns in the order Thermoproteales.

    Science.gov (United States)

    Jay, Zackary J; Inskeep, William P

    2015-07-09

    Intron sequences are common in 16S rRNA genes of specific thermophilic lineages of Archaea, specifically the Thermoproteales (phylum Crenarchaeota). Environmental sequencing (16S rRNA gene and metagenome) from geothermal habitats in Yellowstone National Park (YNP) has expanded the available datasets for investigating 16S rRNA gene introns. The objectives of this study were to characterize and curate archaeal 16S rRNA gene introns from high-temperature habitats, evaluate the conservation and distribution of archaeal 16S rRNA introns in geothermal systems, and determine which "universal" archaeal 16S rRNA gene primers are impacted by the presence of intron sequences. Several new introns were identified and their insertion loci were constrained to thirteen locations across the 16S rRNA gene. Many of these introns encode homing endonucleases, although some introns were short or partial sequences. Pyrobaculum, Thermoproteus, and Caldivirga 16S rRNA genes contained the most abundant and diverse intron sequences. Phylogenetic analysis of introns revealed that sequences within the same locus are distributed biogeographically. The most diverse set of introns were observed in a high-temperature, circumneutral (pH 6) sulfur sediment environment, which also contained the greatest diversity of different Thermoproteales phylotypes. The widespread presence of introns in the Thermoproteales indicates a high probability of misalignments using different "universal" 16S rRNA primers employed in environmental microbial community analysis.

  13. The complete mitochondrial genome of the common sea slater, Ligia oceanica (Crustacea, Isopoda bears a novel gene order and unusual control region features

    Directory of Open Access Journals (Sweden)

    Podsiadlowski Lars

    2006-09-01

    Full Text Available Abstract Background Sequence data and other characters from mitochondrial genomes (gene translocations, secondary structure of RNA molecules are useful in phylogenetic studies among metazoan animals from population to phylum level. Moreover, the comparison of complete mitochondrial sequences gives valuable information about the evolution of small genomes, e.g. about different mechanisms of gene translocation, gene duplication and gene loss, or concerning nucleotide frequency biases. The Peracarida (gammarids, isopods, etc. comprise about 21,000 species of crustaceans, living in many environments from deep sea floor to arid terrestrial habitats. Ligia oceanica is a terrestrial isopod living at rocky seashores of the european North Sea and Atlantic coastlines. Results The study reveals the first complete mitochondrial DNA sequence from a peracarid crustacean. The mitochondrial genome of Ligia oceanica is a circular double-stranded DNA molecule, with a size of 15,289 bp. It shows several changes in mitochondrial gene order compared to other crustacean species. An overview about mitochondrial gene order of all crustacean taxa yet sequenced is also presented. The largest non-coding part (the putative mitochondrial control region of the mitochondrial genome of Ligia oceanica is unexpectedly not AT-rich compared to the remainder of the genome. It bears two repeat regions (4× 10 bp and 3× 64 bp, and a GC-rich hairpin-like secondary structure. Some of the transfer RNAs show secondary structures which derive from the usual cloverleaf pattern. While some tRNA genes are putative targets for RNA editing, trnR could not be localized at all. Conclusion Gene order is not conserved among Peracarida, not even among isopods. The two isopod species Ligia oceanica and Idotea baltica show a similarly derived gene order, compared to the arthropod ground pattern and to the amphipod Parhyale hawaiiensis, suggesting that most of the translocation events were already

  14. 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, ...

  15. 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

  16. 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.

  17. 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

  18. The complete mitogenome of the whale shark parasitic copepod Pandarus rhincodonicus norman, Newbound & Knott (Crustacea; Siphonostomatoida; Pandaridae)--a new gene order for the copepoda.

    Science.gov (United States)

    Austin, Christopher M; Tan, Mun Hua; Lee, Yin Peng; Croft, Laurence J; Meekan, Mark G; Pierce, Simon J; Gan, Han Ming

    2016-01-01

    The complete mitochondrial genome of the parasitic copepod Pandarus rhincodonicus was obtained from a partial genome scan using the HiSeq sequencing system. The Pandarus rhincodonicus mitogenome has 14,480 base pairs (62% A+T content) made up of 12 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a putative 384 bp non-coding AT-rich region. This Pandarus mitogenome sequence is the first for the family Pandaridae, the second for the order Siphonostomatoida and the sixth for the Copepoda.

  19. ALIGNMENTS OF GROUP GALAXIES WITH NEIGHBORING GROUPS

    International Nuclear Information System (INIS)

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

    2009-01-01

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

  20. Parallel and convergent evolution of the dim-light vision gene RH1 in bats (Order: Chiroptera).

    Science.gov (United States)

    Shen, Yong-Yi; Liu, Jie; Irwin, David M; Zhang, Ya-Ping

    2010-01-21

    Rhodopsin, encoded by the gene Rhodopsin (RH1), is extremely sensitive to light, and is responsible for dim-light vision. Bats are nocturnal mammals that inhabit poor light environments. Megabats (Old-World fruit bats) generally have well-developed eyes, while microbats (insectivorous bats) have developed echolocation and in general their eyes were degraded, however, dramatic differences in the eyes, and their reliance on vision, exist in this group. In this study, we examined the rod opsin gene (RH1), and compared its evolution to that of two cone opsin genes (SWS1 and M/LWS). While phylogenetic reconstruction with the cone opsin genes SWS1 and M/LWS generated a species tree in accord with expectations, the RH1 gene tree united Pteropodidae (Old-World fruit bats) and Yangochiroptera, with very high bootstrap values, suggesting the possibility of convergent evolution. The hypothesis of convergent evolution was further supported when nonsynonymous sites or amino acid sequences were used to construct phylogenies. Reconstructed RH1 sequences at internal nodes of the bat species phylogeny showed that: (1) Old-World fruit bats share an amino acid change (S270G) with the tomb bat; (2) Miniopterus share two amino acid changes (V104I, M183L) with Rhinolophoidea; (3) the amino acid replacement I123V occurred independently on four branches, and the replacements L99M, L266V and I286V occurred each on two branches. The multiple parallel amino acid replacements that occurred in the evolution of bat RH1 suggest the possibility of multiple convergences of their ecological specialization (i.e., various photic environments) during adaptation for the nocturnal lifestyle, and suggest that further attention is needed on the study of the ecology and behavior of bats.

  1. Origin and higher-level diversification of acariform mites - evidence from nuclear ribosomal genes, extensive taxon sampling, and secondary structure alignment.

    Science.gov (United States)

    Pepato, A R; Klimov, P B

    2015-09-02

    traditionally regarded as the sister-group to Bdelloidea (Eupodina), but our analyses show their close relationships to Parasitengona. Non-trivial relationships recovered by our analyses with high support (i.e., basal arrangement of endeostigmatid lineages, the position of marine mites, polyphyly of Eupodina) had been proposed by previous underappreciated morphological studies. Thus, we update currently the accepted taxonomic classification to reflect these results: the superfamily Halacaroidea Murray, 1877 is moved from the infraorder Eupodina Krantz, 1978 to Anystina van der Hammen, 1972; and the subfamily Erythracarinae Oudemans, 1936 (formerly in Anystidae Oudemans, 1902) is elevated to family rank, Erythracaridae stat. ressur., leaving Anystidae only with the nominal subfamily. Our study also shows that a clade comprising early derivative Endeostigmata (Alycidae, Nanorchestidae, Nematalycidae, and maybe Alicorhagiidae) should be treated as a taxon with the same rank as Sarcoptiformes and Trombidiformes, and the scope of the superfamily Bdelloidea should be changed. Before turning those findings into nomenclatural changes, however, we consider that our study calls for (i) finding shared apomorphies of the early derivative Endeostigmata clade and the clade including the remaining Acariformes; (ii) a well-supported hypothesis for Alicorhagiidae placement; (iii) sampling the families Proterorhagiidae, Proteonematalycidae and Grandjeanicidae not yet included in molecular analyses; (iv) undertake a denser sampling of clades traditionally placed in Eupodina, Anystina (Trombidiformes) and Palaeosomata (Sarcoptiformes), since consensus networks and Internode certainty (IC) and IC All (ICA) indices indicate high levels of conflict in these tree regions. Our study shows that regions of ambiguous alignment may provide useful phylogenetic signal when secondary structure information is used to guide the alignment procedure and provides an R implementation to the Bayesian Relative Rates

  2. 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...

  3. 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...

  4. Digging deeper: new gene order rearrangements and distinct patterns of codons usage in mitochondrial genomes among shrimps from the Axiidea, Gebiidea and Caridea (Crustacea: Decapoda

    Directory of Open Access Journals (Sweden)

    Mun Hua Tan

    2017-03-01

    Full Text Available Background Whole mitochondrial DNA is being increasingly utilized for comparative genomic and phylogenetic studies at deep and shallow evolutionary levels for a range of taxonomic groups. Although mitogenome sequences are deposited at an increasing rate into public databases, their taxonomic representation is unequal across major taxonomic groups. In the case of decapod crustaceans, several infraorders, including Axiidea (ghost shrimps, sponge shrimps, and mud lobsters and Caridea (true shrimps are still under-represented, limiting comprehensive phylogenetic studies that utilize mitogenomic information. Methods Sequence reads from partial genome scans were generated using the Illumina MiSeq platform and mitogenome sequences were assembled from these low coverage reads. In addition to examining phylogenetic relationships within the three infraorders, Axiidea, Gebiidea, and Caridea, we also investigated the diversity and frequency of codon usage bias and mitogenome gene order rearrangements. Results We present new mitogenome sequences for five shrimp species from Australia that includes two ghost shrimps, Callianassa ceramica and Trypaea australiensis, along with three caridean shrimps, Macrobrachium bullatum, Alpheus lobidens, and Caridina cf. nilotica. Strong differences in codon usage were discovered among the three infraorders and significant gene order rearrangements were observed. While the gene order rearrangements are congruent with the inferred phylogenetic relationships and consistent with taxonomic classification, they are unevenly distributed within and among the three infraorders. Discussion Our findings suggest potential for mitogenome rearrangements to be useful phylogenetic markers for decapod crustaceans and at the same time raise important questions concerning the drivers of mitogenome evolution in different decapod crustacean lineages.

  5. Unscented Kalman filter for SINS alignment

    Institute of Scientific and Technical Information of China (English)

    Zhou Zhanxin; Gao Yanan; Chen Jiabin

    2007-01-01

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

  6. Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition

    Directory of Open Access Journals (Sweden)

    O'Brien Kimberly

    2008-06-01

    Full Text Available Abstract Background The Solanaceae family contains a number of important crop species including potato (Solanum tuberosum which is grown for its underground storage organ known as a tuber. Albeit the 4th most important food crop in the world, other than a collection of ~220,000 Expressed Sequence Tags, limited genomic sequence information is currently available for potato and advances in potato yield and nutrition content would be greatly assisted through access to a complete genome sequence. While morphologically diverse, Solanaceae species such as potato, tomato, pepper, and eggplant share not only genes but also gene order thereby permitting highly informative comparative genomic analyses. Results In this study, we report on analysis 89.9 Mb of potato genomic sequence representing 10.2% of the genome generated through end sequencing of a potato bacterial artificial chromosome (BAC clone library (87 Mb and sequencing of 22 potato BAC clones (2.9 Mb. The GC content of potato is very similar to Solanum lycopersicon (tomato and other dicotyledonous species yet distinct from the monocotyledonous grass species, Oryza sativa. Parallel analyses of repetitive sequences in potato and tomato revealed substantial differences in their abundance, 34.2% in potato versus 46.3% in tomato, which is consistent with the increased genome size per haploid genome of these two Solanum species. Specific classes and types of repetitive sequences were also differentially represented between these two species including a telomeric-related repetitive sequence, ribosomal DNA, and a number of unclassified repetitive sequences. Comparative analyses between tomato and potato at the gene level revealed a high level of conservation of gene content, genic feature, and gene order although discordances in synteny were observed. Conclusion Genomic level analyses of potato and tomato confirm that gene sequence and gene order are conserved between these solanaceous species and that

  7. 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...

  8. 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...

  9. 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...

  10. An approximation to the temporal order in endogenous circadian rhythms of genes implicated in human adipose tissue metabolism

    Science.gov (United States)

    Although it is well established that human adipose tissue (AT) shows circadian rhythmicity, published studies have been discussed as if tissues or systems showed only one or few circadian rhythms at a time. To provide an overall view of the internal temporal order of circadian rhythms in human AT in...

  11. Mitochondrial and nuclear genes suggest that stony corals are monophyletic but most families of stony corals are not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria.

    Directory of Open Access Journals (Sweden)

    Hironobu Fukami

    Full Text Available Modern hard corals (Class Hexacorallia; Order Scleractinia are widely studied because of their fundamental role in reef building and their superb fossil record extending back to the Triassic. Nevertheless, interpretations of their evolutionary relationships have been in flux for over a decade. Recent analyses undermine the legitimacy of traditional suborders, families and genera, and suggest that a non-skeletal sister clade (Order Corallimorpharia might be imbedded within the stony corals. However, these studies either sampled a relatively limited array of taxa or assembled trees from heterogeneous data sets. Here we provide a more comprehensive analysis of Scleractinia (127 species, 75 genera, 17 families and various outgroups, based on two mitochondrial genes (cytochrome oxidase I, cytochrome b, with analyses of nuclear genes (ss-tubulin, ribosomal DNA of a subset of taxa to test unexpected relationships. Eleven of 16 families were found to be polyphyletic. Strikingly, over one third of all families as conventionally defined contain representatives from the highly divergent "robust" and "complex" clades. However, the recent suggestion that corallimorpharians are true corals that have lost their skeletons was not upheld. Relationships were supported not only by mitochondrial and nuclear genes, but also often by morphological characters which had been ignored or never noted previously. The concordance of molecular characters and more carefully examined morphological characters suggests a future of greater taxonomic stability, as well as the potential to trace the evolutionary history of this ecologically important group using fossils.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. Spike Pattern Recognition for Automatic Collimation Alignment

    CERN Document Server

    Azzopardi, Gabriella; Salvachua Ferrando, Belen Maria; Mereghetti, Alessio; Redaelli, Stefano; CERN. Geneva. ATS Department

    2017-01-01

    The LHC makes use of a collimation system to protect its sensitive equipment by intercepting potentially dangerous beam halo particles. The appropriate collimator settings to protect the machine against beam losses relies on a very precise alignment of all the collimators with respect to the beam. The beam center at each collimator is then found by touching the beam halo using an alignment procedure. Until now, in order to determine whether a collimator is aligned with the beam or not, a user is required to follow the collimator’s BLM loss data and detect spikes. A machine learning (ML) model was trained in order to automatically recognize spikes when a collimator is aligned. The model was loosely integrated with the alignment implementation to determine the classification performance and reliability, without effecting the alignment process itself. The model was tested on a number of collimators during this MD and the machine learning was able to output the classifications in real-time.

  18. Gene

    Data.gov (United States)

    U.S. Department of Health & Human Services — Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes,...

  19. 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...

  20. 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

  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. Design of practical alignment device in KSTAR Thomson diagnostic

    Energy Technology Data Exchange (ETDEWEB)

    Lee, J. H., E-mail: jhlee@nfri.re.kr [National Fusion Research Institute, Daejeon (Korea, Republic of); University of Science and Technology (UST), Daejeon (Korea, Republic of); Lee, S. H. [National Fusion Research Institute, Daejeon (Korea, Republic of); Yamada, I. [National Institute for Fusion Science, Toki (Japan)

    2016-11-15

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

  3. 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.

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

    International Nuclear Information System (INIS)

    Potter, J.D.

    1995-01-01

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

  6. Cloning of fusion protein gene of Newcastle disease virus into a baculovirus derived bacmid shuttle vector, in order to express it in insect cell line

    Directory of Open Access Journals (Sweden)

    Hashemzadeh MS

    2015-05-01

    Full Text Available Abstract Background: Newcastle disease virus (NDV is one of the major pathogens in poultry and vaccination is intended to control the disease, as an effective solution, yet. Fusion protein (F on surface of NDV, has a fundamental role in virus pathogenicity and can induce protective immunity, alone. With this background, here our aim was to construct a baculovirus derived recombinant bacmid shuttle vector (encoding F-protein in order to express it in insect cell line. Materials and Methods: In this experimental study, at first complete F gene from avirulent strain La Sota of NDV was amplified by RT-PCR to produce F cDNA. The amplicon was cloned into T/A cloning vector and afterwards into pFastBac Dual donor plasmid. After the verification of cloning process by two methods, PCR and enzymatic digestion analysis, the accuracy of F gene sequence was confirmed by sequencing. Finally, F-containing recombinant bacmid was subsequently generated in DH10Bac cell and the construct production was confirmed by a special PCR panel, using F specific primers and M13 universal primers. Results: Analysis of confirmatory tests showed that the recombinant bacmid, expressing of F-protein gene in correct sequence and framework, has been constructed successfully. Conclusion: The product of this F-containing recombinant bacmid, in addition to its independent application in the induction of protective immunity, can be used with the other individual recombinant baculoviruses, expressing HN and NP genes to produce NDV-VLPs in insect cell line.

  7. 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...

  8. 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...

  9. 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.

  10. 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

  11. 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

  12. 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.

  13. Strategic alignment of Corporate Real Estate

    NARCIS (Netherlands)

    Appel - Meulenbroek, H.A.J.A.; Brown, M.G.; Ramakers, Y

    2010-01-01

    Purpose/value: With the growing complexity of organizations, it becomes increasingly important to tune the strategies of different business functions. In order to add maximum value to the organization, real estate strategies have to be aligned with corporate strategy. The purpose of this paper is to

  14. 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

  15. Predicting RNA hyper-editing with a novel tool when unambiguous alignment is impossible.

    Science.gov (United States)

    McKerrow, Wilson H; Savva, Yiannis A; Rezaei, Ali; Reenan, Robert A; Lawrence, Charles E

    2017-07-10

    Repetitive elements are now known to have relevant cellular functions, including self-complementary sequences that form double stranded (ds) RNA. There are numerous pathways that determine the fate of endogenous dsRNA, and misregulation of endogenous dsRNA is a driver of autoimmune disease, particularly in the brain. Unfortunately, the alignment of high-throughput, short-read sequences to repeat elements poses a dilemma: Such sequences may align equally well to multiple genomic locations. In order to differentiate repeat elements, current alignment methods depend on sequence variation in the reference genome. Reads are discarded when no such variations are present. However, RNA hyper-editing, a possible fate for dsRNA, introduces enough variation to distinguish between repeats that are otherwise identical. To take advantage of this variation, we developed a new algorithm, RepProfile, that simultaneously aligns reads and predicts novel variations. RepProfile accurately aligns hyper-edited reads that other methods discard. In particular we predict hyper-editing of Drosophila melanogaster repeat elements in vivo at levels previously described only in vitro, and provide validation by Sanger sequencing sixty-two individual cloned sequences. We find that hyper-editing is concentrated in genes involved in cell-cell communication at the synapse, including some that are associated with neurodegeneration. We also find that hyper-editing tends to occur in short runs. Previous studies of RNA hyper-editing discarded ambiguously aligned reads, ignoring hyper-editing in long, perfect dsRNA - the perfect substrate for hyper-editing. We provide a method that simulation and Sanger validation show accurately predicts such RNA editing, yielding a superior picture of hyper-editing.

  16. 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...

  17. 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...

  18. 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...

  19. 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...

  20. 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...

  1. 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...

  2. 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.

  3. 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.

  4. 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.

  5. Alignment of the ATLAS Inner Detector Tracking System

    CERN Document Server

    Lacuesta, V; The ATLAS collaboration

    2010-01-01

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

  6. Advanced Alignment of the ATLAS Inner Detector

    CERN Document Server

    Stahlman, JM; The ATLAS collaboration

    2012-01-01

    The primary goal of the ATLAS Inner Detector (ID) is to measure the trajectories of charged particles in the high particle density environment of the Large Hadron Collider (LHC) collisions. This is achieved using a combination of different technologies, including silicon pixels, silicon microstrips, and gaseous drift-tubes, all immersed in a 2 Tesla magnetic field. With over one million alignable degrees of freedom, it is crucial that an accurate model of the detector positions be produced using an automated and robust algorithm in order to achieve good tracking performance. This has been accomplished using a variety of alignment techniques resulting in near optimal hit and momentum resolutions.

  7. 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.

  8. Fractional Order Element Based Impedance Matching

    KAUST Repository

    Radwan, Ahmed Gomaa; Salama, Khaled N.; Shamim, Atif

    2014-01-01

    Disclosed are various embodiments of methods and systems related to fractional order element based impedance matching. In one embodiment, a method includes aligning a traditional Smith chart (|.alpha.|=1) with a fractional order Smith chart (|.alpha

  9. Functionalization of vertically aligned carbon nanotubes.

    Science.gov (United States)

    Van Hooijdonk, Eloise; Bittencourt, Carla; Snyders, Rony; Colomer, Jean-François

    2013-01-01

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

  10. 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.

  11. Precision lens assembly with alignment turning system

    Science.gov (United States)

    Ho, Cheng-Fang; Huang, Chien-Yao; Lin, Yi-Hao; Kuo, Hui-Jean; Kuo, Ching-Hsiang; Hsu, Wei-Yao; Chen, Fong-Zhi

    2017-10-01

    The poker chip assembly with high precision lens barrels is widely applied to ultra-high performance optical system. ITRC applies the poker chip assembly technology to the high numerical aperture objective lenses and lithography projection lenses because of its high efficiency assembly process. In order to achieve high precision lens cell for poker chip assembly, an alignment turning system (ATS) is developed. The ATS includes measurement, alignment and turning modules. The measurement module is equipped with a non-contact displacement sensor (NCDS) and an autocollimator (ACM). The NCDS and ACM are used to measure centration errors of the top and the bottom surface of a lens respectively; then the amount of adjustment of displacement and tilt with respect to the rotational axis of the turning machine for the alignment module can be determined. After measurement, alignment and turning processes on the ATS, the centration error of a lens cell with 200 mm in diameter can be controlled within 10 arcsec. Furthermore, a poker chip assembly lens cell with three sub-cells is demonstrated, each sub-cells are measured and accomplished with alignment and turning processes. The lens assembly test for five times by each three technicians; the average transmission centration error of assembly lens is 12.45 arcsec. The results show that ATS can achieve high assembly efficiency for precision optical systems.

  12. Analyzing and synthesizing phylogenies using tree alignment graphs.

    Directory of Open Access Journals (Sweden)

    Stephen A Smith

    Full Text Available Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG. The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees, we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to

  13. Analyzing and synthesizing phylogenies using tree alignment graphs.

    Science.gov (United States)

    Smith, Stephen A; Brown, Joseph W; Hinchliff, Cody E

    2013-01-01

    Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG). The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees), we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to observe.

  14. Alignment of dust grains in ionized regions

    Science.gov (United States)

    Anderson, Nels; Watson, William D.

    1993-01-01

    The rate at which charged dust grains in a plasma are torqued by passing ions and electrons is calculated. When photo-emission of electrons is not important, attraction of ions by the grain monopole potential increases the rate at which the grains' spins are dealigned by nearly an order of magnitude. Consequently, the energy density of the magnetic field required to align grains in an H II region may be increased by about an order of magnitude. In contrast, electric dipole and quadrupole moments are unlikely to produce large dealignment rates for grains of modest length-to-width ratio. Nonetheless, for positively charged grains these higher-order moments likely prevent monopole repulsion of ions from reducing the dealignment rate far below that for neutral grains. The presence of positive grain charge therefore does not greatly facilitate grain alignment in an H II region.

  15. 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’....

  16. 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...

  17. Development of a multiplex assay for genus- and species-specific detection of Phytophthora based on differences in mitochondrial gene order.

    Science.gov (United States)

    Bilodeau, Guillaume J; Martin, Frank N; Coffey, Michael D; Blomquist, Cheryl L

    2014-07-01

    A molecular diagnostic assay for Phytophthora spp. that is specific, sensitive, has both genus- and species-specific detection capabilities multiplexed, and can be used to systematically develop markers for detection of a wide range of species would facilitate research and regulatory efforts. To address this need, a marker system was developed based on the high copy sequences of the mitochondrial DNA utilizing gene orders that were highly conserved in the genus Phytophthora but different in the related genus Pythium and plants to reduce the importance of highly controlled annealing temperatures for specificity. An amplification primer pair designed from conserved regions of the atp9 and nad9 genes produced an amplicon of ≈340 bp specific for the Phytophthora spp. tested. The TaqMan probe for the genus-specific Phytophthora test was designed from a conserved portion of the atp9 gene whereas variable intergenic spacer sequences were used for designing the species-specific TaqMan probes. Specific probes were developed for 13 species and the P. citricola species complex. In silico analysis suggests that species-specific probes could be developed for at least 70 additional described and provisional species; the use of locked nucleic acids in TaqMan probes should expand this list. A second locus spanning three tRNAs (trnM-trnP-trnM) was also evaluated for genus-specific detection capabilities. At 206 bp, it was not as useful for systematic development of a broad range of species-specific probes as the larger 340-bp amplicon. All markers were validated against a test panel that included 87 Phytophthora spp., 14 provisional Phytophthora spp., 29 Pythium spp., 1 Phytopythium sp., and 39 plant species. Species-specific probes were validated further against a range of geographically diverse isolates to ensure uniformity of detection at an intraspecific level, as well as with other species having high levels of sequence similarity to ensure specificity. Both diagnostic

  18. 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.

  19. A value-based maturity model for IT alignment in networked businesses

    NARCIS (Netherlands)

    Santana Tapia, R.G.

    Business-IT alignment can be achieved at various levels of maturity. Supposing that an organization has tried to achieve business-IT alignment, a question to face is: how is that organization going to know the level of maturity of its alignment situation in order to plan future ways of action? That

  20. Node fingerprinting: an efficient heuristic for aligning biological networks.

    Science.gov (United States)

    Radu, Alex; Charleston, Michael

    2014-10-01

    With the continuing increase in availability of biological data and improvements to biological models, biological network analysis has become a promising area of research. An emerging technique for the analysis of biological networks is through network alignment. Network alignment has been used to calculate genetic distance, similarities between regulatory structures, and the effect of external forces on gene expression, and to depict conditional activity of expression modules in cancer. Network alignment is algorithmically complex, and therefore we must rely on heuristics, ideally as efficient and accurate as possible. The majority of current techniques for network alignment rely on precomputed information, such as with protein sequence alignment, or on tunable network alignment parameters, which may introduce an increased computational overhead. Our presented algorithm, which we call Node Fingerprinting (NF), is appropriate for performing global pairwise network alignment without precomputation or tuning, can be fully parallelized, and is able to quickly compute an accurate alignment between two biological networks. It has performed as well as or better than existing algorithms on biological and simulated data, and with fewer computational resources. The algorithmic validation performed demonstrates the low computational resource requirements of NF.

  1. 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.

  2. 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.

  3. A MEMORY EFFICIENT HARDWARE BASED PATTERN MATCHING AND PROTEIN ALIGNMENT SCHEMES FOR HIGHLY COMPLEX DATABASES

    OpenAIRE

    Bennet, M.Anto; Sankaranarayanan, S.; Deepika, M.; Nanthini, N.; Bhuvaneshwari, S.; Priyanka, M.

    2017-01-01

    Protein sequence alignment to find correlation between different species, or genetic mutations etc. is the most computational intensive task when performing protein comparison. To speed-up the alignment, Systolic Arrays (SAs) have been used. In order to avoid the internal-loop problem which reduces the performance, pipeline interleaving strategy has been presented. This strategy is applied to an SA for Smith Waterman (SW) algorithm which is an alignment algorithm to locally align two proteins...

  4. Magnetic Alignment of Block Copolymer Microdomains by Intrinsic Chain Anisotropy.

    Science.gov (United States)

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

    2015-12-18

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

  5. 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.

  6. Alignment of the ATLAS central muon spectrometer

    CERN Document Server

    Chevallier, F

    2008-01-01

    The muon spectrometer of the ATLAS experiment is one of the largest detectors ever built. At the LHC, new physics signs could appear through high momenta muons (1 TeV). Identification and precise momentum measurement of such muons are two of the main challenges of the ATLAS muon spectrometer. In order to get a good resolution for high energy muons (i.e. 10% at 1 TeV), the accuracy on the alignment of precision chambers must be of the order of 50 microns. Several procedures have been developed to reach such a precision. This document describes complementary techniques used to align the muon sub-detectors, and their results : the optical system, the muon cosmic rays and the straight tracks coming from collisions.

  7. 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...

  8. 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

  9. Alignment sensing and control in advanced LIGO

    International Nuclear Information System (INIS)

    Barsotti, L; Evans, M; Fritschel, P

    2010-01-01

    The advanced LIGO detectors are currently in their final design stage, and the installation phase will start at the end of 2010: they will have about 10 times better sensitivity than initial LIGO, with a sensitive band ranging from 10 Hz to 10 kHz. As compared with previous LIGO detectors, there will be increased complexity in the optical configuration, improved seismic isolation system and significantly higher power circulating in the arm cavities. In the new detectors, the control of the angular orientation of the mirrors will be particularly challenging. The advanced LIGO (aLIGO) mirrors need to have a residual angular motion of the order of 1 nrad RMS in order to achieve high sensitivity. In the high power regime, the torque induced by radiation pressure effects will be comparable with the restoring torque of the mirror suspension, such that we must think of the opto-mechanical response, instead of just the mechanical response. These modifications have to be considered in order to design the control strategy for keeping the mirrors well aligned. Moreover, to meet the sensitivity target the alignment control noise coupled to the gravitational-wave channel must be well below 6x10 -18 m/√Hz at 10 Hz. We developed a model of the alignment sensing and control scheme of aLIGO which takes into account radiation pressure effects and meets the noise target.

  10. Long Read Alignment with Parallel MapReduce Cloud Platform

    Science.gov (United States)

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

    2015-01-01

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

  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. 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...

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

    International Nuclear Information System (INIS)

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

    2005-01-01

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

  14. 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.

  15. Advanced Alignment of the ATLAS Tracking System

    CERN Document Server

    Butti, P; The ATLAS collaboration

    2014-01-01

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

  16. 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.

  17. Nucleotide sequence alignment of hdcA from Gram-positive bacteria.

    Science.gov (United States)

    Diaz, Maria; Ladero, Victor; Redruello, Begoña; Sanchez-Llana, Esther; Del Rio, Beatriz; Fernandez, Maria; Martin, Maria Cruz; Alvarez, Miguel A

    2016-03-01

    The decarboxylation of histidine -carried out mainly by some gram-positive bacteria- yields the toxic dietary biogenic amine histamine (Ladero et al. 2010 〈10.2174/157340110791233256〉 [1], Linares et al. 2016 〈http://dx.doi.org/10.1016/j.foodchem.2015.11.013〉〉 [2]). The reaction is catalyzed by a pyruvoyl-dependent histidine decarboxylase (Linares et al. 2011 〈10.1080/10408398.2011.582813〉 [3]), which is encoded by the gene hdcA. In order to locate conserved regions in the hdcA gene of Gram-positive bacteria, this article provides a nucleotide sequence alignment of all the hdcA sequences from Gram-positive bacteria present in databases. For further utility and discussion, see 〈http://dx.doi.org/ 10.1016/j.foodcont.2015.11.035〉〉 [4].

  18. Aligning for accountable care: Strategic practices for change in accountable care organizations.

    Science.gov (United States)

    Hilligoss, Brian; Song, Paula H; McAlearney, Ann Scheck

    Alignment within accountable care organizations (ACOs) is crucial if these new entities are to achieve their lofty goals. However, the concept of alignment remains underexamined, and we know little about the work entailed in creating alignment. The aim of this study was to develop the concept of aligning by identifying and describing the strategic practices administrators use to align the structures, processes, and behaviors of their organizations and individual providers in pursuit of accountable care. We conducted 2-year qualitative case studies of four ACOs that have assumed full risk for the costs and quality of care for defined populations. Five strategic aligning practices were used by all four ACOs. Informing both aligns providers' understandings with the goals and value proposition of the ACO and aligns the providers' attention with the drivers of performance. Involving both aligns ACO leaders' understandings with the realities facing providers and aligns the policies of the ACO with the needs of providers. Enhancing both aligns the operations of individual provider practices with the operations of the ACO and aligns the trust of providers with the ACO. Motivating aligns what providers value with the goals of the ACO. Finally, evolving is a metapractice of learning and adapting that guides the execution of the other four practices. Our findings suggest that there are second-order cognitive (e.g., understandings and attention) and cultural (e.g., trust and values) levels of alignment, as well as a first-order operational level (organizational structures, processes, and incentives). A well-aligned organization may require ongoing repositioning at each of these levels, as well as attention to both cooperative and coordinative dimensions of alignment. Implications for research and practice are discussed.

  19. 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_...

  20. 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.

  1. Intradomain Textures in Block Copolymers: Multizone Alignment and Biaxiality

    Science.gov (United States)

    Prasad, Ishan; Seo, Youngmi; Hall, Lisa M.; Grason, Gregory M.

    2017-06-01

    Block copolymer (BCP) melt assembly has been studied for decades, focusing largely on self-organized spatial patterns of periodically ordered segment density. Here, we demonstrate that underlying the well-known composition profiles (i.e., ordered lamella, cylinders, spheres, and networks) are generic and heterogeneous patterns of segment orientation that couple strongly to morphology, even in the absence of specific factors that promote intra or interchain segment alignment. We employ both self-consistent field theory and coarse-grained simulation methods to measure polar and nematic order parameters of segments in a freely jointed chain model of diblock melts. We show that BCP morphologies have a multizone texture, with segments predominantly aligned normal and parallel to interdomain interfaces in the respective brush and interfacial regions of the microdomain. Further, morphologies with anisotropically curved interfaces (i.e., cylinders and networks) exhibit biaxial order that is aligned to the principal curvature axes of the interface.

  2. 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

  3. CMS Tracker Alignment Performance Results 2016

    CERN Document Server

    CMS Collaboration

    2017-01-01

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

  4. 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.

  5. ARMY CYBER STRUCTURE ALIGNMENT

    Science.gov (United States)

    2016-02-16

    content/?q=historic-cyber-unit-begins- daily-action . 14 John M. McHugh , Secretary of the Army, HQDA General Order 2014-02, Affirmation of Secretary of...support-plays-role-in-tactical-operations/75545442/. McHugh , John M., Secretary of the Army, HQDA General Order 2014-02, Affirmation of Secretary of

  6. THE EXPERIENCE OF THE TRANSFORMATION OF SOME CULTIVATED PLANTS WITH THE GENE UGT ENCODING THE SYNTHESIS OF UDPG-TRANSFERASE IN ORDER TO CHANGE THE HORMONAL STATUS

    Directory of Open Access Journals (Sweden)

    Rekoslavskaya N.I.

    2012-08-01

    Full Text Available The gene ugt/iaglu was isolated from cDNA library obtained from seedlings of Zea mays L. Positive clones prepared by Lambda ZAPII (Stratagene, USA procedure were screened via western blot with antibodies to UDPG-transferase from corn endosperm raised in rabbit serum. The plasmid pBluescript harboring the gene ugt/iaglu was placed into Escherichia coli (E.coli DH5a under T7/T3 promoter. The gene ugt/iaglu was sequenced and the size was determined as much as 1740 bp. The UDPG-transferase or by trivial name Indoleacetic acid (IAA - glucose synthase (IAGlu-synthase binds IAA with glucose from UDPG thereby making the temporary inactivation and storing of this phytohormone which is capable to be released after the demand from cells. Several cultivated plants were used for transfromation with the gene ugt/iaglu from corn: tomato, potato, lettuce, egg-plant, pepper, strawberry, cucumber, squash, aspen, poplar, pine and others. All plants transformed with the gene ugt/iaglu showed fast growth, better flowering and harvest. The insertion and expression of the gene ugt/iaglu was confirmed in transformed tomato, potato and aspen with PCR, RT-PCR, southern and northern blottings. The contents of free IAA and its bound form IAGlu were higher as much as twice in tomato, potato and aspen transformed with the gene ugt/iaglu. The harvest of tomato was 3-4 times higher in transgenic tomato. The amount of potato tubers and their whole masses were 1.5 - 2 times higher in transgenic potato of several varieties in comparison to control.

  7. CMS silicon tracker alignment strategy with the Millepede II algorithm

    International Nuclear Information System (INIS)

    Flucke, G; Schleper, P; Steinbrueck, G; Stoye, M

    2008-01-01

    The positions of the silicon modules of the CMS tracker will be known to O(100 μm) from survey measurements, mounting precision and the hardware alignment system. However, in order to fully exploit the capabilities of the tracker, these positions need to be known to a precision of a few μm. Only a track-based alignment procedure can reach this required precision. Such an alignment procedure is a major challenge given that about 50000 geometry constants need to be measured. Making use of the novel χ 2 minimization program Millepede II an alignment strategy has been developed in which all detector components are aligned simultaneously and all correlations between their position parameters taken into account. Different simulated data, such as Z 0 decays and muons originated in air showers were used for the study. Additionally information about the mechanical structure of the tracker, and initial position uncertainties have been used as input for the alignment procedure. A proof of concept of this alignment strategy is demonstrated using simulated data

  8. Improving scanner wafer alignment performance by target optimization

    Science.gov (United States)

    Leray, Philippe; Jehoul, Christiane; Socha, Robert; Menchtchikov, Boris; Raghunathan, Sudhar; Kent, Eric; Schoonewelle, Hielke; Tinnemans, Patrick; Tuffy, Paul; Belen, Jun; Wise, Rich

    2016-03-01

    In the process nodes of 10nm and below, the patterning complexity along with the processing and materials required has resulted in a need to optimize alignment targets in order to achieve the required precision, accuracy and throughput performance. Recent industry publications on the metrology target optimization process have shown a move from the expensive and time consuming empirical methodologies, towards a faster computational approach. ASML's Design for Control (D4C) application, which is currently used to optimize YieldStar diffraction based overlay (DBO) metrology targets, has been extended to support the optimization of scanner wafer alignment targets. This allows the necessary process information and design methodology, used for DBO target designs, to be leveraged for the optimization of alignment targets. In this paper, we show how we applied this computational approach to wafer alignment target design. We verify the correlation between predictions and measurements for the key alignment performance metrics and finally show the potential alignment and overlay performance improvements that an optimized alignment target could achieve.

  9. Advanced Alignment of the ATLAS Tracking System

    CERN Document Server

    Pedraza Lopez, S; The ATLAS collaboration

    2012-01-01

    In order to reconstruct trajectories of charged particles, ATLAS is equipped with a tracking system built using different technologies embedded in a 2T solenoidal magnetic field. ATLAS physics goals require high resolution, unbiased measurement of all charged particle kinematic parameters in order to assure accurate invariant mass reconstruction and interaction and decay vertex finding. These critically depend on the systematic effects related to the alignment of the tracking system. In order to eliminate malicious systematic deformations, various advanced tools and techniques have been put in place. These include information from known mass resonances, energy of electrons and positrons measured by the electromagnetic calorimeters, etc. Despite being stable under normal running conditions, ATLAS tracking system responses to sudden environ-mental changes (temperature, magnetic field) by small collective deformations. These have to be identified and corrected in order to assure uniform, highest quality tracking...

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. Long Read Alignment with Parallel MapReduce Cloud Platform

    Directory of Open Access Journals (Sweden)

    Ahmed Abdulhakim Al-Absi

    2015-01-01

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

  15. 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.

  16. A Python Script for Aligning the STIS Echelle Blaze Function

    Science.gov (United States)

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

    2018-01-01

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

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

    International Nuclear Information System (INIS)

    Arce, P.

    1999-01-01

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

  18. 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.

  19. Loss of activity-dependent Arc gene expression in the retrosplenial cortex after hippocampal inactivation: Interaction in a higher-order memory circuit

    Czech Academy of Sciences Publication Activity Database

    Kubík, Štěpán; Miyashita, T.; Kubik-Zahorodna, Agnieszka; Guzowski, J. F.

    2012-01-01

    Roč. 97, č. 1 (2012), s. 124-131 ISSN 1074-7427 Institutional research plan: CEZ:AV0Z50110509 Keywords : hippocampus * spatial memory * water maze * immediate-early gene * Arc * retrosplenial cortex Subject RIV: FH - Neurology Impact factor: 3.327, year: 2012

  20. 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.

  1. 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.

  2. Functionalization of vertically aligned carbon nanotubes

    Directory of Open Access Journals (Sweden)

    Eloise Van Hooijdonk

    2013-02-01

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

  3. 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

  4. 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.

  5. 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....

  6. 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...

  7. 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

  8. 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.

  9. 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

  10. Alignment of business and information strategies and its impact on business performance

    DEFF Research Database (Denmark)

    Johansson, Björn; Sudzina, Frantisek; Pucihar, Andreja

    2014-01-01

    people perceived their business strategy and information strategy to be aligned. Respondents’ statements from the questionnaire survey on their perceived alignment between business strategy and information strategy were checked against the firms’ revenue growth. The analysis of perceived alignment...... between business strategy, information strategy, and revenue growth shows that there is a significant relationship between alignment and revenue growth in Slovenia, and this link is positive. Managers should aim to align business and information strategies in order to achieve better business performance.......Alignment between business strategy and information strategy has been focused on for several years with research suggesting different explanations to how this alignment influences a firm’s performance. This article presents results from an investigation of firms in Slovenia about how business...

  11. Measuring the Maturity of IT and Business Strategies Alignment in Organization: Case Study of SAIPA-Yadak Company

    Directory of Open Access Journals (Sweden)

    Mohmmad Reza Taghva

    2010-04-01

    Full Text Available IT strategic planning towards realizing organizational is one of the most important topics among managers of leading companies. It is known as alignment of IT and business strategies. The alignment factors identified in Luftman model on IT-Business Alignment form the basis of the present study. Luftman model is comprised of five levels, each level consisting of six factors. A questionnaire was designed and distributed among managemers in Saipa Yadak in order to identify the impact of each alignment factor. Thereafter in order to measure the extent of IT-Business alignment, another questionnaire was devised to determine company’s current status. Finally a balanced alignment factor was calculated. Results indicate that Saipa Yadak is at the third alignment level according to Luftman model. This illustrates a stage of total focus. Tactics are offered for approaching the fourth level of alignment.

  12. 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

  13. Only marginal alignment of disc galaxies

    Science.gov (United States)

    Andrae, René; Jahnke, Knud

    2011-12-01

    Testing theories of angular-momentum acquisition of rotationally supported disc galaxies is the key to understanding the formation of this type of galaxies. The tidal-torque theory aims to explain this acquisition process in a cosmological framework and predicts positive autocorrelations of angular-momentum orientation and spiral-arm handedness, i.e. alignment of disc galaxies, on short distance scales of 1 Mpc h-1. This disc alignment can also cause systematic effects in weak-lensing measurements. Previous observations claimed discovering these correlations but are overly optimistic in the reported level of statistical significance of the detections. Errors in redshift, ellipticity and morphological classifications were not taken into account, although they have a significant impact. We explain how to rigorously propagate all the important errors through the estimation process. Analysing disc galaxies in the Sloan Digital Sky Survey (SDSS) data base, we find that positive autocorrelations of spiral-arm handedness and angular-momentum orientations on distance scales of 1 Mpc h-1 are plausible but not statistically significant. Current data appear not good enough to constrain parameters of theory. This result agrees with a simple hypothesis test in the Local Group, where we also find no evidence for disc alignment. Moreover, we demonstrate that ellipticity estimates based on second moments are strongly biased by galactic bulges even for Scd galaxies, thereby corrupting correlation estimates and overestimating the impact of disc alignment on weak-lensing studies. Finally, we discuss the potential of future sky surveys. We argue that photometric redshifts have too large errors, i.e. PanSTARRS and LSST cannot be used. Conversely, the EUCLID project will not cover the relevant redshift regime. We also discuss the potentials and problems of front-edge classifications of galaxy discs in order to improve the autocorrelation estimates of angular-momentum orientation.

  14. 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

  15. Light-Driven Alignment

    CERN Document Server

    Antonyuk, Boris P

    2009-01-01

    This book deals with influencing the properties of solids by light-driven electron transport. The theoretical basis of these effects, light-driven ordering and self-organisation, as well as optical motors are presented. With light as a tool, new ways to produce materials are opened.

  16. Parallel evolution of the glycogen synthase 1 (muscle) gene Gys1 between Old World and New World fruit bats (Order: Chiroptera).

    Science.gov (United States)

    Fang, Lu; Shen, Bin; Irwin, David M; Zhang, Shuyi

    2014-10-01

    Glycogen synthase, which catalyzes the synthesis of glycogen, is especially important for Old World (Pteropodidae) and New World (Phyllostomidae) fruit bats that ingest high-carbohydrate diets. Glycogen synthase 1, encoded by the Gys1 gene, is the glycogen synthase isozyme that functions in muscles. To determine whether Gys1 has undergone adaptive evolution in bats with carbohydrate-rich diets, in comparison to insect-eating sister bat taxa, we sequenced the coding region of the Gys1 gene from 10 species of bats, including two Old World fruit bats (Pteropodidae) and a New World fruit bat (Phyllostomidae). Our results show no evidence for positive selection in the Gys1 coding sequence on the ancestral Old World and the New World Artibeus lituratus branches. Tests for convergent evolution indicated convergence of the sequences and one parallel amino acid substitution (T395A) was detected on these branches, which was likely driven by natural selection.

  17. PEP-II IR-2 Alignment

    International Nuclear Information System (INIS)

    Seryi, A

    2004-01-01

    This paper describes the first results and preliminary analysis obtained with several alignment monitoring systems recently installed in the PEP-II interaction region. The hydrostatic level system, stretched wire system, and laser tracker have been installed in addition to the existing tiltmeters and LVDT sensors. These systems detected motion of the left raft, which correlated primarily with the low energy ring (LER) current. The motion is of the order of 120 micrometers. The cause was identified as synchrotron radiation heating the beampipe, causing its expansion which then results in its deformation and offset of the IR quadrupoles. We also discuss further plans on measurements, analysis and means to counteract this motion

  18. CMS Tracker Alignment Performance Results Summer 2016

    CERN Document Server

    CMS Collaboration

    2016-01-01

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

  19. 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)

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

    Science.gov (United States)

    Eernisse, D J

    1992-04-01

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

  1. 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

  2. Birth order modifies the effect of IL13 gene polymorphisms on serum IgE at age 10 and skin prick test at ages 4, 10 and 18: a prospective birth cohort study

    Science.gov (United States)

    2010-01-01

    Background Susceptibility to atopy originates from effects of the environment on genes. Birth order has been identified as a risk factor for atopy and evidence for some candidate genes has been accumulated; however no study has yet assessed a birth order-gene interaction. Objective To investigate the interaction of IL13 polymorphisms with birth order on allergic sensitization at ages 4, 10 and 18 years. Methods Mother-infant dyads were recruited antenatally and followed prospectively to age 18 years. Questionnaire data (at birth, age 4, 10, 18); skin prick test (SPT) at ages 4, 10, 18; total serum IgE and specific inhalant screen at age 10; and genotyping for IL13 were collected. Three SNPs were selected from IL13: rs20541 (exon 4, nonsynonymous SNP), rs1800925 (promoter region) and rs2066960 (intron 1). Analysis included multivariable log-linear regression analyses using repeated measurements to estimate prevalence ratios (PRs). Results Of the 1456 participants, birth order information was available for 83.2% (1212/1456); SPT was performed on 67.4% at age 4, 71.2% at age 10 and 58.0% at age 18. The prevalence of atopy (sensitization to one or more food or aeroallergens) increased from 19.7% at age 4, to 26.7% at 10 and 41.1% at age 18. Repeated measurement analysis indicated interaction between rs20541 and birth order on SPT. The stratified analyses demonstrated that the effect of IL13 on SPT was restricted only to first-born children (p = 0.007; adjusted PR = 1.35; 95%CI = 1.09, 1.69). Similar findings were noted for firstborns regarding elevated total serum IgE at age 10 (p = 0.007; PR = 1.73; 1.16, 2.57) and specific inhalant screen (p = 0.034; PR = 1.48; 1.03, 2.13). Conclusions This is the first study to show an interaction between birth order and IL13 polymorphisms on allergic sensitization. Future functional genetic research need to determine whether or not birth order is related to altered expression and methylation of the IL13 gene. PMID:20403202

  3. Birth order modifies the effect of IL13 gene polymorphisms on serum IgE at age 10 and skin prick test at ages 4, 10 and 18: a prospective birth cohort study

    Directory of Open Access Journals (Sweden)

    Ogbuanu Ikechukwu U

    2010-04-01

    Full Text Available Abstract Background Susceptibility to atopy originates from effects of the environment on genes. Birth order has been identified as a risk factor for atopy and evidence for some candidate genes has been accumulated; however no study has yet assessed a birth order-gene interaction. Objective To investigate the interaction of IL13 polymorphisms with birth order on allergic sensitization at ages 4, 10 and 18 years. Methods Mother-infant dyads were recruited antenatally and followed prospectively to age 18 years. Questionnaire data (at birth, age 4, 10, 18; skin prick test (SPT at ages 4, 10, 18; total serum IgE and specific inhalant screen at age 10; and genotyping for IL13 were collected. Three SNPs were selected from IL13: rs20541 (exon 4, nonsynonymous SNP, rs1800925 (promoter region and rs2066960 (intron 1. Analysis included multivariable log-linear regression analyses using repeated measurements to estimate prevalence ratios (PRs. Results Of the 1456 participants, birth order information was available for 83.2% (1212/1456; SPT was performed on 67.4% at age 4, 71.2% at age 10 and 58.0% at age 18. The prevalence of atopy (sensitization to one or more food or aeroallergens increased from 19.7% at age 4, to 26.7% at 10 and 41.1% at age 18. Repeated measurement analysis indicated interaction between rs20541 and birth order on SPT. The stratified analyses demonstrated that the effect of IL13 on SPT was restricted only to first-born children (p = 0.007; adjusted PR = 1.35; 95%CI = 1.09, 1.69. Similar findings were noted for firstborns regarding elevated total serum IgE at age 10 (p = 0.007; PR = 1.73; 1.16, 2.57 and specific inhalant screen (p = 0.034; PR = 1.48; 1.03, 2.13. Conclusions This is the first study to show an interaction between birth order and IL13 polymorphisms on allergic sensitization. Future functional genetic research need to determine whether or not birth order is related to altered expression and methylation of the IL13 gene.

  4. 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.

  5. Crowdsourcing RNA structural alignments with an online computer game.

    Science.gov (United States)

    Waldispühl, Jérôme; Kam, Arthur; Gardner, Paul P

    2015-01-01

    The annotation and classification of ncRNAs is essential to decipher molecular mechanisms of gene regulation in normal and disease states. A database such as Rfam maintains alignments, consensus secondary structures, and corresponding annotations for RNA families. Its primary purpose is the automated, accurate annotation of non-coding RNAs in genomic sequences. However, the alignment of RNAs is computationally challenging, and the data stored in this database are often subject to improvements. Here, we design and evaluate Ribo, a human-computing game that aims to improve the accuracy of RNA alignments already stored in Rfam. We demonstrate the potential of our techniques and discuss the feasibility of large scale collaborative annotation and classification of RNA families.

  6. Strategic Alignment and New Product Development

    DEFF Research Database (Denmark)

    Acur, Nuran; Kandemir, Destan; Boer, Harry

    2012-01-01

    Strategic alignment is widely accepted as a prerequisite for a firm’s success, but insight into the role of alignment in, and its impact on, the new product evelopment (NPD) process and its performance is less well developed. Most publications on this topic either focus on one form of alignment...... 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...

  7. On the Efficiency of Grain Alignment in Dark Clouds

    Science.gov (United States)

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

    1997-11-01

    A quantitative analysis of grain alignment in the filamentary dark cloud L1755 in Ophiuchus is presented. We show that the observed decrease of the polarization-to-extinction ratio for the inner parts of this quiescent dark cloud can be explained as a result of the decrease of the efficiency of grain alignment. We make quantitative estimates of grain alignment efficiency for six mechanisms involving grains with either thermal or suprathermal rotation, interacting with either magnetic field or gaseous flow. We also make semiquantitative estimates of grain alignment by radiative torques. We show that in conditions typical of dark cloud interiors, all known major mechanisms of grain alignment fail. All the studied mechanisms predict polarization at least an order of magnitude below the currently detectable levels of ~1%. On the contrary, in the dark cloud environments where Av sight, including the interiors of dark quiescent clouds, where no alignment is possible. We dedicate this paper to the memory of Edward M. Purcell and Lyman Spitzer, Jr., two pioneers in the quantitative study of the interstellar medium.

  8. Spatio-temporal alignment of pedobarographic image sequences.

    Science.gov (United States)

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

    2011-07-01

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

  9. Cryogenic Pupil Alignment Test Architecture for Aberrated Pupil Images

    Science.gov (United States)

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

    2009-01-01

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

  10. 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.

  11. 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...

  12. 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.

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

    Science.gov (United States)

    Malod-Dognin, Noël; Pržulj, Nataša

    2015-07-01

    Discovering and understanding patterns in networks of protein-protein interactions (PPIs) is a central problem in systems biology. Alignments between these networks aid functional understanding as they uncover important information, such as evolutionary conserved pathways, protein complexes and functional orthologs. A few methods have been proposed for global PPI network alignments, but because of NP-completeness of underlying sub-graph isomorphism problem, producing topologically and biologically accurate alignments remains a challenge. We introduce a novel global network alignment tool, Lagrangian GRAphlet-based ALigner (L-GRAAL), which directly optimizes both the protein and the interaction functional conservations, using a novel alignment search heuristic based on integer programming and Lagrangian relaxation. We compare L-GRAAL with the state-of-the-art network aligners on the largest available PPI networks from BioGRID and observe that L-GRAAL uncovers the largest common sub-graphs between the networks, as measured by edge-correctness and symmetric sub-structures scores, which allow transferring more functional information across networks. We assess the biological quality of the protein mappings using the semantic similarity of their Gene Ontology annotations and observe that L-GRAAL best uncovers functionally conserved proteins. Furthermore, we introduce for the first time a measure of the semantic similarity of the mapped interactions and show that L-GRAAL also uncovers best functionally conserved interactions. In addition, we illustrate on the PPI networks of baker's yeast and human the ability of L-GRAAL to predict new PPIs. Finally, L-GRAAL's results are the first to show that topological information is more important than sequence information for uncovering functionally conserved interactions. L-GRAAL is coded in C++. Software is available at: http://bio-nets.doc.ic.ac.uk/L-GRAAL/. n.malod-dognin@imperial.ac.uk Supplementary data are available at

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. Measurement of the attosecond emission from aligned molecules

    International Nuclear Information System (INIS)

    Boutu, W.; Merdji, H.; Fitour, R.; Monchicourt, P.; Breger, P.; Carre, B.; Salieres, P.

    2006-01-01

    Complete test of publication follows. Recently, a number of papers have demonstrated the interest of high-order harmonic generation (HHG) from molecules aligned with respect to the laser polarization. Itatani et al. (Nature 432, 867 (2004)) have shown that a precise characterization of the harmonic emission allows performing a tomographic reconstruction of the molecular orbitals that radiate. Kanai et al. (Nature 435, 470 (2005)) have evidenced quantum interferences in the recombination process of HHG that are directly related to the molecular structure. In all of these papers, only the HHG intensity was measured. The relative harmonic phase, though more difficult to measure, contains important information on the interference process, and is needed for an ab initio tomographic reconstruction. Finally, while the attosecond emission from atoms has been thoroughly studied, in particular by our group (Mairesse et al., Science (302, 1540 (2003)), it has not been investigated in molecules. In a first experiment (Wabnitz et al., EPJD (2006)), we measured the amplitude and relative phase of harmonics radiated by un-aligned nitrogen molecules. Small but reproducible deviations from the phase of harmonics generated in argon (same ionization potential as nitrogen) were measured for low orders. In a recent experiment, we have measured, up to high order, the harmonic amplitude and relative phase for aligned molecules (N 2 and CO 2 ). In order to align the molecules, we used the so-called nonadiabatic technique: a rotational wavepacket is created by a strong enough and short aligning pulse, so that a field-free alignment is obtained at the revival (a few ps after the aligning pulse). The measurement of phase locking between neighboring harmonics was performed through the photoionization of a target gas by the harmonic beam in presence of a sufficiently intense 'dressing' laser beam (RABITT technique). The harmonic phase measured when the CO 2 molecules are aligned parallel to

  19. AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences

    Directory of Open Access Journals (Sweden)

    Claros M Gonzalo

    2010-06-01

    Full Text Available Abstract Background Multiple sequence alignments are used to study gene or protein function, phylogenetic relations, genome evolution hypotheses and even gene polymorphisms. Virtually without exception, all available tools focus on conserved segments or residues. Small divergent regions, however, are biologically important for specific quantitative polymerase chain reaction, genotyping, molecular markers and preparation of specific antibodies, and yet have received little attention. As a consequence, they must be selected empirically by the researcher. AlignMiner has been developed to fill this gap in bioinformatic analyses. Results AlignMiner is a Web-based application for detection of conserved and divergent regions in alignments of conserved sequences, focusing particularly on divergence. It accepts alignments (protein or nucleic acid obtained using any of a variety of algorithms, which does not appear to have a significant impact on the final results. AlignMiner uses different scoring methods for assessing conserved/divergent regions, Entropy being the method that provides the highest number of regions with the greatest length, and Weighted being the most restrictive. Conserved/divergent regions can be generated either with respect to the consensus sequence or to one master sequence. The resulting data are presented in a graphical interface developed in AJAX, which provides remarkable user interaction capabilities. Users do not need to wait until execution is complete and can.even inspect their results on a different computer. Data can be downloaded onto a user disk, in standard formats. In silico and experimental proof-of-concept cases have shown that AlignMiner can be successfully used to designing specific polymerase chain reaction primers as well as potential epitopes for antibodies. Primer design is assisted by a module that deploys several oligonucleotide parameters for designing primers "on the fly". Conclusions AlignMiner can be used

  20. Bacterial genomes lacking long-range correlations may not be modeled by low-order Markov chains: the role of mixing statistics and frame shift of neighboring genes.

    Science.gov (United States)

    Cocho, Germinal; Miramontes, Pedro; Mansilla, Ricardo; Li, Wentian

    2014-12-01

    We examine the relationship between exponential correlation functions and Markov models in a bacterial genome in detail. Despite the well known fact that Markov models generate sequences with correlation function that decays exponentially, simply constructed Markov models based on nearest-neighbor dimer (first-order), trimer (second-order), up to hexamer (fifth-order), and treating the DNA sequence as being homogeneous all fail to predict the value of exponential decay rate. Even reading-frame-specific Markov models (both first- and fifth-order) could not explain the fact that the exponential decay is very slow. Starting with the in-phase coding-DNA-sequence (CDS), we investigated correlation within a fixed-codon-position subsequence, and in artificially constructed sequences by packing CDSs with out-of-phase spacers, as well as altering CDS length distribution by imposing an upper limit. From these targeted analyses, we conclude that the correlation in the bacterial genomic sequence is mainly due to a mixing of heterogeneous statistics at different codon positions, and the decay of correlation is due to the possible out-of-phase between neighboring CDSs. There are also small contributions to the correlation from bases at the same codon position, as well as by non-coding sequences. These show that the seemingly simple exponential correlation functions in bacterial genome hide a complexity in correlation structure which is not suitable for a modeling by Markov chain in a homogeneous sequence. Other results include: use of the (absolute value) second largest eigenvalue to represent the 16 correlation functions and the prediction of a 10-11 base periodicity from the hexamer frequencies. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. Replacing fuel alignment in Germany

    International Nuclear Information System (INIS)

    Poetz, F.; Kalthoff, W.

    1991-01-01

    Up to the end of 1989 varying numbers of broken fuel alignment pins were detected in several German PWRs (80 broken pins in all). The distribution of these broken pins over the core cross-section was more or less random. The problem was due to the stress corrosion cracking of the pin material and was restricted to individual pins. It was concluded that all fuel alignment pins made of Inconel X-750 should be replaced. The development of a new pin, more resistant to intergranular stress corrosion, and the replacement technique are outlined. (author)

  2. 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

  3. 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)

  4. Advanced alignment of the ATLAS tracking system

    CERN Document Server

    AUTHOR|(CDS)2085334; The ATLAS collaboration

    2016-01-01

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

  5. RAPID TRANSFER ALIGNMENT USING FEDERATED KALMAN FILTER

    Institute of Scientific and Technical Information of China (English)

    GUDong-qing; QINYong-yuan; PENGRong; LIXin

    2005-01-01

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

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

    NARCIS (Netherlands)

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

    2015-01-01

    Purpose: Strategic alignment is a theory-based state that is considered as crucial for organizations in order to realize performance gains from information technology (IT) investments and deployments. Within the domain of purchasing and supply chain management there has been a growing interest on

  7. Energy level alignment at Co/AlOx/pentacene interfaces

    NARCIS (Netherlands)

    Popinciuc, M.; Jonkman, H. T.; van Wees, B. J.

    2007-01-01

    X-ray and ultraviolet photoemission spectroscopy (XPS and UPS) experiments were performed in order to study the energy level alignment and electronic structure at Co/AlOx/pentacene interfaces as a function of the aluminum oxide (AlOx) tunnel barrier thickness and the oxidation state of Co. XPS was

  8. Simultaneous alignment and dispersion of carbon nanotubes with lyotropic liquid crystals

    NARCIS (Netherlands)

    Lagerwall, J.P.F.; Scalia, G.; Haluska, M.; Dettlaff-Weglikowska, U.; Giesselmann, F.; Roth, S.

    2006-01-01

    We demonstrate that single-wall carbon nanotubes (SWCNTs) can be macroscopically aligned by means of templating in a lyotropic nematic liquid crystal (LC), a self-assembling anisotropic fluid with orientational but no translational order. The CNTs spontaneously adopt the alignment of the host, as we

  9. Alignment of diabetic feet images

    NARCIS (Netherlands)

    Klein, Almar; van der Heijden, Ferdinand; Slump, Cornelis H.; Uyl, M.J.; Philips, W.

    2007-01-01

    This paper addresses the problem of aligning the images of feet taken at different instances in time. We propose to use SIFT keypoints to find the geometric deformation between two photo’s. We then have a set of landmarks for each image. By finding the corresponding landmarks (i.e. matching the

  10. 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…

  11. Enhancing Teaching through Constructive Alignment.

    Science.gov (United States)

    Biggs, John

    1996-01-01

    An approach to college-level instructional design that incorporates the principles of constructivism, termed "constructive alignment," is described. The process is then illustrated with reference to a professional development unit in educational psychology for teachers, but the model is viewed as generalizable to most units or programs in higher…

  12. Global alignment algorithms implementations | Fatumo ...

    African Journals Online (AJOL)

    In this paper, we implemented the two routes for sequence comparison, that is; the dotplot and Needleman-wunsch algorithm for global sequence alignment. Our algorithms were implemented in python programming language and were tested on Linux platform 1.60GHz, 512 MB of RAM SUSE 9.2 and 10.1 versions.

  13. Novel Real-time Calibration and Alignment Procedure for LHCb Run II

    CERN Multimedia

    Prouve, Claire

    2016-01-01

    In order to achieve optimal detector performance the LHCb experiment has introduced a novel real-time detector alignment and calibration strategy for Run II of the LHC. For the alignment tasks, data is collected and processed at the beginning of each fill while the calibrations are performed for each run. This real time alignment and calibration allows the same constants being used in both the online and offline reconstruction, thus improving the correlation between triggered and offline selected events. Additionally the newly computed alignment and calibration constants can be instantly used in the trigger, making it more efficient. The online alignment and calibration of the RICH detectors also enable the use of hadronic particle identification in the trigger. The computing time constraints are met through the use of a new dedicated framework using the multi-core farm infrastructure for the LHCb trigger. An overview of all alignment and calibration tasks is presented and their performance is shown.

  14. Beam-based alignment of CLIC drive beam decelerator using girders movers

    CERN Document Server

    Sterbini, G

    2011-01-01

    The CLIC drive beams will provide the rf power to accelerate the colliding beams: in order to reach the design performance, an efficient transport of the drive beam has to be ensured in spite of its challenging energy spread and large current intensity. As shown in previous studies, the specifications can be met by coupling a convenient optics design with the state-of-the-art of pre-alignment and beambased alignment techniques. In this paper we consider a novel beam-based alignment scheme that does not require quadrupole movers or dipole correctors but uses the motors already foreseen for the pre-alignment system. This implies potential savings in terms of complexity and cost at the expense of the alignment flexibility: the performance, limitations and sensitivity to pre-alignment tolerances of this method are discussed.

  15. Pairagon+N-SCAN_EST: a model-based gene annotation pipeline

    DEFF Research Database (Denmark)

    Arumugam, Manimozhiyan; Wei, Chaochun; Brown, Randall H

    2006-01-01

    This paper describes Pairagon+N-SCAN_EST, a gene annotation pipeline that uses only native alignments. For each expressed sequence it chooses the best genomic alignment. Systems like ENSEMBL and ExoGean rely on trans alignments, in which expressed sequences are aligned to the genomic loci...... with de novo gene prediction by using N-SCAN_EST. N-SCAN_EST is based on a generalized HMM probability model augmented with a phylogenetic conservation model and EST alignments. It can predict complete transcripts by extending or merging EST alignments, but it can also predict genes in regions without EST...

  16. 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

  17. Keeping speed and distance for aligned motion.

    Science.gov (United States)

    Farkas, Illés J; Kun, Jeromos; Jin, Yi; He, Gaoqi; Xu, Mingliang

    2015-01-01

    The cohesive collective motion (flocking, swarming) of autonomous agents is ubiquitously observed and exploited in both natural and man-made settings, thus, minimal models for its description are essential. In a model with continuous space and time we find that if two particles arrive symmetrically in a plane at a large angle, then (i) radial repulsion and (ii) linear self-propelling toward a fixed preferred speed are sufficient for them to depart at a smaller angle. For this local gain of momentum explicit velocity alignment is not necessary, nor are adhesion or attraction, inelasticity or anisotropy of the particles, or nonlinear drag. With many particles obeying these microscopic rules of motion we find that their spatial confinement to a square with periodic boundaries (which is an indirect form of attraction) leads to stable macroscopic ordering. As a function of the strength of added noise we see--at finite system sizes--a critical slowing down close to the order-disorder boundary and a discontinuous transition. After varying the density of particles at constant system size and varying the size of the system with constant particle density we predict that in the infinite system size (or density) limit the hysteresis loop disappears and the transition becomes continuous. We note that animals, humans, drones, etc., tend to move asynchronously and are often more responsive to motion than positions. Thus, for them velocity-based continuous models can provide higher precision than coordinate-based models. An additional characteristic and realistic feature of the model is that convergence to the ordered state is fastest at a finite density, which is in contrast to models applying (discontinuous) explicit velocity alignments and discretized time. To summarize, we find that the investigated model can provide a minimal description of flocking.

  18. GraphAlignment: Bayesian pairwise alignment of biological networks

    Czech Academy of Sciences Publication Activity Database

    Kolář, Michal; Meier, J.; Mustonen, V.; Lässig, M.; Berg, J.

    2012-01-01

    Roč. 6, November 21 (2012) ISSN 1752-0509 Grant - others:Deutsche Forschungsgemeinschaft(DE) SFB 680; Deutsche Forschungsgemeinschaft(DE) SFB-TR12; Deutsche Forschungsgemeinschaft(DE) BE 2478/2-1 Institutional research plan: CEZ:AV0Z50520514 Keywords : Graph alignment * Biological networks * Parameter estimation * Bioconductor Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.982, year: 2012

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

    Indian Academy of Sciences (India)

    Carbon nanotube; arc discharge; characterization; alignment; nanoscratch. 1. Introduction ... During arc discharge, when the gap between the electrodes is ∼ 1 mm, ..... increase in the D band intensity in the aligned region may not be possibly ...

  20. Alignment of the eight beams Octal 82 laser

    International Nuclear Information System (INIS)

    Josse, Michel.

    1982-10-01

    The OCTAL 82 laser facility is a Neodymium glass laser system, recently put in operation at Limeil, France. It is designed to create high energy light beams during very short periods of time in the nanosecond range and shorter, in order to irradiate and compress microscopic fusion targets to extremely high densities. The alignment is undertaken in two stages, each using a telescope with vidicon detectors connected to a real time computer named ''CENTROIDE'' which displays the digitized image on a color TV screen. First, a refracting telescope is used to inject the front-end beam into the preamplifier assembly and to align all its optical components. Second, a reflecting telescope and ten insertable mirrors are used to align the eight individual power chains and the beam splitter arrays. The alignment method works with a manually controlled closed loop which is the most flexible approach that can meet our dual objectives of reliability and accuracy. The over all alignment of OCTAL 82 was first completed in may 1982 and since that time only minor routine realignments have been made, thereby proving the feasibility of the method

  1. Aperiodic order

    CERN Document Server

    Grimm, Uwe

    2017-01-01

    Quasicrystals are non-periodic solids that were discovered in 1982 by Dan Shechtman, Nobel Prize Laureate in Chemistry 2011. The mathematics that underlies this discovery or that proceeded from it, known as the theory of Aperiodic Order, is the subject of this comprehensive multi-volume series. This second volume begins to develop the theory in more depth. A collection of leading experts, among them Robert V. Moody, cover various aspects of crystallography, generalising appropriately from the classical case to the setting of aperiodically ordered structures. A strong focus is placed upon almost periodicity, a central concept of crystallography that captures the coherent repetition of local motifs or patterns, and its close links to Fourier analysis. The book opens with a foreword by Jeffrey C. Lagarias on the wider mathematical perspective and closes with an epilogue on the emergence of quasicrystals, written by Peter Kramer, one of the founders of the field.

  2. Gene expression

    International Nuclear Information System (INIS)

    Hildebrand, C.E.; Crawford, B.D.; Walters, R.A.; Enger, M.D.

    1983-01-01

    We prepared probes for isolating functional pieces of the metallothionein locus. The probes enabled a variety of experiments, eventually revealing two mechanisms for metallothionein gene expression, the order of the DNA coding units at the locus, and the location of the gene site in its chromosome. Once the switch regulating metallothionein synthesis was located, it could be joined by recombinant DNA methods to other, unrelated genes, then reintroduced into cells by gene-transfer techniques. The expression of these recombinant genes could then be induced by exposing the cells to Zn 2+ or Cd 2+ . We would thus take advantage of the clearly defined switching properties of the metallothionein gene to manipulate the expression of other, perhaps normally constitutive, genes. Already, despite an incomplete understanding of how the regulatory switch of the metallothionein locus operates, such experiments have been performed successfully

  3. Assessing strategic alignment to improve IT effectiveness

    NARCIS (Netherlands)

    Smits, M.T.; Fairchild, A.M.; Ribbers, P.M.A.; Milis, K.; van Geel, E.; Markus, M.L.; Hampe, J.F.; Gricar, J.; Pucihar, A.; Lenart, G.

    2009-01-01

    A long running challenge in both large and small organizations has been aligning information systems services with business needs. Good alignment is assumed to lead to good business results, but there is a need for good instruments to assess strategic alignment and business success in practice.

  4. 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.

  5. Curricular Alignment: A Re-examination.

    Science.gov (United States)

    Anderson, Lorin W.

    2002-01-01

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

  6. Study of CMOS Image Sensors for the Alignment System of the CMS Experiment

    Energy Technology Data Exchange (ETDEWEB)

    Virto, A. L.; Vila, I.; Rodrigo, T.; Matorras, F.; Figueroa, C. F.; Calvo, E.; Calderon, A.; Arce, P.; Oller, J. C.; Molinero, A.; Josa, M. I.; Fuentes, J.; Ferrando, A.; Fernandez, M. G.; Barcala, J. M.

    2002-07-01

    We report on an in-depth study made on commercial CMOS image sensors in order to determine their feasibility for beam light position detection in the CMS multipoint alignment scheme. (Author) 21 refs.

  7. Alignment of the VISA Undulator

    International Nuclear Information System (INIS)

    Ruland, Robert E.

    2000-01-01

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

  8. Position list word aligned hybrid

    DEFF Research Database (Denmark)

    Deliege, Francois; Pedersen, Torben Bach

    2010-01-01

    Compressed bitmap indexes are increasingly used for efficiently querying very large and complex databases. The Word Aligned Hybrid (WAH) bitmap compression scheme is commonly recognized as the most efficient compression scheme in terms of CPU efficiency. However, WAH compressed bitmaps use a lot...... of storage space. This paper presents the Position List Word Aligned Hybrid (PLWAH) compression scheme that improves significantly over WAH compression by better utilizing the available bits and new CPU instructions. For typical bit distributions, PLWAH compressed bitmaps are often half the size of WAH...... bitmaps and, at the same time, offer an even better CPU efficiency. The results are verified by theoretical estimates and extensive experiments on large amounts of both synthetic and real-world data....

  9. Beam based alignment of the SLC final focus sextupoles

    International Nuclear Information System (INIS)

    Emma, P.; Irwin, J.; Phinney, N.; Raimondi, P.; Toge, N.; Walker, N.J.; Ziemann, V.

    1993-05-01

    The strong demagnification inherent in final focus systems requires local cancellation of the resulting chromaticty. Strong sextupole pair separated by a -I transform are positioned π/2 in the betatron phase away from the Interaction Point (IP) in order to cancel chromatic aberrations primarily due to the final quadrupoles. Sextupole alignment is critical in order to provide orthogonal tuning of the chromaticty and, in the case of the SLC, to limit the third and higher order optical aberrations generated from misaligned and 'nested' horizontal and vertical sextupole pairs. Reported here is a novel technique for aligning the beam centroid to the sextupole centers, which uses measurements of the criticality dependent parameter - the beam size at the IP. Results for the SLC final focus sextupoles are presented, where a resolution of <50 μm is achieved

  10. The rigors of aligning performance

    OpenAIRE

    Hart, Andrew; Lucas, James

    2015-01-01

    Approved for public release; distribution is unlimited This Joint Applied Project addresses what can be done within the Naval Facilities Engineering Command Northwest community to better align its goals among competing interests from various stakeholders, while balancing the operational and regulatory constraints that often conflict with stakeholder goals and objectives. As a cross-functional organization, competing interests among the various business lines, support lines, and other stake...

  11. Alignment in double capture processes

    International Nuclear Information System (INIS)

    Moretto-Capelle, P.; Benhenni, M.; Bordenave-Montesquieu, A.; Benoit-Cattin, P.; Gleizes, A.

    1993-01-01

    The electron spectra emitted when a double capture occurs in N 7+ +He and Ne 8+ +He systems at 10 qkeV collisional energy, allow us to determine the angular distributions of the 3 ell 3 ell ' lines through a special spectra fitting procedure which includes interferences between neighbouring states. It is found that the doubly excited states populated in double capture processes are generally aligned

  12. Alignment in double capture processes

    Energy Technology Data Exchange (ETDEWEB)

    Moretto-Capelle, P.; Benhenni, M.; Bordenave-Montesquieu, A.; Benoit-Cattin, P.; Gleizes, A. (IRSAMC, URA CNRS 770, Univ. Paul Sabatier, 118 rte de Narbonne, 31062 Toulouse Cedex (France))

    1993-06-05

    The electron spectra emitted when a double capture occurs in N[sup 7+]+He and Ne[sup 8+]+He systems at 10 qkeV collisional energy, allow us to determine the angular distributions of the 3[ell]3[ell] [prime] lines through a special spectra fitting procedure which includes interferences between neighbouring states. It is found that the doubly excited states populated in double capture processes are generally aligned.

  13. Interest alignment and competitive advantage

    OpenAIRE

    Gottschalg, Oliver; Zollo, Mauricio

    2006-01-01

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

  14. International Business And Aligning CSR

    Directory of Open Access Journals (Sweden)

    Daniel Miret

    2017-11-01

    Full Text Available The labor relationship between the employer and the workers is evaluated and directed by the labor rights which is a group of legal rights that are derived from human rights. Labor rights are more precisely relative to CSR as CSR are based on perspective and point of view of a given corporation. In this perspective implementing the workers and labor rights becomes more difficult compared to the implementation of the CSR. If an international corporation can be able to align CSR with the labor laws the friction between the employees and the corporation and the employee is likely to reduce. There is need to explore whether multinational corporations can be able to align CSR with the labor rights and employee initiatives global market. In this case the analysis focuses on China Brazil and India as the reference countries with cross-sectional secondary data obtained from a survey of the existing sources on the internet. The pertinent question is whether multinational corporations be successful while aligning CSR Corporate Social Responsibility with labor rights and employee initiatives in a competitive global market based on that cross-sectional data. The findings reveal that the uphold of labor rights largely determines morale of the employees and the will to participate in the growth and development of a given business both locally and international. Notably the continued change of CSR has resulted in the replacement of management and government dominated trade unions with more democratic unions of workers that pay attention to the initiatives of the workers. The combination of the internal code of conduct with the workers association labor associations and movements is one of the credible routes that show CSR can be aligned with labor rights.

  15. Axially alignable nuclear fuel pellets

    International Nuclear Information System (INIS)

    Johansson, E.B.; Klahn, D.H.; Marlowe, M.O.

    1978-01-01

    An axially alignable nuclear fuel pellet of the type stacked in end-to-end relationship within a tubular cladding is described. Fuel cladding failures can occur at pellet interface locations due to mechanical interaction between misaligned fuel pellets and the cladding. Mechanical interaction between the cladding and the fuel pellets loads the cladding and causes increased cladding stresses. Nuclear fuel pellets are provided with an end structure that increases plastic deformation of the pellets at the interface between pellets so that lower alignment forces are required to straighten axially misaligned pellets. Plastic deformation of the pellet ends results in less interactions beween the cladding and the fuel pellets and significantly lowers cladding stresses. The geometry of pellets constructed according to the invention also reduces alignment forces required to straighten fuel pellets that are tilted within the cladding. Plastic deformation of the pellets at the pellet interfaces is increased by providing pellets with at least one end face having a centrally-disposed raised area of convex shape so that the mean temperature and shear stress of the contact area is higher than that of prior art pellets

  16. 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)

  17. 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.

  18. Photodissociation of spatially aligned acetaldehyde cations.

    Science.gov (United States)

    Lee, Suk Kyoung; Silva, Ruchira; Kim, Myung Hwa; Shen, Lei; Suits, Arthur G

    2007-07-26

    Photofragment translational energy and angular distributions are reported for the photodissociation of acetaldehyde cations in the wavelength range 354-363 nm obtained using the DC slice ion imaging technique. Vibrationally selected parent ions were produced by 2+1 resonance-enhanced multiphoton ionization (REMPI) via the 3sCH3CO+, and CH4+. The angular distributions reveal that all product channels have a predominantly parallel recoil anisotropy although the lower beta2 parameter of CH3CO+ indicates the concomitant presence of a perpendicular component. Furthermore, the distinct angular distribution of the CH3CO+ fragments shows a large value of the higher order Legendre polynomial term, providing evidence that acetaldehyde cations are spatially aligned during the ionization process.

  19. 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/

  20. 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....

  1. 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

  2. Mining biological databases for candidate disease genes

    Science.gov (United States)

    Braun, Terry A.; Scheetz, Todd; Webster, Gregg L.; Casavant, Thomas L.

    2001-07-01

    The publicly-funded effort to sequence the complete nucleotide sequence of the human genome, the Human Genome Project (HGP), has currently produced more than 93% of the 3 billion nucleotides of the human genome into a preliminary `draft' format. In addition, several valuable sources of information have been developed as direct and indirect results of the HGP. These include the sequencing of model organisms (rat, mouse, fly, and others), gene discovery projects (ESTs and full-length), and new technologies such as expression analysis and resources (micro-arrays or gene chips). These resources are invaluable for the researchers identifying the functional genes of the genome that transcribe and translate into the transcriptome and proteome, both of which potentially contain orders of magnitude more complexity than the genome itself. Preliminary analyses of this data identified approximately 30,000 - 40,000 human `genes.' However, the bulk of the effort still remains -- to identify the functional and structural elements contained within the transcriptome and proteome, and to associate function in the transcriptome and proteome to genes. A fortuitous consequence of the HGP is the existence of hundreds of databases containing biological information that may contain relevant data pertaining to the identification of disease-causing genes. The task of mining these databases for information on candidate genes is a commercial application of enormous potential. We are developing a system to acquire and mine data from specific databases to aid our efforts to identify disease genes. A high speed cluster of Linux of workstations is used to analyze sequence and perform distributed sequence alignments as part of our data mining and processing. This system has been used to mine GeneMap99 sequences within specific genomic intervals to identify potential candidate disease genes associated with Bardet-Biedle Syndrome (BBS).

  3. The pkI gene encoding pyruvate kinase I links to the luxZ gene which enhances bioluminescence of the lux operon from Photobacterium leiognathi.

    Science.gov (United States)

    Lin, J W; Lu, H C; Chen, H Y; Weng, S F

    1997-10-09

    Partial 3'-end nucleotide sequence of the pkI gene (GenBank accession No. AF019143) from Photobacterium leiognathi ATCC 25521 has been determined, and the encoded pyruvate kinase I is deduced. Pyruvate kinase I is the key enzyme of glycolysis, which converts phosphoenol pyruvate to pyruvate. Alignment and comparison of pyruvate kinase Is from P. leiognathi, E. coli and Salmonella typhimurium show that they are homologous. Nucleotide sequence reveals that the pkI gene is linked to the luxZ gene that enhances bioluminescence of the lux operon from P. leiognathi. The gene order of the pkI and luxZ genes is-pk1-ter-->-R&R"-luxZ-ter"-->, whereas ter is transcriptional terminator for the pkI and related genes, and R&R" is the regulatory region and ter" is transcriptional terminator for the luxZ gene. It clearly elicits that the pkI gene and luxZ gene are divided to two operons. Functional analysis confirms that the potential hairpin loop omega T is the transcriptional terminator for the pkI and related genes. It infers that the pkI and related genes are simply linked to the luxZ gene in P. leiognathi genome.

  4. Induced alignment and measurement of dipolar couplings of an SH2 domain through direct binding with filamentous phage

    International Nuclear Information System (INIS)

    Dahlke Ojennus, Deanna; Mitton-Fry, Rachel M.; Wuttke, Deborah S.

    1999-01-01

    Large residual 15 N- 1 H dipolar couplings have been measured in a Src homology II domain aligned at Pf1 bacteriophage concentrations an order of magnitude lower than used for induction of a similar degree of alignment of nucleic acids and highly acidic proteins. An increase in 1 H and 15 N protein linewidths and a decrease in T 2 and T 1 ρ relaxation time constants implicates a binding interaction between the protein and phage as the mechanism of alignment. However, the associated increased linewidth does not preclude the accurate measurement of large dipolar couplings in the aligned protein. A good correlation is observed between measured dipolar couplings and predicted values based on the high resolution NMR structure of the SH2 domain. The observation of binding-induced protein alignment promises to broaden the scope of alignment techniques by extending their applicability to proteins that are able to interact weakly with the alignment medium

  5. Antares beam-alignment-system performance

    International Nuclear Information System (INIS)

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

    1983-01-01

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

  6. A practical strategy for the accurate measurement of residual dipolar couplings in strongly aligned small molecules

    Science.gov (United States)

    Liu, Yizhou; Cohen, Ryan D.; Martin, Gary E.; Williamson, R. Thomas

    2018-06-01

    Accurate measurement of residual dipolar couplings (RDCs) requires an appropriate degree of alignment in order to optimize data quality. An overly weak alignment yields very small anisotropic data that are susceptible to measurement errors, whereas an overly strong alignment introduces extensive anisotropic effects that severely degrade spectral quality. The ideal alignment amplitude also depends on the specific pulse sequence used for the coupling measurement. In this work, we introduce a practical strategy for the accurate measurement of one-bond 13C-1H RDCs up to a range of ca. -300 to +300 Hz, corresponding to an alignment that is an order of magnitude stronger than typically employed for small molecule structural elucidation. This strong alignment was generated in the mesophase of the commercially available poly-γ-(benzyl-L-glutamate) polymer. The total coupling was measured by the simple and well-studied heteronuclear two-dimensional J-resolved experiment, which performs well in the presence of strong anisotropic effects. In order to unequivocally determine the sign of the total coupling and resolve ambiguities in assigning total couplings in the CH2 group, coupling measurements were conducted at an isotropic condition plus two anisotropic conditions of different alignment amplitudes. Most RDCs could be readily extracted from these measurements whereas more complicated spectral effects resulting from strong homonuclear coupling could be interpreted either theoretically or by simulation. Importantly, measurement of these very large RDCs actually offers significantly improved data quality and utility for the structure determination of small organic molecules.

  7. MEANS FOR DETERMINING CENTRIFUGE ALIGNMENT

    Science.gov (United States)

    Smith, W.Q.

    1958-08-26

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

  8. NON-ALIGNEMENT IN AFRICA

    OpenAIRE

    G. Jacobs

    2012-01-01

    The first indications to the Western world that African non-alignment had achieved conscious political form became apparent only in the late 1940's. This strand of thought within the tapestry of Africanism reached its zenith with the declarations of Kwame Nkrumah, Jomo Kenyatta and Julius Nyerere in the years after the Pan-African Congress in Manchester in 1945. The causes of the movement go back far beyond the first official expressions of an African solidarity in the 1940's. As a mature exp...

  9. Alignment of the ATLAS Inner Detector Tracking System

    CERN Document Server

    Heller, C; The ATLAS collaboration

    2011-01-01

    ATLAS is one of the multipurpose experiments that records the products of the LHC proton-proton and heavy ion collisions. In order to reconstruct trajectories of charged particles produced in these collisions, ATLAS is equipped with a tracking system built using two different technologies, silicon planar sensors (pixel and microstrips) and drift-tube based detectors. Together they constitute the ATLAS Inner Detector, which is embedded in a 2 T axial field. Efficiently reconstructing tracks from charged particles traversing the detector, and precisely measure their momenta is of crucial importance for physics analyses. In order to achieve its scientific goals, an alignment of the ATLAS Inner Detector is required to accurately determine its more than 700,000 degrees of freedom. The goal of the alignment is set such that the limited knowledge of the sensor locations should not deteriorate the resolution of track parameters by more than 20% with respect to the intrinsic tracker resolution. The implementation of t...

  10. Evolutionary rates at codon sites may be used to align sequences and infer protein domain function

    Directory of Open Access Journals (Sweden)

    Hazelhurst Scott

    2010-03-01

    Full Text Available Abstract Background Sequence alignments form part of many investigations in molecular biology, including the determination of phylogenetic relationships, the prediction of protein structure and function, and the measurement of evolutionary rates. However, to obtain meaningful results, a significant degree of sequence similarity is required to ensure that the alignments are accurate and the inferences correct. Limitations arise when sequence similarity is low, which is particularly problematic when working with fast-evolving genes, evolutionary distant taxa, genomes with nucleotide biases, and cases of convergent evolution. Results A novel approach was conceptualized to address the "low sequence similarity" alignment problem. We developed an alignment algorithm termed FIRE (Functional Inference using the Rates of Evolution, which aligns sequences using the evolutionary rate at codon sites, as measured by the dN/dS ratio, rather than nucleotide or amino acid residues. FIRE was used to test the hypotheses that evolutionary rates can be used to align sequences and that the alignments may be used to infer protein domain function. Using a range of test data, we found that aligning domains based on evolutionary rates was possible even when sequence similarity was very low (for example, antibody variable regions. Furthermore, the alignment has the potential to infer protein domain function, indicating that domains with similar functions are subject to similar evolutionary constraints. These data suggest that an evolutionary rate-based approach to sequence analysis (particularly when combined with structural data may be used to study cases of convergent evolution or when sequences have very low similarity. However, when aligning homologous gene sets with sequence similarity, FIRE did not perform as well as the best traditional alignment algorithms indicating that the conventional approach of aligning residues as opposed to evolutionary rates remains the

  11. Molecular-alignment dependence in the transfer excitation of H2

    International Nuclear Information System (INIS)

    Wang, Y.D.; McGuire, J.H.; Weaver, O.L.; Corchs, S.E.; Rivarola, R.D.

    1993-01-01

    Molecular-alignment effects in the transfer excitation of H 2 by high-velocity heavy ions are studied using a two-step mechanism with amplitudes evaluated from first-order perturbation theory. Two-electron transfer excitation is treated as a result of two independent collision processes (excitation and electron transfer). Cross sections for each one-electron subprocess as well as the combined two-electron process are calculated as functions of the molecular-alignment angle. Within the independent-electron approximation, the dynamic roles of electron excitation and transfer in conjunction with molecular alignment are explored. While both excitation and transfer cross sections may strongly depend on molecular alignment, it is electron transfer that is largely responsible for the molecular-alignment dependence in the transfer excitation process. Interpretation of some experimental observations based on this model will also be discussed

  12. TMRG studies on spin alignment in molecule-based ferrimagnetics [rapid communication

    Science.gov (United States)

    Liu, Q. M.; Yao, K. L.; Liu, Z. L.

    2005-05-01

    A physical picture of spin alignment in organic molecule-based ferrimagnets is presented from studying the thermal effective magnetic moment of the sublattice by use of the transfer matrix renormalization group. We conclude that the classical antiparallel spin alignment is not the most stable state. The three-spin system tends to parallel alignment when the exchange interaction between the biradical and the monoradical molecules is much weaker than that within the biradical, which can result in the decrease of the effective magnetic moment upon lowering the temperature. More importantly, we give the theoretical evidence that even the antiparallel spin alignment in the biradical monoradical alternating chain does not necessarily lead to ferrimagnetic spin ordering due to the formation of the spin singlet pairs, which suppresses the ferrimagnetic spin alignment.

  13. A novel laser alignment system for tracking detectors using transparent silicon strip sensors

    International Nuclear Information System (INIS)

    Blum, W.; Kroha, H.; Widmann, P.

    1995-02-01

    Modern large-area precision tracking detectors require increasing accuracy of the geometrical alignment over large distances. A novel optical multi-point alignment system has been developed for the muon spectrometer of the ATLAS detector at the Large Hadron Collider. The system uses collimated laser beams as alignment references which are monitored by semi-transparent optical position sensors. The custom designed sensors provide very precise and uniform position information on the order of 1 μm over a wide measurement range. At suitable laser wavelengths, produced by laser diodes, transmission rates above 90% have been achieved which allow to align more than 30 sensors along one laser beam. With this capability and equipped with integrated readout electronics, the alignment system offers high flexibility for precision applications in a wide range of detector systems. (orig.)

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

    DEFF Research Database (Denmark)

    Wernersson, Rasmus; Pedersen, Anders Gorm

    2003-01-01

    The simple fact that proteins are built from 20 amino acids while DNA only contains four different bases, means that the 'signal-to-noise ratio' in protein sequence alignments is much better than in alignments of DNA. Besides this information-theoretical advantage, protein alignments also benefit...... proteins. It is therefore preferable to align coding DNA at the amino acid level and it is for this purpose we have constructed the program RevTrans. RevTrans constructs a multiple DNA alignment by: (i) translating the DNA; (ii) aligning the resulting peptide sequences; and (iii) building a multiple DNA...

  15. Fractional Order Element Based Impedance Matching

    KAUST Repository

    Radwan, Ahmed Gomaa

    2014-06-24

    Disclosed are various embodiments of methods and systems related to fractional order element based impedance matching. In one embodiment, a method includes aligning a traditional Smith chart (|.alpha.|=1) with a fractional order Smith chart (|.alpha.|.noteq.1). A load impedance is located on the traditional Smith chart and projected onto the fractional order Smith chart. A fractional order matching element is determined by transitioning along a matching circle of the fractional order Smith chart based at least in part upon characteristic line impedance. In another embodiment, a system includes a fractional order impedance matching application executed in a computing device. The fractional order impedance matching application includes logic that obtains a first set of Smith chart coordinates at a first order, determines a second set of Smith chart coordinates at a second order, and determines a fractional order matching element from the second set of Smith chart coordinates.

  16. China And The International Order

    Science.gov (United States)

    2018-01-01

    existing order, it stated that China will “take an active part in reforming and developing 13 Feng Zhang, “Chinese Thinking on the South China Sea and the...interests and those that do not align as closely with U.S. interests. China might be challenging 19 Zhang’s “Chinese Thinking on the South China...China Bets on Sensitive U.S. Start-Ups, Worrying the Pentagon,” New York Times, March 22, 2017a; Paul Mozur and Jane Perlez, “China Tech Investment

  17. 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

  18. Nuclear alignment following compound nucleus reactions

    International Nuclear Information System (INIS)

    Butler, P.A.; Nolan, P.J.

    1981-01-01

    A procedure for calculating the alignment of a nuclear state populated by a compound nucleus reaction is given and used to investigate how alignment varies for different types of population mechanisms. The calculations are compared to both predictions of Gaussian models for the state population distribution and to experimental data, for a variety of types of nuclear reactions. The treatment of alignment in the analysis of γ-ray angular distribution is discussed. (orig.)

  19. Clear aligners generations and orthodontic tooth movement.

    Science.gov (United States)

    Hennessy, Joe; Al-Awadhi, Ebrahim A

    2016-03-01

    Clear aligner technology has evolved over the last 15 years, with these appliances continually being modified to increase the range of tooth movements that they can achieve. However, there is very little clinical research available to show how these appliances achieve their results. This article describes the different generations of clear aligners that are available and highlights their use. However, until more clinical research becomes available, aligners cannot be routinely prescribed as an effective alternative to fixed labial appliances.

  20. Sub-cell turning to accomplish micron-level alignment of precision assemblies

    Science.gov (United States)

    Kumler, James J.; Buss, Christian

    2017-08-01

    Higher performance expectations for complex optical systems demand tighter alignment requirements for lens assembly alignment. In order to meet diffraction limited imaging performance over wide spectral bands across the UV and visible wavebands, new manufacturing approaches and tools must be developed if the optical systems will be produced consistently in volume production. This is especially applicable in the field of precision microscope objectives for life science, semiconductor inspection and laser material processing systems. We observe a rising need for the improvement in the optical imaging performance of objective lenses. The key challenge lies in the micron-level decentration and tilt of each lens element. One solution for the production of high quality lens systems is sub-cell assembly with alignment turning. This process relies on an automatic alignment chuck to align the optical axis of a mounted lens to the spindle axis of the machine. Subsequently, the mount is cut with diamond tools on a lathe with respect to the optical axis of the mount. Software controlled integrated measurement technology ensures highest precision. In addition to traditional production processes, further dimensions can be controlled in a very precise manner, e.g. the air gaps between the lenses. Using alignment turning simplifies further alignment steps and reduces the risk of errors. This paper describes new challenges in microscope objective design and manufacturing, and addresses difficulties with standard production processes. A new measurement and alignment technique is described, and strengths and limitations are outlined.

  1. Hybrid hydrogels containing vertically aligned carbon nanotubes with anisotropic electrical conductivity for muscle myofiber fabrication.

    Science.gov (United States)

    Ahadian, Samad; Ramón-Azcón, Javier; Estili, Mehdi; Liang, Xiaobin; Ostrovidov, Serge; Shiku, Hitoshi; Ramalingam, Murugan; Nakajima, Ken; Sakka, Yoshio; Bae, Hojae; Matsue, Tomokazu; Khademhosseini, Ali

    2014-03-19

    Biological scaffolds with tunable electrical and mechanical properties are of great interest in many different fields, such as regenerative medicine, biorobotics, and biosensing. In this study, dielectrophoresis (DEP) was used to vertically align carbon nanotubes (CNTs) within methacrylated gelatin (GelMA) hydrogels in a robust, simple, and rapid manner. GelMA-aligned CNT hydrogels showed anisotropic electrical conductivity and superior mechanical properties compared with pristine GelMA hydrogels and GelMA hydrogels containing randomly distributed CNTs. Skeletal muscle cells grown on vertically aligned CNTs in GelMA hydrogels yielded a higher number of functional myofibers than cells that were cultured on hydrogels with randomly distributed CNTs and horizontally aligned CNTs, as confirmed by the expression of myogenic genes and proteins. In addition, the myogenic gene and protein expression increased more profoundly after applying electrical stimulation along the direction of the aligned CNTs due to the anisotropic conductivity of the hybrid GelMA-vertically aligned CNT hydrogels. We believe that platform could attract great attention in other biomedical applications, such as biosensing, bioelectronics, and creating functional biomedical devices.

  2. Aligned carbon nanotubes patterned photolithographically by silver

    Science.gov (United States)

    Huang, Shaoming; Mau, Albert H. W.

    2003-02-01

    Selective growth of aligned carbon nanotubes (CNTs) by pyrolysis of iron (II) phthalocyanine (FePc) on quartz substrate patterned photolithographically by metallic silver has been demonstrated. Micro/nanopattern of aligned CNTs can be achieved by using a photomask with features on a microscale. With convenient use of simple high-contract black and white films as a photomask, aligned nanotubes patterned with 20 μm resolution in large scale can be fabricated. This practical fabrication of aligned CNTs on patterned conducting substrate could be applied to various device applications of CNTs.

  3. The art of editing RNA structural alignments

    DEFF Research Database (Denmark)

    Andersen, Ebbe Sloth

    2014-01-01

    Manual editing of RNA structural alignments may be considered more art than science, since it still requires an expert biologist to take multiple levels of information into account and be slightly creative when constructing high-quality alignments. Even though the task is rather tedious, it is re......Manual editing of RNA structural alignments may be considered more art than science, since it still requires an expert biologist to take multiple levels of information into account and be slightly creative when constructing high-quality alignments. Even though the task is rather tedious...

  4. Peripheral pin alignment system for fuel assemblies

    International Nuclear Information System (INIS)

    Anthony, A.J.

    1981-01-01

    An alignment system is provided for nuclear fuel assemblies in a nuclear core. The core support structure of the nuclear reactor includes upwardly pointing alignment pins arranged in a square grid and engage peripheral depressions formed in the lateral periphery of the lower ends of each of the fuel assemblies of the core. In a preferred embodiment, the depressions are located at the corners of the fuel assemblies so that each depression includes one-quarter of a cylindrical void. Accordingly, each fuel assembly is positioned and aligned by one-quarter of four separate alignment pins which engage the fuel assemblies at their lower exterior corners. (author)

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

    KAUST Repository

    Cui, Xuefeng

    2015-09-09

    (PROSTA) family of pairwise structure alignment methods [1, 2] that address the fragmentation issue of pockets and interfaces, and automatically align interfaces between any types of biological complexes. Our PROSTA structure alignment methods have two critical advantages comparing to existing structure alignment methods. First, our methods are completely sequence order independent, which is critical to the success of pairwise pocket and interface structure alignments. This is achieved by introducing contact groups that are not limited to backbone fragments, and by employing a maximum weighted bipartite matching solver from the beginning of the alignment process. In addition, our methods incorporate similarities of sequentially and structurally remote residues that potentially model the topology of the global structure. Comparing to existing methods that focus on local structure or whole sequence similarities, topological similarities are more reliable to find near-optimal structure alignments in the initial alignment state. As a result, a significant number of similar pockets and interfaces are newly discovered, and literatures also support that similar functions are shared between biological complexes in our cases studies. The PROSTA web-server and source codes are publicly available at "http://www.cbrc.kaust.edu.sa/prosta/".

  6. Surface-induced ordering of a liquid crystal in the isotropic phase

    International Nuclear Information System (INIS)

    Miyano, K.

    1979-01-01

    A detailed account of a measurement of order parameter of a liquid crystal at the boundary by means of the wall-induced pretransitional birefringence is given. Several surface treatments were studied including surfactants and evaporated films. Although all treatments produced good alignment in the nematic phase, the boundary order parameter (hence the strength of the aligning force) in the isotropic phase differed very much depending on the treatment, indicating the diverse nature of the alignment process

  7. Aligning seminars with Bologna requirements

    DEFF Research Database (Denmark)

    Lueg, Rainer; Lueg, Klarissa; Lauridsen, Ole

    2016-01-01

    Changes in public policy, such as the Bologna Process, require students to be equipped with multifunctional competencies to master relevant tasks in unfamiliar situations. Achieving this goal might imply a change in many curricula toward deeper learning. As a didactical means to achieve deep...... learning results, the authors suggest reciprocal peer tutoring (RPT); as a conceptual framework the authors suggest the SOLO (Structure of Observed Learning Outcomes) taxonomy and constructive alignment as suggested by Biggs and Tang. Our study presents results from the introduction of RPT in a large...... and students, suggest that RPT fosters deeper learning than does teacher-led instruction. Based on these findings, the authors also offer guidelines regarding how to implement RPT and how to overcome barriers....

  8. Scintillation counter: photomultiplier tube alignment

    International Nuclear Information System (INIS)

    Olson, R.E.

    1975-01-01

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

  9. Quantized wobbling excitations with alignments

    International Nuclear Information System (INIS)

    Hamamoto, Ikuko; Hagemann, Gudrun B.

    2003-01-01

    The wobbling excitations in the presence of an appreciable amount of alignment are expected to appear more easily at lower angular momenta of the yrast spectra, compared with those in the textbook example. The large B(E2;I→I-1) value for Δn=1 transitions where n expresses the number of wobbling phonons is shown to be a strongly increasing function of the triaxiality parameter γ, especially for γ > or approx. +20 deg., while it is relatively independent of moments of inertia. On the other hand, the relation of the wobbling phonon energy to the total angular momentum may be used to extract quantitative information on nuclear moments of inertia. It is concluded that the γ value of the triaxial, strongly deformed bands in 163 Lu is about equal to +20 deg. and may be slightly increasing as a function of I

  10. Genes and Gene Therapy

    Science.gov (United States)

    ... correctly, a child can have a genetic disorder. Gene therapy is an experimental technique that uses genes to ... or prevent disease. The most common form of gene therapy involves inserting a normal gene to replace an ...

  11. 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

  12. The development of alignment turning system for precision len cells

    Science.gov (United States)

    Huang, Chien-Yao; Ho, Cheng-Fang; Wang, Jung-Hsing; Chung, Chien-Kai; Chen, Jun-Cheng; Chang, Keng-Shou; Kuo, Ching-Hsiang; Hsu, Wei-Yao; Chen, Fong-Zhi

    2017-08-01

    In general, the drop-in and cell-mounted assembly are used for standard and high performance optical system respectively. The optical performance is limited by the residual centration error and position accuracy of the conventional assembly. Recently, the poker chip assembly with high precision lens barrels that can overcome the limitation of conventional assembly is widely applied to ultra-high performance optical system. ITRC also develops the poker chip assembly solution for high numerical aperture objective lenses and lithography projection lenses. In order to achieve high precision lens cell for poker chip assembly, an alignment turning system (ATS) is developed. The ATS includes measurement, alignment and turning modules. The measurement module including a non-contact displacement sensor and an autocollimator can measure centration errors of the top and the bottom surface of a lens respectively. The alignment module comprising tilt and translation stages can align the optical axis of the lens to the rotating axis of the vertical lathe. The key specifications of the ATS are maximum lens diameter, 400mm, and radial and axial runout of the rotary table < 2 μm. The cutting performances of the ATS are surface roughness Ra < 1 μm, flatness < 2 μm, and parallelism < 5 μm. After measurement, alignment and turning processes on our ATS, the centration error of a lens cell with 200mm in diameter can be controlled in 10 arcsec. This paper also presents the thermal expansion of the hydrostatic rotating table. A poker chip assembly lens cell with three sub-cells is accomplished with average transmission centration error in 12.45 arcsec by fresh technicians. The results show that ATS can achieve high assembly efficiency for precision optical systems.

  13. Angle alignment evokes perceived depth and illusory surfaces.

    Science.gov (United States)

    Shapley, Robert; Maertens, Marianne

    2008-01-01

    There is a distinct visual process that triggers the perception of illusory surfaces and contours along the intersections of aligned, zigzag line patterns. Such illusory contours and surfaces are qualitatively different from illusory contours of the Kanizsa type. The illusory contours and surfaces in this case are not the product of occlusion and do not imply occlusion of one surface by another. Rather, the aligned angles in the patterns are combined by the visual system into the perception of a fold or a 3-D corner, as of stairs on a staircase or a wall ending on a floor. The depth impression is ambiguous and reversible like the Necker cube. Such patterns were used by American Indian artists of the Akimel O'odham (Pima) tribe in basketry, and also by modern European and American artists like Josef Albers, Bridget Riley, Victor Vasarely, and Frank Stella. Our research aims to find out what manipulations of the visual image affect perceived depth in such patterns in order to learn about the perceptual mechanisms. Using paired comparisons, we find that human observers perceive depth in such patterns if, and only if, lines in adjacent regions of the patterns join to form angles, and also if, and only if, the angles are aligned precisely to be consistent with a fold or 3-D corner. The amount of perceived depth is graded, depending on the steepness and the density of angles in the aligned-angle pattern. The required precision of the alignment implies that early retinotopic visual cortical areas may be involved in this perceptual behavior, but the linkage of form with perceived depth suggests involvement of higher cortical areas as well.

  14. An OMG model-based approach for aligning information systems requirements and architectures with business

    OpenAIRE

    Salgado, Carlos Eduardo Rodrigues Teixeira

    2017-01-01

    Tese de Doutoramento (Programa Doutoral em Tecnologias e Sistemas de Informação) The challenges involved in developing information systems (which are able to adapt to rapidly changing business and technological conditions) are directly related to the importance of their alignment with the business counterpart. These challenges comprise issues that cross management and information systems domains, relating and aligning them in order to attain superior performance for the organiz...

  15. Thesaurus maintenance, alignment and publication as linked data: the AGROVOC use case

    OpenAIRE

    Caracciolo, Caterina; Stellato, Armando; Rajbahndari, Sachit; Morshed, Ahsan; Johannsen, Gudrun; Jaques, Yves; Keizer, Johannes

    2012-01-01

    The AGROVOC multilingual thesaurus maintained by the Food and Agriculture Organisation (FAO) of the United Nations is now published as linked data. In order to reach this goal AGROVOC was expressed in Simple Knowledge Organisation System (SKOS) and its concepts provided with dereferenceable URIs. AGROVOC is now aligned with ten other multilingual Knowledge Organisation Systems (KOS) related to agriculture, using the SKOS properties exact match and close match. Alignments were a...

  16. Automated measurement of bolometer line of sight alignment and characteristics for application in ITER

    Energy Technology Data Exchange (ETDEWEB)

    Penzel, Florian Olivier

    2015-07-01

    The line of sight (LOS) alignment and characteristic of a bolometer camera used in a fusion experiment is a crucial parameter for the measurement accuracy of the diagnostic. A robot based LOS measurement device has been developed which allows the fully automatic measurement of the two dimensional transmission function of a bolometer camera. It has been used to optimize camera prototypes for ITER and has been successfully operated in the fusion experiment ASDEX Upgrade in order to measure the LOS alignment.

  17. Phylo-mLogo: an interactive and hierarchical multiple-logo visualization tool for alignment of many sequences

    Directory of Open Access Journals (Sweden)

    Lee DT

    2007-02-01

    Full Text Available Abstract Background When aligning several hundreds or thousands of sequences, such as epidemic virus sequences or homologous/orthologous sequences of some big gene families, to reconstruct the epidemiological history or their phylogenies, how to analyze and visualize the alignment results of many sequences has become a new challenge for computational biologists. Although there are several tools available for visualization of very long sequence alignments, few of them are applicable to the alignments of many sequences. Results A multiple-logo alignment visualization tool, called Phylo-mLogo, is presented in this paper. Phylo-mLogo calculates the variabilities and homogeneities of alignment sequences by base frequencies or entropies. Different from the traditional representations of sequence logos, Phylo-mLogo not only displays the global logo patterns of the whole alignment of multiple sequences, but also demonstrates their local homologous logos for each clade hierarchically. In addition, Phylo-mLogo also allows the user to focus only on the analysis of some important, structurally or functionally constrained sites in the alignment selected by the user or by built-in automatic calculation. Conclusion With Phylo-mLogo, the user can symbolically and hierarchically visualize hundreds of aligned sequences simultaneously and easily check the changes of their amino acid sites when analyzing many homologous/orthologous or influenza virus sequences. More information of Phylo-mLogo can be found at URL http://biocomp.iis.sinica.edu.tw/phylomlogo.

  18. Phrasal alignment in Functional Discourse Grammar

    NARCIS (Netherlands)

    van Rijn, M.

    2011-01-01

    Although the term is alignment is typically associated with morphosyntactic expression of arguments of the Clause, alignment is also relevant to units of the Phrase. In Functional Discourse Grammar a basic distinction is made between two kinds of dependency relations obtaining both within Phrases

  19. SOA-Driven Business-Software Alignment

    NARCIS (Netherlands)

    Shishkov, Boris; van Sinderen, Marten J.; Quartel, Dick; Tsai, W.; Chung, J.; Younas, M.

    2006-01-01

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

  20. 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...

  1. Comparative genomics beyond sequence-based alignments

    DEFF Research Database (Denmark)

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

    2008-01-01

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

  2. The GEM Detector projective alignment simulation system

    International Nuclear Information System (INIS)

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

    1993-01-01

    Precision position knowledge (< 25 microns RMS) of the GEM Detector muon system at the Superconducting Super Collider Laboratory (SSCL) is an important physics requirement necessary to minimize sagitta error in detecting and tracking high energy muons that are deflected by the magnetic field within the GEM Detector. To validate the concept of the sagitta correction function determined by projective alignment of the muon detectors (Cathode Strip Chambers or CSCs), the basis of the proposed GEM alignment scheme, a facility, called the ''Alignment Test Stand'' (ATS), is being constructed. This system simulates the environment that the CSCs and chamber alignment systems are expected to experience in the GEM Detector, albeit without the 0.8 T magnetic field and radiation environment. The ATS experimental program will allow systematic study and characterization of the projective alignment approach, as well as general mechanical engineering of muon chamber mounting concepts, positioning systems and study of the mechanical behavior of the proposed 6 layer CSCs. The ATS will consist of a stable local coordinate system in which mock-ups of muon chambers (i.e., non-working mechanical analogs, representing the three superlayers of a selected barrel and endcap alignment tower) are implemented, together with a sufficient number of alignment monitors to overdetermine the sagitta correction function, providing a self-consistency check. This paper describes the approach to be used for the alignment of the GEM muon system, the design of the ATS, and the experiments to be conducted using the ATS

  3. 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.

  4. Business and IT alignment in context

    NARCIS (Netherlands)

    Silvius, A.J.G.

    2013-01-01

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

  5. Compositions for directed alignment of conjugated polymers

    Science.gov (United States)

    Kim, Jinsang; Kim, Bong-Gi; Jeong, Eun Jeong

    2016-04-19

    Conjugated polymers (CPs) achieve directed alignment along an applied flow field and a dichroic ratio of as high as 16.67 in emission from well-aligned thin films and fully realized anisotropic optoelectronic properties of CPs in field-effect transistor (FET).

  6. 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

  7. STELLAR: fast and exact local alignments

    Directory of Open Access Journals (Sweden)

    Weese David

    2011-10-01

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

  8. Aligning Application Architecture to the Business Context

    NARCIS (Netherlands)

    Wieringa, Roelf J.; Blanken, Henk; Fokkinga, M.M.; Grefen, P.W.P.J.; Eder, J.; Missikoff, M.

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

  9. Alignment of Developments in Higher Education

    Science.gov (United States)

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

    2004-01-01

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

  10. Achieving Organisational Change through Values Alignment

    Science.gov (United States)

    Branson, Christopher M.

    2008-01-01

    Purpose: The purpose of this paper is to, first, establish the interdependency between the successful achievement of organisational change and the attainment of values alignment within an organisation's culture and then, second, to describe an effective means for attaining such values alignment. Design/methodology/approach: Literature from the…

  11. Partial Automated Alignment and Integration System

    Science.gov (United States)

    Kelley, Gary Wayne (Inventor)

    2014-01-01

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

  12. JNK2 promotes endothelial cell alignment under flow.

    Directory of Open Access Journals (Sweden)

    Cornelia Hahn

    Full Text Available Endothelial cells in straight, unbranched segments of arteries elongate and align in the direction of flow, a feature which is highly correlated with reduced atherosclerosis in these regions. The mitogen-activated protein kinase c-Jun N-terminal kinase (JNK is activated by flow and is linked to inflammatory gene expression and apoptosis. We previously showed that JNK activation by flow is mediated by integrins and is observed in cells plated on fibronectin but not on collagen or basement membrane proteins. We now show thatJNK2 activation in response to laminar shear stress is biphasic, with an early peak and a later peak. Activated JNK localizes to focal adhesions at the ends of actin stress fibers, correlates with integrin activation and requires integrin binding to the extracellular matrix. Reducing JNK2 activation by siRNA inhibits alignment in response to shear stress. Cells on collagen, where JNK activity is low, align slowly. These data show that an inflammatory pathway facilitates adaptation to laminar flow, thereby revealing an unexpected connection between adaptation and inflammatory pathways.

  13. MICA: Multiple interval-based curve alignment

    Science.gov (United States)

    Mann, Martin; Kahle, Hans-Peter; Beck, Matthias; Bender, Bela Johannes; Spiecker, Heinrich; Backofen, Rolf

    2018-01-01

    MICA enables the automatic synchronization of discrete data curves. To this end, characteristic points of the curves' shapes are identified. These landmarks are used within a heuristic curve registration approach to align profile pairs by mapping similar characteristics onto each other. In combination with a progressive alignment scheme, this enables the computation of multiple curve alignments. Multiple curve alignments are needed to derive meaningful representative consensus data of measured time or data series. MICA was already successfully applied to generate representative profiles of tree growth data based on intra-annual wood density profiles or cell formation data. The MICA package provides a command-line and graphical user interface. The R interface enables the direct embedding of multiple curve alignment computation into larger analyses pipelines. Source code, binaries and documentation are freely available at https://github.com/BackofenLab/MICA

  14. Ultrasonic inspections of fuel alignment pins

    International Nuclear Information System (INIS)

    Rathgeb, W.; Schmid, R.

    1994-01-01

    As a remedy to the practical problem of defects in fuel alignment pins made of Inconel X750, an inspection technique has been developed which fully meets the requirements of detecting defects. The newly used fuel alignment pins made of austenite are easy to test and therefore satisfy the necessity of further inspections.For the fuel alignment pins of the upper core structure a safe and fast inspection technique was made available. The inspection sensitivity is high and it is possible to give quantitative directions concerning defect orientation and depth. After the required inspections had been concluded in 1989, a total of 18 inspections were carried out in various national and international nuclear power plants in the following years. During this time more than 6000 fuel alignment pines were examined.For the fuel alignment pins the inspection technique provided could increase the understanding of the defect process. This technique contributed to the development of an adaptive and economical repair strategy. ((orig.))

  15. Three dimensional extrusion printing induces polymer molecule alignment and cell organization within engineered cartilage.

    Science.gov (United States)

    Guo, Ting; Ringel, Julia P; Lim, Casey G; Bracaglia, Laura G; Noshin, Maeesha; Baker, Hannah B; Powell, Douglas A; Fisher, John P

    2018-04-16

    Proper cell-material interactions are critical to remain cell function and thus successful tissue regeneration. Many fabrication processes have been developed to create microenvironments to control cell attachment and organization on a three-dimensional (3D) scaffold. However, these approaches often involve heavy engineering and only the surface layer can be patterned. We found that 3D extrusion based printing at high temperature and pressure will result an aligned effect on the polymer molecules, and this molecular arrangement will further induce the cell alignment and different differentiation capacities. In particular, articular cartilage tissue is known to have zonal collagen fiber and cell orientation to support different functions, where collagen fibers and chondrocytes align parallel, randomly, and perpendicular, respectively, to the surface of the joint. Therefore, cell alignment was evaluated in a cartilage model in this study. We used small angle X-ray scattering analysis to substantiate the polymer molecule alignment phenomenon. The cellular response was evaluated both in vitro and in vivo. Seeded mesenchymal stem cells (MSCs) showed different morphology and orientation on scaffolds, as a combined result of polymer molecule alignment and printed scaffold patterns. Gene expression results showed improved superficial zonal chondrogenic marker expression in parallel-aligned group. The cell alignment was successfully maintained in the animal model after 7 days with distinct MSC morphology between the casted and parallel printed scaffolds. This 3D printing induced polymer and cell alignment will have a significant impact on developing scaffold with controlled cell-material interactions for complex tissue engineering while avoiding complicated surface treatment, and therefore provides new concept for effective tissue repairing in future clinical applications. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A, 2018. © 2018 Wiley Periodicals, Inc.

  16. Pathway-engineering for highly-aligned block copolymer arrays.

    Science.gov (United States)

    Choo, Youngwoo; Majewski, Paweł W; Fukuto, Masafumi; Osuji, Chinedum O; Yager, Kevin G

    2017-12-21

    While the ultimate driving force in self-assembly is energy minimization and the corresponding evolution towards equilibrium, kinetic effects can also play a very strong role. These kinetic effects, such as trapping in metastable states, slow coarsening kinetics, and pathway-dependent assembly, are often viewed as complications to be overcome. Here, we instead exploit these effects to engineer a desired final nano-structure in a block copolymer thin film, by selecting a particular ordering pathway through the self-assembly energy landscape. In particular, we combine photothermal shearing with high-temperature annealing to yield hexagonal arrays of block copolymer cylinders that are aligned in a single prescribed direction over macroscopic sample dimensions. Photothermal shearing is first used to generate a highly-aligned horizontal cylinder state, with subsequent thermal processing used to reorient the morphology to the vertical cylinder state in a templated manner. Finally, we demonstrate the successful transfer of engineered morphologies into inorganic replicas.

  17. Measuring and aligning accelerator components to the nanometre scale

    CERN Document Server

    Catalán Lasheras, N; Modena, M

    2014-01-01

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

  18. Diameter modulation of vertically aligned single-walled carbon nanotubes.

    Science.gov (United States)

    Xiang, Rong; Einarsson, Erik; Murakami, Yoichi; Shiomi, Junichiro; Chiashi, Shohei; Tang, Zikang; Maruyama, Shigeo

    2012-08-28

    We demonstrate wide-range diameter modulation of vertically aligned single-walled carbon nanotubes (SWNTs) using a wet chemistry prepared catalyst. In order to ensure compatibility to electronic applications, the current minimum mean diameter of 2 nm for vertically aligned SWNTs is challenged. The mean diameter is decreased to about 1.4 nm by reducing Co catalyst concentrations to 1/100 or by increasing Mo catalyst concentrations by five times. We also propose a novel spectral analysis method that allows one to distinguish absorbance contributions from the upper, middle, and lower parts of a nanotube array. We use this method to quantitatively characterize the slight diameter change observed along the array height. On the basis of further investigation of the array and catalyst particles, we conclude that catalyst aggregation-rather than Ostwald ripening-dominates the growth of metal particles.

  19. Aligning Objectives and Assessment in Responsible Conduct of Research Instruction

    Science.gov (United States)

    Antes, Alison L.; DuBois, James M.

    2014-01-01

    Efforts to advance research integrity in light of concerns about misbehavior in research rely heavily on education in the responsible conduct of research (RCR). However, there is limited evidence for the effectiveness of RCR instruction as a remedy. Assessment is essential in RCR education if the research community wishes to expend the effort of instructors, students, and trainees wisely. This article presents key considerations that instructors and course directors must consider in aligning learning objectives with instructional methods and assessment measures, and it provides illustrative examples. Above all, in order for RCR educators to assess outcomes more effectively, they must align assessment to their learning objectives and attend to the validity of the measures used. PMID:25574258

  20. Thin aligned organic polymer films for liquid crystal devices

    International Nuclear Information System (INIS)

    Foster, Kathryn Ellen

    1997-01-01

    This project was designed to investigate the possibility of producing alignment layers for liquid crystal devices by cross-linking thin films containing anisotropic polymer bound chromophores via irradiation with polarised ultraviolet light. Photocross-linkable polymers find use in microelectronics, liquid crystal displays, printing and UV curable lacquers and inks; so there is an increasing incentive for the development of new varieties of photopolymers in general. The synthesis and characterisation of two new photopolymers that are suitable as potential alignment layers for liquid crystal devices are reported in this thesis. The first polymer contains the anthracene chromophore attached via a spacer unit to a methacrylate backbone and the second used a similarly attached aryl azide group. Copolymers of the new monomers with methyl methacrylate were investigated to establish reactivity ratios in order to understand composition drift during polymerisation. (author)

  1. Tracing magnetic fields with aligned grains

    International Nuclear Information System (INIS)

    Lazarian, A.

    2007-01-01

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

  2. Higher Order Lagrange Finite Elements In M3D

    International Nuclear Information System (INIS)

    Chen, J.; Strauss, H.R.; Jardin, S.C.; Park, W.; Sugiyama, L.E.; Fu, G.; Breslau, J.

    2004-01-01

    The M3D code has been using linear finite elements to represent multilevel MHD on 2-D poloidal planes. Triangular higher order elements, up to third order, are constructed here in order to provide M3D the capability to solve highly anisotropic transport problems. It is found that higher order elements are essential to resolve the thin transition layer characteristic of the anisotropic transport equation, particularly when the strong anisotropic direction is not aligned with one of the Cartesian coordinates. The transition layer is measured by the profile width, which is zero for infinite anisotropy. It is shown that only higher order schemes have the ability to make this layer converge towards zero when the anisotropy gets stronger and stronger. Two cases are considered. One has the strong transport direction partially aligned with one of the element edges, the other doesn't have any alignment. Both cases have the strong transport direction misaligned with the grid line by some angles

  3. Learning of Alignment Rules between Concept Hierarchies

    Science.gov (United States)

    Ichise, Ryutaro; Takeda, Hideaki; Honiden, Shinichi

    With the rapid advances of information technology, we are acquiring much information than ever before. As a result, we need tools for organizing this data. Concept hierarchies such as ontologies and information categorizations are powerful and convenient methods for accomplishing this goal, which have gained wide spread acceptance. Although each concept hierarchy is useful, it is difficult to employ multiple concept hierarchies at the same time because it is hard to align their conceptual structures. This paper proposes a rule learning method that inputs information from a source concept hierarchy and finds suitable location for them in a target hierarchy. The key idea is to find the most similar categories in each hierarchy, where similarity is measured by the κ(kappa) statistic that counts instances belonging to both categories. In order to evaluate our method, we conducted experiments using two internet directories: Yahoo! and LYCOS. We map information instances from the source directory into the target directory, and show that our learned rules agree with a human-generated assignment 76% of the time.

  4. Phylo: a citizen science approach for improving multiple sequence alignment.

    Directory of Open Access Journals (Sweden)

    Alexander Kawrykow

    Full Text Available BACKGROUND: Comparative genomics, or the study of the relationships of genome structure and function across different species, offers a powerful tool for studying evolution, annotating genomes, and understanding the causes of various genetic disorders. However, aligning multiple sequences of DNA, an essential intermediate step for most types of analyses, is a difficult computational task. In parallel, citizen science, an approach that takes advantage of the fact that the human brain is exquisitely tuned to solving specific types of problems, is becoming increasingly popular. There, instances of hard computational problems are dispatched to a crowd of non-expert human game players and solutions are sent back to a central server. METHODOLOGY/PRINCIPAL FINDINGS: We introduce Phylo, a human-based computing framework applying "crowd sourcing" techniques to solve the Multiple Sequence Alignment (MSA problem. The key idea of Phylo is to convert the MSA problem into a casual game that can be played by ordinary web users with a minimal prior knowledge of the biological context. We applied this strategy to improve the alignment of the promoters of disease-related genes from up to 44 vertebrate species. Since the launch in November 2010, we received more than 350,000 solutions submitted from more than 12,000 registered users. Our results show that solutions submitted contributed to improving the accuracy of up to 70% of the alignment blocks considered. CONCLUSIONS/SIGNIFICANCE: We demonstrate that, combined with classical algorithms, crowd computing techniques can be successfully used to help improving the accuracy of MSA. More importantly, we show that an NP-hard computational problem can be embedded in casual game that can be easily played by people without significant scientific training. This suggests that citizen science approaches can be used to exploit the billions of "human-brain peta-flops" of computation that are spent every day playing games

  5. Base-By-Base: single nucleotide-level analysis of whole viral genome alignments.

    Science.gov (United States)

    Brodie, Ryan; Smith, Alex J; Roper, Rachel L; Tcherepanov, Vasily; Upton, Chris

    2004-07-14

    With ever increasing numbers of closely related virus genomes being sequenced, it has become desirable to be able to compare two genomes at a level more detailed than gene content because two strains of an organism may share the same set of predicted genes but still differ in their pathogenicity profiles. For example, detailed comparison of multiple isolates of the smallpox virus genome (each approximately 200 kb, with 200 genes) is not feasible without new bioinformatics tools. A software package, Base-By-Base, has been developed that provides visualization tools to enable researchers to 1) rapidly identify and correct alignment errors in large, multiple genome alignments; and 2) generate tabular and graphical output of differences between the genomes at the nucleotide level. Base-By-Base uses detailed annotation information about the aligned genomes and can list each predicted gene with nucleotide differences, display whether variations occur within promoter regions or coding regions and whether these changes result in amino acid substitutions. Base-By-Base can connect to our mySQL database (Virus Orthologous Clusters; VOCs) to retrieve detailed annotation information about the aligned genomes or use information from text files. Base-By-Base enables users to quickly and easily compare large viral genomes; it highlights small differences that may be responsible for important phenotypic differences such as virulence. It is available via the Internet using Java Web Start and runs on Macintosh, PC and Linux operating systems with the Java 1.4 virtual machine.

  6. Alignment of mapping system for magnet cyclotron DECY-13

    International Nuclear Information System (INIS)

    Idrus Abdul Kudus; Taufik; Kurnia Wibowo

    2016-01-01

    A cyclotron is composed of some main and specific components, such as magnet system, ion source, RF system and extractor. A magnet is one of important component in a cyclotron that serves as ion beam bending so the ion beam trajectory is circular. Magnet design should with the requirement of cyclotron that proton energy is 13 MeV. In the construction of the cyclotron magnet, a mapping tool of the magnetic field is required for analysis in shimming process in order to optimize the magnetic field. The magnetic field mapping process is carried out in the median plane of the magnet poles. The magnetic field mapping is carried out repeatedly during the shimming process. During this process, the mapping tool is possible to experience a shift or change in position, for that it is necessary to alignment in order to make sure that the probe is in the median plane of magnet poles and to ensure their positions are always the same on each repetition mapping. During this process, it is possible to experience a shift mapping tool or change the position, for this it is needed to process alignment to ensure the position of the probe is in the median plane magnetic poles and ensure their positions are always the same on each repetition mapping. Alignment on the mapping tool are the height position, zeroing tesla meter and two hall probe mapping. The parameters form the basis for magnetic field measurements based on the three elements: an alignment system on the engine mapping, mapping tool reference point and stage movement of x-y coordinates. Shifts occur due to change in elevation mapping tool table and center coordinates x and y in the mapping process. Changes made to shift mapping coordinates can be shifted as far as 1 to 2 mm for each hall probe in the x and y coordinates with altitude changes 0.05° mapping table and measurement of tesla meter changes in 0.002 T. (author)

  7. Order Aggressiveness and Order Book Dynamics

    OpenAIRE

    Anthony D. Hall; Nikolaus Hautsch

    2004-01-01

    In this paper, we study the determinants of order aggressiveness and traders' order submission strategy in an open limit order book market. Using order book data from the Australian Stock Exchange, we model traders' aggressiveness in market trading, limit order trading as well as in order cancellations on both sides of the market using a six-dimensional autoregressive intensity model. The information revealed by the open order book plays an important role in explaining the degree of order agg...

  8. 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.

  9. Construction of coffee transcriptome networks based on gene annotation semantics

    Directory of Open Access Journals (Sweden)

    Castillo Luis F.

    2012-12-01

    Full Text Available Gene annotation is a process that encompasses multiple approaches on the analysis of nucleic acids or protein sequences in order to assign structural and functional characteristics to gene models. When thousands of gene models are being described in an organism genome, construction and visualization of gene networks impose novel challenges in the understanding of complex expression patterns and the generation of new knowledge in genomics research. In order to take advantage of accumulated text data after conventional gene sequence analysis, this work applied semantics in combination with visualization tools to build transcriptome networks from a set of coffee gene annotations. A set of selected coffee transcriptome sequences, chosen by the quality of the sequence comparison reported by Basic Local Alignment Search Tool (BLAST and Interproscan, were filtered out by coverage, identity, length of the query, and e-values. Meanwhile, term descriptors for molecular biology and biochemistry were obtained along the Wordnet dictionary in order to construct a Resource Description Framework (RDF using Ruby scripts and Methontology to find associations between concepts. Relationships between sequence annotations and semantic concepts were graphically represented through a total of 6845 oriented vectors, which were reduced to 745 non-redundant associations. A large gene network connecting transcripts by way of relational concepts was created where detailed connections remain to be validated for biological significance based on current biochemical and genetics frameworks. Besides reusing text information in the generation of gene connections and for data mining purposes, this tool development opens the possibility to visualize complex and abundant transcriptome data, and triggers the formulation of new hypotheses in metabolic pathways analysis.

  10. The 3-D alignment of objects in dynamic PET scans using filtered sinusoidal trajectories of sinogram

    International Nuclear Information System (INIS)

    Kostopoulos, Aristotelis E.; Happonen, Antti P.; Ruotsalainen, Ulla

    2006-01-01

    In this study, our goal is to employ a novel 3-D alignment method for dynamic positron emission tomography (PET) scans. Because the acquired data (i.e. sinograms) often contain noise considerably, filtering of the data prior to the alignment presumably improves the final results. In this study, we utilized a novel 3-D stackgram domain approach. In the stackgram domain, the signals along the sinusoidal trajectory signals of the sinogram can be processed separately. In this work, we performed angular stackgram domain filtering by employing well known 1-D filters: the Gaussian low-pass filter and the median filter. In addition, we employed two wavelet de-noising techniques. After filtering we performed alignment of objects in the stackgram domain. The local alignment technique we used is based on similarity comparisons between locus vectors (i.e. the signals along the sinusoidal trajectories of the sinogram) in a 3-D neighborhood of sequences of the stackgrams. Aligned stackgrams can be transformed back to sinograms (Method 1), or alternatively directly to filtered back-projected images (Method 2). In order to evaluate the alignment process, simulated data with different kinds of additive noises were used. The results indicated that the filtering prior to the alignment can be important concerning the accuracy

  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. 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.

  13. 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.

  14. Genes and proteins of Escherichia coli K-12.

    Science.gov (United States)

    Riley, M

    1998-01-01

    GenProtEC is a database of Escherichia coli genes and their gene products, classified by type of function and physiological role and with citations to the literature for each. Also present are data on sequence similarities among E.coli proteins, representing groups of paralogous genes, with PAM values, percent identity of amino acids, length of alignment and percent aligned. GenProtEC can be accessed at the URL http://www.mbl.edu/html/ecoli.html

  15. Alignment and stability of future machines

    International Nuclear Information System (INIS)

    Shiltsev, V.D.

    1996-06-01

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

  16. Automatic Angular alignment of LHC Collimators

    CERN Document Server

    Azzopardi, Gabriella; Salvachua Ferrando, Belen Maria; Mereghetti, Alessio; Bruce, Roderik; Redaelli, Stefano; CERN. Geneva. ATS Department

    2017-01-01

    The LHC is equipped with a complex collimation system to protect sensitive equipment from unavoidable beam losses. Collimators are positioned close to the beam using an alignment procedure. Until now they have always been aligned assuming no tilt between the collimator and the beam, however, tank misalignments or beam envelope angles at large-divergence locations could introduce a tilt limiting the collimation performance. Three different algorithms were implemented to automatically align a chosen collimator at various angles. The implementation was tested on a number of collimators during this MD and no human intervention was required.

  17. NOVA integrated alignment/diagnostic sensors

    International Nuclear Information System (INIS)

    1978-01-01

    Under Contract 3772003 to the Lawrence Livermore Laboratory, Aerojet ElectroSystems Company has investigated a number of alignment system design topics for the NOVA and SHIVA upgrade lasers. Prior reports dealt with the Main Beam Alignment System, and with Multipass Amplifier Alignment Concepts. This report, which completes the contract, examines ways in which the Return Beam Diagnostic (RBD) package and Incident Beam Diagnostic (IBD) packages may be reconfigured to a more integrated package. In particular, the report shows that the RBD optics may be directly integrated in the Pointing Focus and Centering (PFC) sensor, and that the IBD optics may use the same basic common configuration as the PFC/RBD package

  18. Accessing the molecular frame through strong-field alignment of distributions of gas phase molecules

    Science.gov (United States)

    Reid, Katharine L.

    2018-03-01

    A rationale for creating highly aligned distributions of molecules is that it enables vector properties referenced to molecule-fixed axes (the molecular frame) to be determined. In the present work, the degree of alignment that is necessary for this to be achieved in practice is explored. Alignment is commonly parametrized in experiments by a single parameter, ?, which is insufficient to enable predictive calculations to be performed. Here, it is shown that, if the full distribution of molecular axes takes a Gaussian form, this single parameter can be used to determine the complete set of alignment moments needed to characterize the distribution. In order to demonstrate the degree of alignment that is required to approach the molecular frame, the alignment moments corresponding to a few chosen values of ? are used to project a model molecular frame photoelectron angular distribution into the laboratory frame. These calculations show that ? needs to approach 0.9 in order to avoid significant blurring to be caused by averaging. This article is part of the theme issue `Modern theoretical chemistry'.

  19. 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

  20. Orthodontics Align Crooked Teeth and Boost Self-Esteem

    Science.gov (United States)

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

  1. Simultaneous alignment and Lorentz angle calibration in the CMS silicon tracker using Millepede II

    CERN Document Server

    Bartosik, Nazar

    2013-01-01

    The CMS silicon tracker consists of 25 684 sensors that provide measurements of trajectories of charged particles that are used by almost every physics analysis at CMS. In order to achieve high measurement precision, the positions and orientations of all sensors have to be determined very accurately. This is achieved by track-based alignment using the global fit approach of the Millepede II program. This approach is capable of determining about 200 000 parameters simultaneously.The alignment precision reached such a high level that even small calibration inaccuracies are noticeable. Therefore the alignment framework has been extended to treat position sensitive calibration parameters. Of special interest is the Lorentz angle which affects the hit positions due to the drift of the signal electrons in the magnetic field. We present the results from measurements of the Lorentz angle and its time dependence during full 2012 data taking period as well as general description of the alignment and calibration procedu...

  2. Program for PET image alignment: Effects on calculated differences in cerebral metabolic rates for glucose

    International Nuclear Information System (INIS)

    Phillips, R.L.; London, E.D.; Links, J.M.; Cascella, N.G.

    1990-01-01

    A program was developed to align positron emission tomography images from multiple studies on the same subject. The program allowed alignment of two images with a fineness of one-tenth the width of a pixel. The indications and effects of misalignment were assessed in eight subjects from a placebo-controlled double-blind crossover study on the effects of cocaine on regional cerebral metabolic rates for glucose. Visual examination of a difference image provided a sensitive and accurate tool for assessing image alignment. Image alignment within 2.8 mm was essential to reduce variability of measured cerebral metabolic rates for glucose. Misalignment by this amount introduced errors on the order of 20% in the computed metabolic rate for glucose. These errors propagate to the difference between metabolic rates for a subject measured in basal versus perturbed states

  3. 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

  4. Alignment of time-resolved data from high throughput experiments.

    Science.gov (United States)

    Abidi, Nada; Franke, Raimo; Findeisen, Peter; Klawonn, Frank

    2016-12-01

    To better understand the dynamics of the underlying processes in cells, it is necessary to take measurements over a time course. Modern high-throughput technologies are often used for this purpose to measure the behavior of cell products like metabolites, peptides, proteins, [Formula: see text]RNA or mRNA at different points in time. Compared to classical time series, the number of time points is usually very limited and the measurements are taken at irregular time intervals. The main reasons for this are the costs of the experiments and the fact that the dynamic behavior usually shows a strong reaction and fast changes shortly after a stimulus and then slowly converges to a certain stable state. Another reason might simply be missing values. It is common to repeat the experiments and to have replicates in order to carry out a more reliable analysis. The ideal assumptions that the initial stimulus really started exactly at the same time for all replicates and that the replicates are perfectly synchronized are seldom satisfied. Therefore, there is a need to first adjust or align the time-resolved data before further analysis is carried out. Dynamic time warping (DTW) is considered as one of the common alignment techniques for time series data with equidistant time points. In this paper, we modified the DTW algorithm so that it can align sequences with measurements at different, non-equidistant time points with large gaps in between. This type of data is usually known as time-resolved data characterized by irregular time intervals between measurements as well as non-identical time points for different replicates. This new algorithm can be easily used to align time-resolved data from high-throughput experiments and to come across existing problems such as time scarcity and existing noise in the measurements. We propose a modified method of DTW to adapt requirements imposed by time-resolved data by use of monotone cubic interpolation splines. Our presented approach

  5. Hydrodynamic Equations for Flocking Models without Velocity Alignment

    Science.gov (United States)

    Peruani, Fernando

    2017-10-01

    The spontaneous emergence of collective motion patterns is usually associated with the presence of a velocity alignment mechanism that mediates the interactions among the moving individuals. Despite of this widespread view, it has been shown recently that several flocking behaviors can emerge in the absence of velocity alignment and as a result of short-range, position-based, attractive forces that act inside a vision cone. Here, we derive the corresponding hydrodynamic equations of a microscopic position-based flocking model, reviewing and extending previous reported results. In particular, we show that three distinct macroscopic collective behaviors can be observed: i) the coarsening of aggregates with no orientational order, ii) the emergence of static, elongated nematic bands, and iii) the formation of moving, locally polar structures, which we call worms. The derived hydrodynamic equations indicate that active particles interacting via position-based interactions belong to a distinct class of active systems fundamentally different from other active systems, including velocity-alignment-based flocking systems.

  6. Representation and alignment of sung queries for music information retrieval

    Science.gov (United States)

    Adams, Norman H.; Wakefield, Gregory H.

    2005-09-01

    The pursuit of robust and rapid query-by-humming systems, which search melodic databases using sung queries, is a common theme in music information retrieval. The retrieval aspect of this database problem has received considerable attention, whereas the front-end processing of sung queries and the data structure to represent melodies has been based on musical intuition and historical momentum. The present work explores three time series representations for sung queries: a sequence of notes, a ``smooth'' pitch contour, and a sequence of pitch histograms. The performance of the three representations is compared using a collection of naturally sung queries. It is found that the most robust performance is achieved by the representation with highest dimension, the smooth pitch contour, but that this representation presents a formidable computational burden. For all three representations, it is necessary to align the query and target in order to achieve robust performance. The computational cost of the alignment is quadratic, hence it is necessary to keep the dimension small for rapid retrieval. Accordingly, iterative deepening is employed to achieve both robust performance and rapid retrieval. Finally, the conventional iterative framework is expanded to adapt the alignment constraints based on previous iterations, further expediting retrieval without degrading performance.

  7. Magnetic field-aligned particle precipitation

    International Nuclear Information System (INIS)

    Carlson, W.

    1985-01-01

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

  8. The Alignment of the CMS Silicon Tracker

    CERN Document Server

    Lampen, Pekka Tapio

    2013-01-01

    The CMS all-silicon tracker consists of 16588 modules, embedded in a solenoidal magnet providing a field of B = 3.8 T. The targeted performance requires that the alignment determines the module positions with a precision of a few micrometers. Ultimate local precision is reached by the determination of sensor curvatures, challenging the algorithms to determine about 200k parameters simultaneously, as is feasible with the Millepede II program. The main remaining challenge are global distortions that systematically bias the track parameters and thus physics measurements. They are controlled by adding further information into the alignment workflow, e.g. the mass of decaying resonances or track data taken with B = 0 T. To make use of the latter and also to integrate the determination of the Lorentz angle into the alignment procedure, the alignment framework has been extended to treat position sensitive calibration parameters. This is relevant since due to the increased LHC luminosity in 2012, the Lorentz angle ex...

  9. Robust and Efficient Parametric Face Alignment

    NARCIS (Netherlands)

    Tzimiropoulos, Georgios; Zafeiriou, Stefanos; Pantic, Maja

    2011-01-01

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

  10. EURRECA—Framework for Aligning Micronutrient Recommendations

    NARCIS (Netherlands)

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

    2013-01-01

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

  11. Commissioning the CMS alignment and calibration framework

    International Nuclear Information System (INIS)

    Futyan, David

    2010-01-01

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

  12. Commissioning the CMS Alignment and Calibration Framework

    CERN Document Server

    Futyan, David

    2009-01-01

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

  13. 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.)

  14. Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.

    Directory of Open Access Journals (Sweden)

    Xin He

    2009-03-01

    Full Text Available Cross-species comparison has emerged as a powerful paradigm for predicting cis-regulatory modules (CRMs and understanding their evolution. The comparison requires reliable sequence alignment, which remains a challenging task for less conserved noncoding sequences. Furthermore, the existing models of DNA sequence evolution generally do not explicitly treat the special properties of CRM sequences. To address these limitations, we propose a model of CRM evolution that captures different modes of evolution of functional transcription factor binding sites (TFBSs and the background sequences. A particularly novel aspect of our work is a probabilistic model of gains and losses of TFBSs, a process being recognized as an important part of regulatory sequence evolution. We present a computational framework that uses this model to solve the problems of CRM alignment and prediction. Our alignment method is similar to existing methods of statistical alignment but uses the conserved binding sites to improve alignment. Our CRM prediction method deals with the inherent uncertainties of binding site annotations and sequence alignment in a probabilistic framework. In simulated as well as real data, we demonstrate that our program is able to improve both alignment and prediction of CRM sequences over several state-of-the-art methods. Finally, we used alignments produced by our program to study binding site conservation in genome-wide binding data of key transcription factors in the Drosophila blastoderm, with two intriguing results: (i the factor-bound sequences are under strong evolutionary constraints even if their neighboring genes are not expressed in the blastoderm and (ii binding sites in distal bound sequences (relative to transcription start sites tend to be more conserved than those in proximal regions. Our approach is implemented as software, EMMA (Evolutionary Model-based cis-regulatory Module Analysis, ready to be applied in a broad biological context.

  15. libgapmis: extending short-read alignments.

    Science.gov (United States)

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

    2013-01-01

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

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

    Science.gov (United States)

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

    2017-12-01

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

  17. Polarization and alignment of nucleus fission fragments

    International Nuclear Information System (INIS)

    Barabanov, A.L.; Grechukhin, D.P.

    1987-01-01

    Correlation of fragment orientation with orientation axis of fissile nucleus and with n-vector f vector of fragment divergence is considered. Estimations of polarization and alignment of fission fragments of preliminarily oriented nuclei in correlation (with n-vector f recording) and integral (with n-vector f averaging) experiments were conducted. It is shown that high sensitivity of polarization and fragment alignment to the character of nucleus movement at the stage of descent from barrier to rupture point exists

  18. 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).

  19. Fiber optics welder having movable aligning mirror

    Science.gov (United States)

    Higgins, Robert W.; Robichaud, Roger E.

    1981-01-01

    A system for welding fiber optic waveguides together. The ends of the two fibers to be joined together are accurately, collinearly aligned in a vertical orientation and subjected to a controlled, diffuse arc to effect welding and thermal conditioning. A front-surfaced mirror mounted at a 45.degree. angle to the optical axis of a stereomicroscope mounted for viewing the junction of the ends provides two orthogonal views of the interface during the alignment operation.

  20. 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

  1. 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...

  2. 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.

  3. 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

  4. 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

  5. An Alignment of J-PARC Linac

    CERN Document Server

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

    2005-01-01

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

  6. 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...

  7. Aligning Biomolecular Networks Using Modular Graph Kernels

    Science.gov (United States)

    Towfic, Fadi; Greenlee, M. Heather West; Honavar, Vasant

    Comparative analysis of biomolecular networks constructed using measurements from different conditions, tissues, and organisms offer a powerful approach to understanding the structure, function, dynamics, and evolution of complex biological systems. We explore a class of algorithms for aligning large biomolecular networks by breaking down such networks into subgraphs and computing the alignment of the networks based on the alignment of their subgraphs. The resulting subnetworks are compared using graph kernels as scoring functions. We provide implementations of the resulting algorithms as part of BiNA, an open source biomolecular network alignment toolkit. Our experiments using Drosophila melanogaster, Saccharomyces cerevisiae, Mus musculus and Homo sapiens protein-protein interaction networks extracted from the DIP repository of protein-protein interaction data demonstrate that the performance of the proposed algorithms (as measured by % GO term enrichment of subnetworks identified by the alignment) is competitive with some of the state-of-the-art algorithms for pair-wise alignment of large protein-protein interaction networks. Our results also show that the inter-species similarity scores computed based on graph kernels can be used to cluster the species into a species tree that is consistent with the known phylogenetic relationships among the species.

  8. 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.

  9. 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.

  10. 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

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

    Science.gov (United States)

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

    1998-06-01

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

  12. Remote alignment of Low beta quadrupoles with micrometric resolution

    CERN Document Server

    Acar, M; Herty, A; Mainaud-Durand, H; Marin, A; Quesnel, J P

    2008-01-01

    Considering their location in a high radiation environment and the alignment tolerancesrequested, the low beta quadrupoles of LHC will be positioned remotely (controlling 5 degrees of freedom), with a displacement resolution of few microns in horizontal and vertical. Stepping motor gearbox assemblies are plugged into the jacks which support the cryomagnets in order to move them to the desired position regarding the quality of the beam collisions in the detectors. This displacement will be monitored in real time by the sensors located on the magnets. This paper describes the positioning strategy implemented as well as the software tools used to manage it.

  13. Impact polarization and alignment creation parameters via stepwise excitation processes

    International Nuclear Information System (INIS)

    Csanak, G.; Cartwright, D.C.; Kazantsev, S.A.; Bray, I.

    1998-01-01

    W report here results from first order many body theory, distorted wave approximation, and converged close coupling calculations for polarization fractions and alignment creation parameters in the case of 2 1 S → n 1 P(n 3 - 5), 2 3 S → n 1 P(n = 2 - 5), 2 1 S → n 1 D(n = 3 - 5), 2 3 S → n 1 D(n = 3 - 5), 2 3 S → n 3 D(n = 3 - 5), and 2 1 S → n 3 D(n = 3 - 5) excitations in helium for electron impact energies from threshold to several hundred eV. (author)

  14. Active illumination and appearance model for face alignment

    DEFF Research Database (Denmark)

    Kahraman, Fatih; Gokmen, M.; Darkner, Sune

    2010-01-01

    Illumination conditions have an explicit effect on the performance of face recognition systems. In particular, varying the illumination upon the face imposes such, complex effects that the identification often fails to provide a stable performance level. In this paper, we propose an approach......, integrating face identity and illumination models in order to reach acceptable and stable face recognition rates. For this purpose, Active Appearance Model (A AM) and illumination model of faces are combined in order to obtain an illumination invariant face localization. The proposed method is an integrated......, is sufficient. There is no need to build complex models for illumination. As a result, this paper has presented a simple and efficient method for face modeling and face alignment in order to increase the performance of face localization by means of the proposed illumination invariant AIA method for face...

  15. LCGbase: A Comprehensive Database for Lineage-Based Co-regulated Genes.

    Science.gov (United States)

    Wang, Dapeng; Zhang, Yubin; Fan, Zhonghua; Liu, Guiming; Yu, Jun

    2012-01-01

    Animal genes of different lineages, such as vertebrates and arthropods, are well-organized and blended into dynamic chromosomal structures that represent a primary regulatory mechanism for body development and cellular differentiation. The majority of genes in a genome are actually clustered, which are evolutionarily stable to different extents and biologically meaningful when evaluated among genomes within and across lineages. Until now, many questions concerning gene organization, such as what is the minimal number of genes in a cluster and what is the driving force leading to gene co-regulation, remain to be addressed. Here, we provide a user-friendly database-LCGbase (a comprehensive database for lineage-based co-regulated genes)-hosting information on evolutionary dynamics of gene clustering and ordering within animal kingdoms in two different lineages: vertebrates and arthropods. The database is constructed on a web-based Linux-Apache-MySQL-PHP framework and effective interactive user-inquiry service. Compared to other gene annotation databases with similar purposes, our database has three comprehensible advantages. First, our database is inclusive, including all high-quality genome assemblies of vertebrates and representative arthropod species. Second, it is human-centric since we map all gene clusters from other genomes in an order of lineage-ranks (such as primates, mammals, warm-blooded, and reptiles) onto human genome and start the database from well-defined gene pairs (a minimal cluster where the two adjacent genes are oriented as co-directional, convergent, and divergent pairs) to large gene clusters. Furthermore, users can search for any adjacent genes and their detailed annotations. Third, the database provides flexible parameter definitions, such as the distance of transcription start sites between two adjacent genes, which is extendable to genes that flanking the cluster across species. We also provide useful tools for sequence alignment, gene

  16. Molecular identification of the ompL1 gene within Leptospira interrogans standard serovars.

    Science.gov (United States)

    Dezhbord, Mehrangiz; Esmaelizad, Majid; Khaki, Pejvak; Fotohi, Fariba; Zarehparvar Moghaddam, Athena

    2014-06-11

    Leptospirosis, caused by infection with pathogenic Leptospira species, is one of the most prevalent zoonotic diseases in the world. Current leptospiral vaccines are mainly multivalent dead whole-cell mixtures made of several local dominant serovars. Therefore, design and construction of an efficient recombinant vaccine for leptospirosis control is very important. OmpL1 is an immunogenic porin protein that could be of special significance in vaccination and serodiagnosis for leptospirosis. Three strains belonging to pathogenic L. interrogans were analyzed. The specific primers for proliferation of the ompL1 gene were designed. The amplified gene was cloned. In order to investigate the ompL1 nucleotide sequence and homological analysis of this gene, ompL1 genes cloned from standard vaccinal Leptospira serovars prevalent in Iran were sequenced and cloned. PCR amplification of the ompL1 gene using the designed primers resulted in a 963 bp ompL1 gene product. The PCR based on the ompL1 gene detected all pathogenic reference serovars of Leptospira spp. tested. Based on alignment and phylogenetic analysis, although the ompL1 nucleotide sequence was slightly different within three vaccinal serovars (100%-85% identity), amino acid alignment of the OmpL1 proteins revealed that there would be inconsiderable difference among them. The ompL1 gene of the three isolates was well conserved, differing only by a total of 6 bp and the proteins by 2 amino acids. The cloned gene could be further used for expression and recombinant OmpL1 as an efficient and conserved antigen, and may be a useful vaccine candidate against leptospirosis in our region.

  17. Pathways toward unidirectional alignment in block copolymer thin films on faceted surfaces

    Science.gov (United States)

    Gunkel, Ilja; Gu, Xiaodan; Sarje, Abhinav; Hexemer, Alexander; Russell, Thomas

    2015-03-01

    Solvent vapor annealing (SVA) has been shown recently to be an effective means to produce long-range lateral order in block copolymer (BCP) thin films in relatively short times. Furthermore, using substrates with faceted surfaces allows for generating unidirectionally aligned BCP microdomains on the size scale of an entire wafer. While in recent years SVA has been largely demystified, the detailed pathways toward obtaining unidirectional alignment still remain unclear. Grazing-incidence X-ray scattering (GISAXS) is a very powerful tool for characterizing the structure and morphology of BCPs in thin films, and is particularly useful for studying structural changes in BCP thin films during SVA. We here present in situ GISAXS experiments on cylinder-forming PS-b-P2VP BCP thin films on faceted Sapphire substrates during annealing in THF. We show that the degree of alignment of cylindrical microdomains is greatly enhanced at solvent concentrations close to the order-disorder transition of the copolymer. Furthermore, we observed that inducing disorder by further increasing the solvent concentration and subsequent quenching to the ordered (not yet glassy) state induced the highest degree of alignment with nearly unidirectional alignment of the microdomains in less than 30 min.

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

    Science.gov (United States)

    Burke, Christopher J.; Grason, Gregory M.

    2018-05-01

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

  19. Order aggressiveness and order book dynamics

    DEFF Research Database (Denmark)

    Hall, Anthony D.; Hautsch, Nikolaus

    2006-01-01

    In this paper, we study the determinants of order aggressiveness and traders’ order submission strategy in an open limit order book market. Applying an order classification scheme, we model the most aggressive market orders, limit orders as well as cancellations on both sides of the market...... employing a six-dimensional autoregressive conditional intensity model. Using order book data from the Australian Stock Exchange, we find that market depth, the queued volume, the bid-ask spread, recent volatility, as well as recent changes in both the order flow and the price play an important role...... in explaining the determinants of order aggressiveness. Overall, our empirical results broadly confirm theoretical predictions on limit order book trading. However, we also find evidence for behavior that can be attributed to particular liquidity and volatility effects...

  20. 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

  1. 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.

  2. The relationship between Business Strategy, IT Strategy and Alignment Capability

    NARCIS (Netherlands)

    Drs. A.J.G. Silvius

    2009-01-01

    Aligning business and IT strategy is a prominent area of concern. Organizations that successfully align their business strategy and their IT strategy, outperform their non-aligned peers (Chan et al., 1997). This chapter explores the relationship between business strategy, IT strategy and alignment

  3. SU-E-J-24: Image-Guidance Using Cone-Beam CT for Stereotactic Body Radiotherapy (SBRT) of Lung Cancer Patients: Bony Alignment or Soft Tissue Alignment?

    Science.gov (United States)

    Wang, L; Turaka, A; Meyer, J; Spoka, D; Jin, L; Fan, J; Ma, C

    2012-06-01

    To assess the reliability of soft tissue alignment by comparing pre- and post-treatment cone-beam CT (CBCT) for image guidance in stereotactic body radiotherapy (SBRT) of lung cancers. Our lung SBRT procedures require all patients undergo 4D CT scan in order to obtain patient-specific target motion information through reconstructed 4D data using the maximum-intensity projection (MIP) algorithm. The internal target volume (ITV) was outlined directly from the MIP images and a 3-5 mm margin expansion was then applied to the ITV to create the PTV. Conformal treatment planning was performed on the helical images, to which the MIP images were fused. Prior to each treatment, CBCT was used for image guidance by comparing with the simulation CT and for patient relocalization based on the bony anatomy. Any displacement of the patient bony structure would be considered as setup errors and would be corrected by couch shifts. Theoretically, as the PTV definition included target internal motion, no further shifts other than setup corrections should be made. However, it is our practice to have treating physicians further check target localization within the PTV. Whenever the shifts based on the soft-tissue alignment (that is, target alignment) exceeded a certain value (e.g. 5 mm), a post-treatment CBCT was carried out to ensure that the tissue alignment is reliable by comparing between pre- and post-treatment CBCT. Pre- and post-CBCT has been performed for 7 patients so far who had shifts beyond 5 mm despite bony alignment. For all patients, post CBCT confirmed that the visualized target position was kept in the same position as before treatment after adjusting for soft-tissue alignment. For the patient population studied, it is shown that soft-tissue alignment is necessary and reliable in the lung SBRT for individual cases. © 2012 American Association of Physicists in Medicine.

  4. ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes.

    Science.gov (United States)

    Otto, Thomas Dan; Catanho, Marcos; Tristão, Cristian; Bezerra, Márcia; Fernandes, Renan Mathias; Elias, Guilherme Steinberger; Scaglia, Alexandre Capeletto; Bovermann, Bill; Berstis, Viktors; Lifschitz, Sergio; de Miranda, Antonio Basílio; Degrave, Wim

    2010-03-01

    Many analyses in modern biological research are based on comparisons between biological sequences, resulting in functional, evolutionary and structural inferences. When large numbers of sequences are compared, heuristics are often used resulting in a certain lack of accuracy. In order to improve and validate results of such comparisons, we have performed radical all-against-all comparisons of 4 million protein sequences belonging to the RefSeq database, using an implementation of the Smith-Waterman algorithm. This extremely intensive computational approach was made possible with the help of World Community Grid, through the Genome Comparison Project. The resulting database, ProteinWorldDB, which contains coordinates of pairwise protein alignments and their respective scores, is now made available. Users can download, compare and analyze the results, filtered by genomes, protein functions or clusters. ProteinWorldDB is integrated with annotations derived from Swiss-Prot, Pfam, KEGG, NCBI Taxonomy database and gene ontology. The database is a unique and valuable asset, representing a major effort to create a reliable and consistent dataset of cross-comparisons of the whole protein content encoded in hundreds of completely sequenced genomes using a rigorous dynamic programming approach. The database can be accessed through http://proteinworlddb.org

  5. An Overview of DNA Microarray Grid Alignment and Foreground Separation Approaches

    Directory of Open Access Journals (Sweden)

    Bajcsy Peter

    2006-01-01

    Full Text Available This paper overviews DNA microarray grid alignment and foreground separation approaches. Microarray grid alignment and foreground separation are the basic processing steps of DNA microarray images that affect the quality of gene expression information, and hence impact our confidence in any data-derived biological conclusions. Thus, understanding microarray data processing steps becomes critical for performing optimal microarray data analysis. In the past, the grid alignment and foreground separation steps have not been covered extensively in the survey literature. We present several classifications of existing algorithms, and describe the fundamental principles of these algorithms. Challenges related to automation and reliability of processed image data are outlined at the end of this overview paper.

  6. Alignment-free phylogeny of whole genomes using underlying subwords

    Directory of Open Access Journals (Sweden)

    Comin Matteo

    2012-12-01

    Full Text Available Abstract Background With the progress of modern sequencing technologies a large number of complete genomes are now available. Traditionally the comparison of two related genomes is carried out by sequence alignment. There are cases where these techniques cannot be applied, for example if two genomes do not share the same set of genes, or if they are not alignable to each other due to low sequence similarity, rearrangements and inversions, or more specifically to their lengths when the organisms belong to different species. For these cases the comparison of complete genomes can be carried out only with ad hoc methods that are usually called alignment-free methods. Methods In this paper we propose a distance function based on subword compositions called Underlying Approach (UA. We prove that the matching statistics, a popular concept in the field of string algorithms able to capture the statistics of common words between two sequences, can be derived from a small set of “independent” subwords, namely the irredundant common subwords. We define a distance-like measure based on these subwords, such that each region of genomes contributes only once, thus avoiding to count shared subwords a multiple number of times. In a nutshell, this filter discards subwords occurring in regions covered by other more significant subwords. Results The Underlying Approach (UA builds a scoring function based on this set of patterns, called underlying. We prove that this set is by construction linear in the size of input, without overlaps, and can be efficiently constructed. Results show the validity of our method in the reconstruction of phylogenetic trees, where the Underlying Approach outperforms the current state of the art methods. Moreover, we show that the accuracy of UA is achieved with a very small number of subwords, which in some cases carry meaningful biological information. Availability http://www.dei.unipd.it/∼ciompin/main/underlying.html

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

    Science.gov (United States)

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

    2015-01-01

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

  8. The impact of two-loop effects on the scenario of MSSM Higgs alignment without decoupling

    Energy Technology Data Exchange (ETDEWEB)

    Haber, Howard E.; Stefaniak, Tim [University of California, Santa Cruz Institute for Particle Physics (SCIPP) and Department of Physics, Santa Cruz, CA (United States); Heinemeyer, Sven [Campus of International Excellence UAM+CSIC, Madrid (Spain); Universidad Autonoma de Madrid, Instituto de Fisica Teorica, (UAM/CSIC), Madrid (Spain); Instituto de Fisica de Cantabria (CSIC-UC), Santander (Spain)

    2017-11-15

    In multi-Higgs models, the properties of one neutral scalar state approximate those of the Standard Model (SM) Higgs boson in a limit where the corresponding scalar field is roughly aligned in field space with the scalar doublet vacuum expectation value. In a scenario of alignment without decoupling, a SM-like Higgs boson can be accompanied by additional scalar states whose masses are of a similar order of magnitude. In the Minimal Supersymmetric Standard Model (MSSM), alignment without decoupling can be achieved due to an accidental cancellation of tree-level and radiative loop-level effects. In this paper we assess the impact of the leading two-loop O(α{sub s}h{sub t}{sup 2}) corrections on the Higgs alignment condition in the MSSM. These corrections are sizable and important in the relevant regions of parameter space and furthermore give rise to solutions of the alignment condition that are not present in the approximate one-loop description. We provide a comprehensive numerical comparison of the alignment condition obtained in the approximate one-loop and two-loop approximations, and discuss its implications for phenomenologically viable regions of the MSSM parameter space. (orig.)

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-08-15

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

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

    Science.gov (United States)

    Yang, Zhengfan; Penczek, Pawel A

    2008-08-01

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

  11. Automatic alignment device for focal spot measurements in the center of the field for mammography

    International Nuclear Information System (INIS)

    Vieira, Marcelo A.C.; Watanabe, Alex O.; Oliveira Junior, Paulo D.; Schiabel, Homero

    2010-01-01

    Some quality control procedures used for mammography, such as focal spot evaluation, requires previous alignment of the measurement equipment with the X-ray central beam. However, alignment procedures are, in general, the most difficult task and the one that needs more time to be performed. Moreover, the operator sometimes is exposed to radiation during this procedure. This work presents an automatic alignment system for mammographic equipment that allows locating the central ray of the radiation beam and, immediately, aligns with it by dislocating itself automatically along the field. The system consists on a bidirectional moving device, connected to a CCD sensor for digital radiographic image acquisition. A computational analysis of a radiographic image, acquired at any position on the field, is performed in order to determine its positioning under the X-ray beam. Finally, a mechanical system for two moving directions, electronically controlled by a microcontroller under USB communication, makes the system to align automatically with the radiation beam central ray. The alignment process is fully automatic, fast and accurate, with no operator exposure to radiation, which allows a considerable time saving for quality control procedures achievement for mammography. (author)

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

    International Nuclear Information System (INIS)

    Yang Zhengfan; Penczek, Pawel A.

    2008-01-01

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

  13. Quantification of Cardiomyocyte Alignment from Three-Dimensional (3D) Confocal Microscopy of Engineered Tissue.

    Science.gov (United States)

    Kowalski, William J; Yuan, Fangping; Nakane, Takeichiro; Masumoto, Hidetoshi; Dwenger, Marc; Ye, Fei; Tinney, Joseph P; Keller, Bradley B

    2017-08-01

    Biological tissues have complex, three-dimensional (3D) organizations of cells and matrix factors that provide the architecture necessary to meet morphogenic and functional demands. Disordered cell alignment is associated with congenital heart disease, cardiomyopathy, and neurodegenerative diseases and repairing or replacing these tissues using engineered constructs may improve regenerative capacity. However, optimizing cell alignment within engineered tissues requires quantitative 3D data on cell orientations and both efficient and validated processing algorithms. We developed an automated method to measure local 3D orientations based on structure tensor analysis and incorporated an adaptive subregion size to account for multiple scales. Our method calculates the statistical concentration parameter, κ, to quantify alignment, as well as the traditional orientational order parameter. We validated our method using synthetic images and accurately measured principal axis and concentration. We then applied our method to confocal stacks of cleared, whole-mount engineered cardiac tissues generated from human-induced pluripotent stem cells or embryonic chick cardiac cells and quantified cardiomyocyte alignment. We found significant differences in alignment based on cellular composition and tissue geometry. These results from our synthetic images and confocal data demonstrate the efficiency and accuracy of our method to measure alignment in 3D tissues.

  14. 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.

  15. Evolution of shiva laser alignment systems

    International Nuclear Information System (INIS)

    Boyd, R.D.

    1980-07-01

    The Shiva oscillator pulse is preamplified and divided into twenty beams. Each beam is then amplified, spatially filtered, directed, and focused onto a target a few hundred micrometers in size producing optical intensities up to 10 16 W/cm 2 . The laser was designed and built with three automatic alignment systems: the oscillator alignment system, which aligns each of the laser's three oscillators to a reference beamline; the chain input pointing system, which points each beam into its respective chain; and the chain output pointing, focusing and centering system which points, centers and focuses the beam onto the target. Recently the alignment of the laser's one hundred twenty spatial filter pinholes was also automated. This system uses digitized video images of back-illuminated pinholes and computer analysis to determine current positions. The offset of each current position from a desired center point is then translated into stepper motor commands and the pinhole is moved the proper distance. While motors for one pinhole are moving, the system can digitize, analyze, and send commands to other motors, allowing the system to efficiently align several pinholes in parallel

  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. Unsupervised image matching based on manifold alignment.

    Science.gov (United States)

    Pei, Yuru; Huang, Fengchun; Shi, Fuhao; Zha, Hongbin

    2012-08-01

    This paper challenges the issue of automatic matching between two image sets with similar intrinsic structures and different appearances, especially when there is no prior correspondence. An unsupervised manifold alignment framework is proposed to establish correspondence between data sets by a mapping function in the mutual embedding space. We introduce a local similarity metric based on parameterized distance curves to represent the connection of one point with the rest of the manifold. A small set of valid feature pairs can be found without manual interactions by matching the distance curve of one manifold with the curve cluster of the other manifold. To avoid potential confusions in image matching, we propose an extended affine transformation to solve the nonrigid alignment in the embedding space. The comparatively tight alignments and the structure preservation can be obtained simultaneously. The point pairs with the minimum distance after alignment are viewed as the matchings. We apply manifold alignment to image set matching problems. The correspondence between image sets of different poses, illuminations, and identities can be established effectively by our approach.

  18. 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

  19. Enabling Process Alignment for IT Entrepreneurship

    Directory of Open Access Journals (Sweden)

    Sonia D. Bot

    2012-11-01

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

  20. 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.

  1. 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.

  2. Engineering muscle cell alignment through 3D bioprinting.

    Science.gov (United States)

    Mozetic, Pamela; Giannitelli, Sara Maria; Gori, Manuele; Trombetta, Marcella; Rainer, Alberto

    2017-09-01

    Processing of hydrogels represents a main challenge for the prospective application of additive manufacturing (AM) to soft tissue engineering. Furthermore, direct manufacturing of tissue precursors with a cell density similar to native tissues has the potential to overcome the extensive in vitro culture required for conventional cell-seeded scaffolds seeking to fabricate constructs with tailored structural and functional properties. In this work, we present a simple AM methodology that exploits the thermoresponsive behavior of a block copolymer (Pluronic ® ) as a means to obtain good shape retention at physiological conditions and to induce cellular alignment. Pluronic/alginate blends have been investigated as a model system for the processing of C2C12 murine myoblast cell line. Interestingly, C2C12 cell model demonstrated cell alignment along the deposition direction, potentially representing a new avenue to tailor the resulting cell histoarchitecture during AM process. Furthermore, the fabricated constructs exhibited high cell viability, as well as a significantly improved expression of myogenic genes vs. conventional 2D cultures. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 2582-2588, 2017. © 2017 Wiley Periodicals, Inc.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-11-10

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

  4. SAMMate: a GUI tool for processing short read alignments in SAM/BAM format

    Directory of Open Access Journals (Sweden)

    Flemington Erik

    2011-01-01

    Full Text Available Abstract Background Next Generation Sequencing (NGS technology generates tens of millions of short reads for each DNA/RNA sample. A key step in NGS data analysis is the short read alignment of the generated sequences to a reference genome. Although storing alignment information in the Sequence Alignment/Map (SAM or Binary SAM (BAM format is now standard, biomedical researchers still have difficulty accessing this information. Results We have developed a Graphical User Interface (GUI software tool named SAMMate. SAMMate allows biomedical researchers to quickly process SAM/BAM files and is compatible with both single-end and paired-end sequencing technologies. SAMMate also automates some standard procedures in DNA-seq and RNA-seq data analysis. Using either standard or customized annotation files, SAMMate allows users to accurately calculate the short read coverage of genomic intervals. In particular, for RNA-seq data SAMMate can accurately calculate the gene expression abundance scores for customized genomic intervals using short reads originating from both exons and exon-exon junctions. Furthermore, SAMMate can quickly calculate a whole-genome signal map at base-wise resolution allowing researchers to solve an array of bioinformatics problems. Finally, SAMMate can export both a wiggle file for alignment visualization in the UCSC genome browser and an alignment statistics report. The biological impact of these features is demonstrated via several case studies that predict miRNA targets using short read alignment information files. Conclusions With just a few mouse clicks, SAMMate will provide biomedical researchers easy access to important alignment information stored in SAM/BAM files. Our software is constantly updated and will greatly facilitate the downstream analysis of NGS data. Both the source code and the GUI executable are freely available under the GNU General Public License at http://sammate.sourceforge.net.

  5. 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.

  6. LumiCal alignment system - Status report

    CERN Document Server

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

    2015-01-01

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

  7. Plasmonic Properties of Vertically Aligned Nanowire Arrays

    Directory of Open Access Journals (Sweden)

    Hua Qi

    2012-01-01

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

  8. Alignment analysis of a vertical sodium pump

    International Nuclear Information System (INIS)

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

    1981-01-01

    With the objective of identifying important alignment features of pumps such as FFTF, HALLAM, EBR II, PNC, PHENIX, and CRBR, alignment of the vertical sodium pump for the Clinch River Breeder Reactor Plant (CRBRP) is investigated. The CRBRP pump includes a flexibly coupled pump shaft and motor shaft, two oil-film tilting-pad hydrodynamic radial bearings in the motor plus a vertical thrust bearing, and two sodium hydrostatic bearings straddling the double-suction centrifugal impeller in the pump. The assembled CRBRP prototype pump shows smooth predictable vibration behavior experienced during water test. An ealier swing check of the pump shaft about the motor shaft hub demonstrated that the pump is relatively insensitive to manufacturing and assembly tolerances, a consequence of close dimensional control and unique alignment features. (orig./GL)

  9. Mechanical alignment of substrates to a mask

    Science.gov (United States)

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

    2016-11-08

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

  10. Tracker Alignment Performance Plots after Commissioning

    CERN Document Server

    CMS Collaboration

    2017-01-01

    During the LHC shutdown in Winter 2016/17, the CMS pixel detector, the inner component of the CMS Tracker, was replaced by the Phase-1 upgrade detector. Among others improvements, the new pixel detector consists of four instead of three layers in the central barrel region (BPIX) and three instead of two disks in the endcap regions (FPIX). In this report, performance plots of pixel detector alignment results are presented, which were obtained with both cosmic-ray and pp collision data acquired at the beginning of the 2017 LHC operation. Alignment constants have been derived for each data-taking period to the level of single module positions in both the pixel and the strip detectors. The complete understanding of the alignment and biases was derived by using two algorithms, Millepede-II and HipPy. The results confirm each other.

  11. Prosody and alignment: a sequential perspective

    Science.gov (United States)

    Szczepek Reed, Beatrice

    2010-12-01

    In their analysis of a corpus of classroom interactions in an inner city high school, Roth and Tobin describe how teachers and students accomplish interactional alignment by prosodically matching each other's turns. Prosodic matching, and specific prosodic patterns are interpreted as signs of, and contributions to successful interactional outcomes and positive emotions. Lack of prosodic matching, and other specific prosodic patterns are interpreted as features of unsuccessful interactions, and negative emotions. This forum focuses on the article's analysis of the relation between interpersonal alignment, emotion and prosody. It argues that prosodic matching, and other prosodic linking practices, play a primarily sequential role, i.e. one that displays the way in which participants place and design their turns in relation to other participants' turns. Prosodic matching, rather than being a conversational action in itself, is argued to be an interactional practice (Schegloff 1997), which is not always employed for the accomplishment of `positive', or aligning actions.

  12. Precision alignment and calibration of optical systems using computer generated holograms

    Science.gov (United States)

    Coyle, Laura Elizabeth

    As techniques for manufacturing and metrology advance, optical systems are being designed with more complexity than ever before. Given these prescriptions, alignment and calibration can be a limiting factor in their final performance. Computer generated holograms (CGHs) have several unique properties that make them powerful tools for meeting these demanding tolerances. This work will present three novel methods for alignment and calibration of optical systems using computer generated holograms. Alignment methods using CGHs require that the optical wavefront created by the CGH be related to a mechanical datum to locate it space. An overview of existing methods is provided as background, then two new alignment methods are discussed in detail. In the first method, the CGH contact Ball Alignment Tool (CBAT) is used to align a ball or sphere mounted retroreflector (SMR) to a Fresnel zone plate pattern with micron level accuracy. The ball is bonded directly onto the CGH substrate and provides permanent, accurate registration between the optical wavefront and a mechanical reference to locate the CGH in space. A prototype CBAT was built and used to align and bond an SMR to a CGH. In the second method, CGH references are used to align axi-symmetric optics in four degrees of freedom with low uncertainty and real time feedback. The CGHs create simultaneous 3D optical references where the zero order reflection sets tilt and the first diffracted order sets centration. The flexibility of the CGH design can be used to accommodate a wide variety of optical systems and maximize sensitivity to misalignments. A 2-CGH prototype system was aligned multiplied times and the alignment uncertainty was quantified and compared to an error model. Finally, an enhanced calibration method is presented. It uses multiple perturbed measurements of a master sphere to improve the calibration of CGH-based Fizeau interferometers ultimately measuring aspheric test surfaces. The improvement in the

  13. SMC Progressively Aligns Chromosomal Arms in Caulobacter crescentus but Is Antagonized by Convergent Transcription

    Directory of Open Access Journals (Sweden)

    Ngat T. Tran

    2017-08-01

    Full Text Available The structural maintenance of chromosomes (SMC complex plays an important role in chromosome organization and segregation in most living organisms. In Caulobacter crescentus, SMC is required to align the left and the right arms of the chromosome that run in parallel down the long axis of the cell. However, the mechanism of SMC-mediated alignment of chromosomal arms remains elusive. Here, using genome-wide methods and microscopy of single cells, we show that Caulobacter SMC is recruited to the centromeric parS site and that SMC-mediated arm alignment depends on the chromosome-partitioning protein ParB. We provide evidence that SMC likely tethers the parS-proximal regions of the chromosomal arms together, promoting arm alignment. Furthermore, we show that highly transcribed genes near parS that are oriented against SMC translocation disrupt arm alignment, suggesting that head-on transcription interferes with SMC translocation. Our results demonstrate a tight interdependence of bacterial chromosome organization and global patterns of transcription.

  14. Design of multiple sequence alignment algorithms on parallel, distributed memory supercomputers.

    Science.gov (United States)

    Church, Philip C; Goscinski, Andrzej; Holt, Kathryn; Inouye, Michael; Ghoting, Amol; Makarychev, Konstantin; Reumann, Matthias

    2011-01-01

    The challenge of comparing two or more genomes that have undergone recombination and substantial amounts of segmental loss and gain has recently been addressed for small numbers of genomes. However, datasets of hundreds of genomes are now common and their sizes will only increase in the future. Multiple sequence alignment of hundreds of genomes remains an intractable problem due to quadratic increases in compute time and memory footprint. To date, most alignment algorithms are designed for commodity clusters without parallelism. Hence, we propose the design of a multiple sequence alignment algorithm on massively parallel, distributed memory supercomputers to enable research into comparative genomics on large data sets. Following the methodology of the sequential progressiveMauve algorithm, we design data structures including sequences and sorted k-mer lists on the IBM Blue Gene/P supercomputer (BG/P). Preliminary results show that we can reduce the memory footprint so that we can potentially align over 250 bacterial genomes on a single BG/P compute node. We verify our results on a dataset of E.coli, Shigella and S.pneumoniae genomes. Our implementation returns results matching those of the original algorithm but in 1/2 the time and with 1/4 the memory footprint for scaffold building. In this study, we have laid the basis for multiple sequence alignment of large-scale datasets on a massively parallel, distributed memory supercomputer, thus enabling comparison of hundreds instead of a few genome sequences within reasonable time.

  15. FunGene: the functional gene pipeline and repository.

    Science.gov (United States)

    Fish, Jordan A; Chai, Benli; Wang, Qiong; Sun, Yanni; Brown, C Titus; Tiedje, James M; Cole, James R

    2013-01-01

    Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer. While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/) offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

  16. FunGene: the Functional Gene Pipeline and Repository

    Directory of Open Access Journals (Sweden)

    Jordan A. Fish

    2013-10-01

    Full Text Available Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer.While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/ offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

  17. 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.

  18. Wire alignment system for ATF LINAC

    International Nuclear Information System (INIS)

    Hayano, H.; Takeda, S.; Matsumoto, H.; Matsui, T.

    1994-01-01

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

  19. Alignment and geodesy for the ESRF project

    International Nuclear Information System (INIS)

    Roux, D.

    1990-01-01

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

  20. 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.

  1. Spreadsheet macros for coloring sequence alignments.

    Science.gov (United States)

    Haygood, M G

    1993-12-01

    This article describes a set of Microsoft Excel macros designed to color amino acid and nucleotide sequence alignments for review and preparation of visual aids. The colored alignments can then be modified to emphasize features of interest. Procedures for importing and coloring sequences are described. The macro file adds a new menu to the menu bar containing sequence-related commands to enable users unfamiliar with Excel to use the macros more readily. The macros were designed for use with Macintosh computers but will also run with the DOS version of Excel.

  2. 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

  3. Aligning European OA policies with Horizon 2020

    OpenAIRE

    Picarra, Mafalda; Angelaki, Marina; Dogan, Guleda; Guy, Marieke; Artusio, Claudio

    2015-01-01

    This article considers that the Horizon 2020 (H2020) Open Access (OA) policy can be adopted as a policy model in European Research Area (ERA) countries for the development and increasing alignment of OA policies. Accordingly, the OA policy landscape in five ERA countries – Greece, Italy, the Netherlands, Turkey and the UK – is assessed and the extent of alignment or divergence of those policies with the H2020 OA policy is examined. The article concludes by considering some of the impacts that...

  4. Cloning and analysis of calmodulin gene from Porphyra yezoensis Ueda (Bangiales, Rhodophyta)

    Science.gov (United States)

    Wang, Mengqiang; Mao, Yunxiang; Zhuang, Yunyun; Kong, Fanna; Sui, Zhenghong

    2009-09-01

    In order to understand the mechanisms of signal transduction and anti-desiccation mechanisms of Porphyra yezoensis, cDNA and its genomic sequence of Calmodulin gene (CaM) was cloned by the technique of polymerase chain reaction (PCR) based on the analysis of P. yezoensis ESTs from dbEST database. The result shows that the full-length cDNA of CaM consists of 603 bps including an ORF encoding for 151 amino acids and a terminate codon UGA, while the length of genomic sequence is 1231 bps including 2 exons and 1 intron. The average GC content of the coding region is 58.77%, while the GC content of the third position of this gene is as high as 82.23%. Four Ca2+ binding sites (EF-hand) are found in this gene. The predicted molecular mass of the deduced peptide is 16688.72 Da and the pI is 4.222. By aligning with known CaM genes, the similarity of CaM gene sequence with homologous genes in Chlamydomonas incerta and Chlamydomonas reinhardtii is 72.7% and 72.2% respectively, and the similarity of the deduced amino acid sequence of CaM gene with homologous genes in C. incerta and C. reinhardtii are both 71.5%. This is the first report on CaM from a species of Rhodophyta.

  5. Covering vertically aligned carbon nanotubes with a multiferroic compound

    KAUST Repository

    Mahajan, Amit; Rodriguez, Brian J.; Saravanan, K. Venkata; Ramana, E. Venkata; Da Costa, Pedro M. F. J.; Vilarinho, Paula M.

    2014-01-01

    This work highlights the possible use of vertically-aligned multiwall carbon nanotubes (VA-MWCNTs) as bottom electrodes for microelectronics, for example for memory applications. As a proof of concept BiFeO3 (BFO) films were fabricated in-situ deposited on the surface of VA-MWCNTs by RF (radio frequency) magnetron sputtering. For in situ deposition temperature of 400 °C and deposition time up to 2 h, BFO films cover the MWCNTs and no damage occurs either in the film or MWCNTs. In spite of the macroscopic lossy polarization behaviour, the ferroelectric nature, domain structure and switching of these conformal BFO films was verified by piezo force microscopy. G type antiferromagnetic ordering with weak ferromagnetic ordering loop was proved for BFO films on VA-MWCNTs having a coercive field of 700 Oe.

  6. Covering vertically aligned carbon nanotubes with a multiferroic compound

    KAUST Repository

    Mahajan, Amit

    2014-10-30

    This work highlights the possible use of vertically-aligned multiwall carbon nanotubes (VA-MWCNTs) as bottom electrodes for microelectronics, for example for memory applications. As a proof of concept BiFeO3 (BFO) films were fabricated in-situ deposited on the surface of VA-MWCNTs by RF (radio frequency) magnetron sputtering. For in situ deposition temperature of 400 °C and deposition time up to 2 h, BFO films cover the MWCNTs and no damage occurs either in the film or MWCNTs. In spite of the macroscopic lossy polarization behaviour, the ferroelectric nature, domain structure and switching of these conformal BFO films was verified by piezo force microscopy. G type antiferromagnetic ordering with weak ferromagnetic ordering loop was proved for BFO films on VA-MWCNTs having a coercive field of 700 Oe.

  7. Collagen fiber alignment and biaxial mechanical behavior of porcine urinary bladder derived extracellular matrix

    NARCIS (Netherlands)

    Gilbert, Thomas W.; Wognum, Silvia; Joyce, Erinn M.; Freytes, Donald O.; Sacks, Michael S.; Badylak, Stephen F.

    2008-01-01

    The collagen fiber alignment and biomechanical behavior of naturally occurring extracellular matrix (ECM) scaffolds are important considerations for the design of medical devices from these materials. Both should be considered in order to produce a device to meet tissue specific mechanical

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

    CERN Document Server

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

    2003-01-01

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

  9. A Case Study of the Alignment between Curriculum and Assessment in the New York State Earth Science Standards-Based System

    Science.gov (United States)

    Contino, Julie

    2013-01-01

    In a standards-based system, it is important for all components of the system to align in order to achieve the intended goals. No Child Left Behind law mandates that assessments be fully aligned with state standards, be valid, reliable and fair, be reported to all stakeholders, and provide evidence that all students in the state are meeting the…

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

    Science.gov (United States)

    Lizotte, Todd E.

    2011-10-01

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

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

    CERN Document Server

    Chatrchyan, S; Sirunyan, A M; Adam, W; Arnold, B; Bergauer, H; Bergauer, T; Dragicevic, M; Eichberger, M; Erö, J; Friedl, M; Frühwirth, R; Ghete, V M; Hammer, J; Hänsel, S; Hoch, M; Hörmann, N; Hrubec, J; Jeitler, M; Kasieczka, G; Kastner, K; Krammer, M; Liko, D; Magrans de Abril, I; Mikulec, I; Mittermayr, F; Neuherz, B; Oberegger, M; Padrta, M; Pernicka, M; Rohringer, H; Schmid, S; Schöfbeck, R; Schreiner, T; Stark, R; Steininger, H; Strauss, J; Taurok, A; Teischinger, F; Themel, T; Uhl, D; Wagner, P; Waltenberger, W; Walzel, G; Widl, E; Wulz, C E; Chekhovsky, V; Dvornikov, O; Emeliantchik, I; Litomin, A; Makarenko, V; Marfin, I; Mossolov, V; Shumeiko, N; Solin, A; Stefanovitch, R; Suarez Gonzalez, J; Tikhonov, A; Fedorov, A; Karneyeu, A; Korzhik, M; Panov, V; Zuyeuski, R; Kuchinsky, P; Beaumont, W; Benucci, L; Cardaci, M; De Wolf, E A; Delmeire, E; Druzhkin, D; Hashemi, M; Janssen, X; Maes, T; Mucibello, L; Ochesanu, S; Rougny, R; Selvaggi, M; Van Haevermaet, H; Van Mechelen, P; Van Remortel, N; Adler, V; Beauceron, S; Blyweert, S; D'Hondt, J; De Weirdt, S; Devroede, O; Heyninck, J; Kalogeropoulos, A; Maes, J; Maes, M; Mozer, M U; Tavernier, S; Van Doninck, W; Van Mulders, P; Villella, I; Bouhali, O; Chabert, E C; Charaf, O; Clerbaux, B; De Lentdecker, G; Dero, V; Elgammal, S; Gay, A P R; Hammad, G H; Marage, P E; Rugovac, S; Vander Velde, C; Vanlaer, P; Wickens, J; Grunewald, M; Klein, B; Marinov, A; Ryckbosch, D; Thyssen, F; Tytgat, M; Vanelderen, L; Verwilligen, P; Basegmez, S; Bruno, G; Caudron, J; Delaere, C; Demin, P; Favart, D; Giammanco, A; Grégoire, G; Lemaitre, V; Militaru, O; Ovyn, S; Piotrzkowski, K; Quertenmont, L; Schul, N; Beliy, N; Daubie, E; Alves, G A; Pol, M E; Souza, M H G; Carvalho, W; De Jesus Damiao, D; De Oliveira Martins, C; Fonseca De Souza, S; Mundim, L; Oguri, V; Santoro, A; Silva Do Amaral, S M; Sznajder, A; Fernandez Perez Tomei, T R; Ferreira Dias, M A; Gregores, E M; Novaes, S F; Abadjiev, K; Anguelov, T; Damgov, J; Darmenov, N; Dimitrov, L; Genchev, V; Iaydjiev, P; Piperov, S; Stoykova, S; Sultanov, G; Trayanov, R; Vankov, I; Dimitrov, A; Dyulendarova, M; Kozhuharov, V; Litov, L; Marinova, E; Mateev, M; Pavlov, B; Petkov, P; Toteva, Z; Chen, G M; Chen, H S; Guan, W; Jiang, C H; Liang, D; Liu, B; Meng, X; Tao, J; Wang, J; Wang, Z; Xue, Z; Zhang, Z; Ban, Y; Cai, J; Ge, Y; Guo, S; Hu, Z; Mao, Y; Qian, S J; Teng, H; Zhu, B; Avila, C; Baquero Ruiz, M; Carrillo Montoya, C A; Gomez, A; Gomez Moreno, B; Ocampo Rios, A A; Osorio Oliveros, A F; Reyes Romero, D; Sanabria, J C; Godinovic, N; Lelas, K; Plestina, R; Polic, D; Puljak, I; Antunovic, Z; Dzelalija, M; Brigljevic, V; Duric, S; Kadija, K; Morovic, S; Fereos, R; Galanti, M; Mousa, J; Papadakis, A; Ptochos, F; Razis, P A; Tsiakkouri, D; Zinonos, Z; Hektor, A; Kadastik, M; Kannike, K; Müntel, M; Raidal, M; Rebane, L; Anttila, E; Czellar, S; Härkönen, J; Heikkinen, A; Karimäki, V; Kinnunen, R; Klem, J; Kortelainen, M J; Lampén, T; Lassila-Perini, K; Lehti, S; Lindén, T; 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Lumb, N; Mirabito, L; Perries, S; Vander Donckt, M; Verdier, P; Djaoshvili, N; Roinishvili, N; Roinishvili, V; Amaglobeli, N; Adolphi, R; Anagnostou, G; Brauer, R; Braunschweig, W; Edelhoff, M; Esser, H; Feld, L; Karpinski, W; Khomich, A; Klein, K; Mohr, N; Ostaptchouk, A; Pandoulas, D; Pierschel, G; Raupach, F; Schael, S; Schultz von Dratzig, A; Schwering, G; Sprenger, D; Thomas, M; Weber, M; Wittmer, B; Wlochal, M; Actis, O; Altenhöfer, G; Bender, W; Biallass, P; Erdmann, M; Fetchenhauer, G; Frangenheim, J; Hebbeker, T; Hilgers, G; Hinzmann, A; Hoepfner, K; Hof, C; Kirsch, M; Klimkovich, T; Kreuzer, P; Lanske, D; Merschmeyer, M; Meyer, A; Philipps, B; Pieta, H; Reithler, H; Schmitz, S A; Sonnenschein, L; Sowa, M; Steggemann, J; Szczesny, H; Teyssier, D; Zeidler, C; Bontenackels, M; Davids, M; Duda, M; Flügge, G; Geenen, H; Giffels, M; Haj Ahmad, W; Hermanns, T; Heydhausen, D; Kalinin, S; Kress, T; Linn, A; Nowack, A; Perchalla, L; Poettgens, M; Pooth, O; Sauerland, P; Stahl, A; Tornier, D; 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Osborne, I; Paul, T; Reucroft, S; Swain, J; Taylor, L; Tuura, L; Anastassov, A; Gobbi, B; Kubik, A; Ofierzynski, R A; Pozdnyakov, A; Schmitt, M; Stoynev, S; Velasco, M; Won, S; Antonelli, L; Berry, D; Hildreth, M; Jessop, C; Karmgard, D J; Kolberg, T; Lannon, K; Lynch, S; Marinelli, N; Morse, D M; Ruchti, R; Slaunwhite, J; Warchol, J; Wayne, M; Bylsma, B; Durkin, L S; Gilmore, J; Gu, J; Killewald, P; Ling, T Y; Williams, G; Adam, N; Berry, E; Elmer, P; Garmash, A; Gerbaudo, D; Halyo, V; Hunt, A; Jones, J; Laird, E; Marlow, D; Medvedeva, T; Mooney, M; Olsen, J; Piroué, P; Stickland, D; Tully, C; Werner, J S; Wildish, T; Xie, Z; Zuranski, A; Acosta, J G; Bonnett Del Alamo, M; Huang, X T; Lopez, A; Mendez, H; Oliveros, S; Ramirez Vargas, J E; Santacruz, N; Zatzerklyany, A; Alagoz, E; Antillon, E; Barnes, V E; Bolla, G; Bortoletto, D; Everett, A; Garfinkel, A F; Gecse, Z; Gutay, L; Ippolito, N; Jones, M; Koybasi, O; Laasanen, A T; Leonardo, N; Liu, C; Maroussov, V; Merkel, P; Miller, D H; Neumeister, N; Sedov, A; Shipsey, I; Yoo, H D; Zheng, Y; Jindal, P; Parashar, N; Cuplov, V; Ecklund, K M; Geurts, F J M; Liu, J H; Maronde, D; Matveev, M; Padley, B P; Redjimi, R; Roberts, J; Sabbatini, L; Tumanov, A; Betchart, B; Bodek, A; Budd, H; Chung, Y S; de Barbaro, P; Demina, R; Flacher, H; Gotra, Y; Harel, A; Korjenevski, S; Miner, D C; Orbaker, D; Petrillo, G; Vishnevskiy, D; Zielinski, M; Bhatti, A; Demortier, L; Goulianos, K; Hatakeyama, K; Lungu, G; Mesropian, C; Yan, M; Atramentov, O; Bartz, E; Gershtein, Y; Halkiadakis, E; Hits, D; Lath, A; Rose, K; Schnetzer, S; Somalwar, S; Stone, R; Thomas, S; Watts, T L; Cerizza, G; Hollingsworth, M; Spanier, S; Yang, Z C; York, A; Asaadi, J; Aurisano, A; Eusebi, R; Golyash, A; Gurrola, A; Kamon, T; Nguyen, C N; Pivarski, J; Safonov, A; Sengupta, S; Toback, D; Weinberger, M; Akchurin, N; Berntzon, L; Gumus, K; Jeong, C; Kim, H; Lee, S W; Popescu, S; Roh, Y; Sill, A; Volobouev, I; Washington, E; Wigmans, R; Yazgan, E; Engh, D; Florez, C; Johns, W; Pathak, S; Sheldon, P; Andelin, D; Arenton, M W; Balazs, M; Boutle, S; Buehler, M; Conetti, S; Cox, B; Hirosky, R; Ledovskoy, A; Neu, C; Phillips II, D; Ronquest, M; Yohay, R; Gollapinni, S; Gunthoti, K; Harr, R; Karchin, P E; Mattson, M; Sakharov, A; Anderson, M; Bachtis, M; Bellinger, J N; Carlsmith, D; Crotty, I; Dasu, S; Dutta, S; Efron, J; Feyzi, F; Flood, K; Gray, L; Grogg, K S; Grothe, M; Hall-Wilton, R; Jaworski, M; Klabbers, P; Klukas, J; Lanaro, A; Lazaridis, C; Leonard, J; Loveless, R; Magrans de Abril, M; Mohapatra, A; Ott, G; Polese, G; Reeder, D; Savin, A; Smith, W H; Sourkov, A; Swanson, J; Weinberg, M; Wenman, D; Wensveen, M; White, A

    2010-01-01

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

  13. Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%

    DEFF Research Database (Denmark)

    Havgaard, Jakob Hull; Lyngsø, Rune B.; Stormo, Gary D.

    2005-01-01

    detect two genes with low sequence similarity, where the genes are part of a larger genomic region. Results: Here we present such an approach for pairwise local alignment which is based on FILDALIGN and the Sankoff algorithm for simultaneous structural alignment of multiple sequences. We include...... the ability to conduct mutual scans of two sequences of arbitrary length while searching for common local structural motifs of some maximum length. This drastically reduces the complexity of the algorithm. The scoring scheme includes structural parameters corresponding to those available for free energy....... The structure prediction performance for a family is typically around 0.7 using Matthews correlation coefficient. In case (2), the algorithm is successful at locating RNA families with an average sensitivity of 0.8 and a positive predictive value of 0.9 using a BLAST-like hit selection scheme. Availability...

  14. Stimulating Strategically Aligned Behaviour among Employees

    NARCIS (Netherlands)

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

    2008-01-01

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

  15. Aligning English Language Testing with Curriculum

    Science.gov (United States)

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

    2016-01-01

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

  16. 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.

  17. Aligning Technology Education Teaching with Brain Development

    Science.gov (United States)

    Katsioloudis, Petros

    2015-01-01

    This exploratory study was designed to determine if there is a level of alignment between technology education curriculum and theories of intellectual development. The researcher compared Epstein's Brain Growth Theory and Piaget's Status of Intellectual Development with technology education curriculum from Australia, England, and the United…

  18. 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 ...

  19. Alignment of Partnering with Construction IT

    Directory of Open Access Journals (Sweden)

    Eleni Papadonikolaki

    2017-11-01

     As the construction industry evolves into an information-driven sector, the alignment of construction IT with inter-organisational management is preeminent for managing the inherent complexities of the industry. In parallel, embracing inter-organisational approaches for information management such as BIM is a promisingway forward for SCM and construction management.

  20. 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)

  1. 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 ...

  2. Stimulating Strategically Aligned Behaviour Among Employees

    NARCIS (Netherlands)

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

    2007-01-01

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

  3. Constructive Alignment and the SOLO Taxonomy

    DEFF Research Database (Denmark)

    Brabrand, Claus; Dahl, Bettina

    2008-01-01

    the science faculties at University of Aarhus, Denmark (AU) and the University of Southern Denmark (SDU) that had been rewritten to explicitly incorporate course objectives, interpreted as intended learning outcomes (ILOs), using the principles of Constructive Alignment and the SOLO Taxonomy. In this paper we...

  4. Alignment of voids in the cosmic web

    NARCIS (Netherlands)

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

    2008-01-01

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

  5. 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

  6. 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.

  7. 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

  8. Local Alignments for Fine-Grained Categorization

    NARCIS (Netherlands)

    Gavves, E.; Fernando, B.; Snoek, C.G.M.; Smeulders, A.W.M.; Tuytelaars, T.

    2015-01-01

    The aim of this paper is fine-grained categorization without human interaction. Different from prior work, which relies on detectors for specific object parts, we propose to localize distinctive details by roughly aligning the objects using just the overall shape. Then, one may proceed to the

  9. Constructing Aligned Assessments Using Automated Test Construction

    Science.gov (United States)

    Porter, Andrew; Polikoff, Morgan S.; Barghaus, Katherine M.; Yang, Rui

    2013-01-01

    We describe an innovative automated test construction algorithm for building aligned achievement tests. By incorporating the algorithm into the test construction process, along with other test construction procedures for building reliable and unbiased assessments, the result is much more valid tests than result from current test construction…

  10. Alignment Challenges for a Future Linear Collider

    CERN Document Server

    Durand, H; Stern, G

    2013-01-01

    The preservation of ultra-low emittances in the main linac and Beam Delivery System area is one of the main challenges for linear colliders. This requires alignment tolerances never achieved before at that scale, down to the micrometre level. As a matter of fact, in the LHC, the goal for the smoothing of the components was to obtain a 1σ deviation with respect to a smooth curve of 0.15 mm over a 150 m long sliding window, while for the CLIC project for example, it corresponds to 10 μm over a sliding window of 200 m in the Beam Delivery System area. Two complementary strategies are being studied to fulfil these requirements: the development and validation of long range alignment systems over a few hundreds of metres and short range alignment systems over a few metres. The studies undertaken, with associated tests setups and the latest results will be detailed, as well as their application for the alignment of both CLIC and ILC colliders.

  11. 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

  12. 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...

  13. Systematic Image Based Optical Alignment and Tensegrity

    Science.gov (United States)

    Zeiders, Glenn W.; Montgomery, Edward E, IV (Technical Monitor)

    2001-01-01

    This presentation will review the objectives and current status of two Small Business Innovative Research being performed by the Sirius Group, under the direction of MSFC. They all relate to the development of advanced optical systems technologies for automated segmented mirror alignment techniques and fundamental design methodologies for ultralight structures. These are important to future astronomical missions in space.

  14. Aligning Pedagogy with Physical Learning Spaces

    Science.gov (United States)

    van Merriënboer, Jeroen J. G.; McKenney, Susan; Cullinan, Dominic; Heuer, Jos

    2017-01-01

    The quality of education suffers when pedagogies are not aligned with physical learning spaces. For example, the architecture of the triple-decker Victorian schools across England fits the information transmission model that was dominant in the industrial age, but makes it more difficult to implement student-centred pedagogies that better fit a…

  15. Alignment modification for pencil eye shields

    International Nuclear Information System (INIS)

    Evans, M.D.; Pla, M.; Podgorsak, E.B.

    1989-01-01

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

  16. Face Alignment Using Boosting and Evolutionary Search

    NARCIS (Netherlands)

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

    2010-01-01

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

  17. Mechanical equipment for magnet measurement and alignment

    International Nuclear Information System (INIS)

    Harvey, A.

    1992-05-01

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

  18. Security Policy Alignment: A Formal Approach

    NARCIS (Netherlands)

    Pieters, Wolter; Dimkov, T.; Pavlovic, Dusko

    2013-01-01

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

  19. 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)

  20. A Clustal Alignment Improver Using Evolutionary Algorithms

    DEFF Research Database (Denmark)

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

    2002-01-01

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