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Sample records for multiple-sequence local alignment

  1. Mulan: Multiple-Sequence Local Alignment and Visualization for Studying Function and Evolution

    SciTech Connect

    Ovcharenko, I; Loots, G; Giardine, B; Hou, M; Ma, J; Hardison, R; Stubbs, L; Miller, W

    2004-07-14

    Multiple sequence alignment analysis is a powerful approach for understanding phylogenetic relationships, annotating genes and detecting functional regulatory elements. With a growing number of partly or fully sequenced vertebrate genomes, effective tools for performing multiple comparisons are required to accurately and efficiently assist biological discoveries. Here we introduce Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved over evolutionary time. Mulan brings together several novel algorithms: the tba multi-aligner program for rapid identification of local sequence conservation and the multiTF program for detecting evolutionarily conserved transcription factor binding sites in multiple alignments. In addition, Mulan supports two-way communication with the GALA database; alignments of multiple species dynamically generated in GALA can be viewed in Mulan, and conserved transcription factor binding sites identified with Mulan/multiTF can be integrated and overlaid with extensive genome annotation data using GALA. Local multiple alignments computed by Mulan ensure reliable representation of short-and large-scale genomic rearrangements in distant organisms. Mulan allows for interactive modification of critical conservation parameters to differentially predict conserved regions in comparisons of both closely and distantly related species. We illustrate the uses and applications of the Mulan tool through multi-species comparisons of the GATA3 gene locus and the identification of elements that are conserved differently in avians than in other genomes allowing speculation on the evolution of birds. Source code for the aligners and the aligner-evaluation software can be freely downloaded from http://bio.cse.psu.edu/.

  2. An efficient method for multiple sequence alignment

    SciTech Connect

    Kim, J.; Pramanik, S.

    1994-12-31

    Multiple sequence alignment has been a useful method in the study of molecular evolution and sequence-structure relationships. This paper presents a new method for multiple sequence alignment based on simulated annealing technique. Dynamic programming has been widely used to find an optimal alignment. However, dynamic programming has several limitations to obtain optimal alignment. It requires long computation time and cannot apply certain types of cost functions. We describe detail mechanisms of simulated annealing for multiple sequence alignment problem. It is shown that simulated annealing can be an effective approach to overcome the limitations of dynamic programming in multiple sequence alignment problem.

  3. Two Hybrid Algorithms for Multiple Sequence Alignment

    NASA Astrophysics Data System (ADS)

    Naznin, Farhana; Sarker, Ruhul; Essam, Daryl

    2010-01-01

    In order to design life saving drugs, such as cancer drugs, the design of Protein or DNA structures has to be accurate. These structures depend on Multiple Sequence Alignment (MSA). MSA is used to find the accurate structure of Protein and DNA sequences from existing approximately correct sequences. To overcome the overly greedy nature of the well known global progressive alignment method for multiple sequence alignment, we have proposed two different algorithms in this paper; one is using an iterative approach with a progressive alignment method (PAMIM) and the second one is using a genetic algorithm with a progressive alignment method (PAMGA). Both of our methods started with a "kmer" distance table to generate single guide-tree. In the iterative approach, we have introduced two new techniques: the first technique is to generate Guide-trees with randomly selected sequences and the second is of shuffling the sequences inside that tree. The output of the tree is a multiple sequence alignment which has been evaluated by the Sum of Pairs Method (SPM) considering the real value data from PAM250. In our second GA approach, these two techniques are used to generate an initial population and also two different approaches of genetic operators are implemented in crossovers and mutation. To test the performance of our two algorithms, we have compared these with the existing well known methods: T-Coffee, MUSCEL, MAFFT and Probcon, using BAliBase benchmarks. The experimental results show that the first algorithm works well for some situations, where other existing methods face difficulties in obtaining better solutions. The proposed second method works well compared to the existing methods for all situations and it shows better performance over the first one.

  4. Identifying subset errors in multiple sequence alignments.

    PubMed

    Roy, Aparna; Taddese, Bruck; Vohra, Shabana; Thimmaraju, Phani K; Illingworth, Christopher J R; Simpson, Lisa M; Mukherjee, Keya; Reynolds, Christopher A; Chintapalli, Sree V

    2014-01-01

    Multiple sequence alignment (MSA) accuracy is important, but there is no widely accepted method of judging the accuracy that different alignment algorithms give. We present a simple approach to detecting two types of error, namely block shifts and the misplacement of residues within a gap. Given a MSA, subsets of very similar sequences are generated through the use of a redundancy filter, typically using a 70-90% sequence identity cut-off. Subsets thus produced are typically small and degenerate, and errors can be easily detected even by manual examination. The errors, albeit minor, are inevitably associated with gaps in the alignment, and so the procedure is particularly relevant to homology modelling of protein loop regions. The usefulness of the approach is illustrated in the context of the universal but little known [K/R]KLH motif that occurs in intracellular loop 1 of G protein coupled receptors (GPCR); other issues relevant to GPCR modelling are also discussed.

  5. Protein multiple sequence alignment by hybrid bio-inspired algorithms.

    PubMed

    Cutello, Vincenzo; Nicosia, Giuseppe; Pavone, Mario; Prizzi, Igor

    2011-03-01

    This article presents an immune inspired algorithm to tackle the Multiple Sequence Alignment (MSA) problem. MSA is one of the most important tasks in biological sequence analysis. Although this paper focuses on protein alignments, most of the discussion and methodology may also be applied to DNA alignments. The problem of finding the multiple alignment was investigated in the study by Bonizzoni and Vedova and Wang and Jiang, and proved to be a NP-hard (non-deterministic polynomial-time hard) problem. The presented algorithm, called Immunological Multiple Sequence Alignment Algorithm (IMSA), incorporates two new strategies to create the initial population and specific ad hoc mutation operators. It is based on the 'weighted sum of pairs' as objective function, to evaluate a given candidate alignment. IMSA was tested using both classical benchmarks of BAliBASE (versions 1.0, 2.0 and 3.0), and experimental results indicate that it is comparable with state-of-the-art multiple alignment algorithms, in terms of quality of alignments, weighted Sums-of-Pairs (SP) and Column Score (CS) values. The main novelty of IMSA is its ability to generate more than a single suboptimal alignment, for every MSA instance; this behaviour is due to the stochastic nature of the algorithm and of the populations evolved during the convergence process. This feature will help the decision maker to assess and select a biologically relevant multiple sequence alignment. Finally, the designed algorithm can be used as a local search procedure to properly explore promising alignments of the search space.

  6. Multiple sequence alignment with hierarchical clustering.

    PubMed Central

    Corpet, F

    1988-01-01

    An algorithm is presented for the multiple alignment of sequences, either proteins or nucleic acids, that is both accurate and easy to use on microcomputers. The approach is based on the conventional dynamic-programming method of pairwise alignment. Initially, a hierarchical clustering of the sequences is performed using the matrix of the pairwise alignment scores. The closest sequences are aligned creating groups of aligned sequences. Then close groups are aligned until all sequences are aligned in one group. The pairwise alignments included in the multiple alignment form a new matrix that is used to produce a hierarchical clustering. If it is different from the first one, iteration of the process can be performed. The method is illustrated by an example: a global alignment of 39 sequences of cytochrome c. PMID:2849754

  7. Progressive multiple sequence alignments from triplets

    PubMed Central

    Kruspe, Matthias; Stadler, Peter F

    2007-01-01

    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 (mis)match scores. PMID:17631683

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

    PubMed

    Zhang, Zefeng; Lin, Hao; Li, Ming

    2007-01-01

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

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

    PubMed

    Afridi, Muhammad Ishaq

    2013-01-01

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

  10. Genetic algorithms with permutation coding for multiple sequence alignment.

    PubMed

    Ben Othman, Mohamed Tahar; Abdel-Azim, Gamil

    2013-08-01

    Multiple sequence alignment (MSA) is one of the topics of bio informatics that has seriously been researched. It is known as NP-complete problem. It is also considered as one of the most important and daunting tasks in computational biology. Concerning this a wide number of heuristic algorithms have been proposed to find optimal alignment. Among these heuristic algorithms are genetic algorithms (GA). The GA has mainly two major weaknesses: it is time consuming and can cause local minima. One of the significant aspects in the GA process in MSA is to maximize the similarities between sequences by adding and shuffling the gaps of Solution Coding (SC). Several ways for SC have been introduced. One of them is the Permutation Coding (PC). We propose a hybrid algorithm based on genetic algorithms (GAs) with a PC and 2-opt algorithm. The PC helps to code the MSA solution which maximizes the gain of resources, reliability and diversity of GA. The use of the PC opens the area by applying all functions over permutations for MSA. Thus, we suggest an algorithm to calculate the scoring function for multiple alignments based on PC, which is used as fitness function. The time complexity of the GA is reduced by using this algorithm. Our GA is implemented with different selections strategies and different crossovers. The probability of crossover and mutation is set as one strategy. Relevant patents have been probed in the topic.

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

    PubMed

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

    2016-11-15

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

  12. Quantifying the Displacement of Mismatches in Multiple Sequence Alignment Benchmarks

    PubMed Central

    Bawono, Punto; van der Velde, Arjan; Abeln, Sanne; Heringa, Jaap

    2015-01-01

    Multiple Sequence Alignment (MSA) methods are typically benchmarked on sets of reference alignments. The quality of the alignment can then be represented by the sum-of-pairs (SP) or column (CS) scores, which measure the agreement between a reference and corresponding query alignment. Both the SP and CS scores treat mismatches between a query and reference alignment as equally bad, and do not take the separation into account between two amino acids in the query alignment, that should have been matched according to the reference alignment. This is significant since the magnitude of alignment shifts is often of relevance in biological analyses, including homology modeling and MSA refinement/manual alignment editing. In this study we develop a new alignment benchmark scoring scheme, SPdist, that takes the degree of discordance of mismatches into account by measuring the sequence distance between mismatched residue pairs in the query alignment. Using this new score along with the standard SP score, we investigate the discriminatory behavior of the new score by assessing how well six different MSA methods perform with respect to BAliBASE reference alignments. The SP score and the SPdist score yield very similar outcomes when the reference and query alignments are close. However, for more divergent reference alignments the SPdist score is able to distinguish between methods that keep alignments approximately close to the reference and those exhibiting larger shifts. We observed that by using SPdist together with SP scoring we were able to better delineate the alignment quality difference between alternative MSA methods. With a case study we exemplify why it is important, from a biological perspective, to consider the separation of mismatches. The SPdist scoring scheme has been implemented in the VerAlign web server (http://www.ibi.vu.nl/programs/veralignwww/). The code for calculating SPdist score is also available upon request. PMID:25993129

  13. A Convex Atomic-Norm Approach to Multiple Sequence Alignment and Motif Discovery

    PubMed Central

    Yen, Ian E. H.; Lin, Xin; Zhang, Jiong; Ravikumar, Pradeep; Dhillon, Inderjit S.

    2016-01-01

    Multiple Sequence Alignment and Motif Discovery, known as NP-hard problems, are two fundamental tasks in Bioinformatics. Existing approaches to these two problems are based on either local search methods such as Expectation Maximization (EM), Gibbs Sampling or greedy heuristic methods. In this work, we develop a convex relaxation approach to both problems based on the recent concept of atomic norm and develop a new algorithm, termed Greedy Direction Method of Multiplier, for solving the convex relaxation with two convex atomic constraints. Experiments show that our convex relaxation approach produces solutions of higher quality than those standard tools widely-used in Bioinformatics community on the Multiple Sequence Alignment and Motif Discovery problems. PMID:27559428

  14. An enhanced algorithm for multiple sequence alignment of protein sequences using genetic algorithm

    PubMed Central

    Kumar, Manish

    2015-01-01

    One of the most fundamental operations in biological sequence analysis is multiple sequence alignment (MSA). The basic of multiple sequence alignment problems is to determine the most biologically plausible alignments of protein or DNA sequences. In this paper, an alignment method using genetic algorithm for multiple sequence alignment has been proposed. Two different genetic operators mainly crossover and mutation were defined and implemented with the proposed method in order to know the population evolution and quality of the sequence aligned. The proposed method is assessed with protein benchmark dataset, e.g., BALIBASE, by comparing the obtained results to those obtained with other alignment algorithms, e.g., SAGA, RBT-GA, PRRP, HMMT, SB-PIMA, CLUSTALX, CLUSTAL W, DIALIGN and PILEUP8 etc. Experiments on a wide range of data have shown that the proposed algorithm is much better (it terms of score) than previously proposed algorithms in its ability to achieve high alignment quality. PMID:27065770

  15. Multiple sequence alignment with user-defined anchor points

    PubMed Central

    Morgenstern, Burkhard; Prohaska, Sonja J; Pöhler, Dirk; Stadler, Peter F

    2006-01-01

    Background Automated software tools for multiple alignment often fail to produce biologically meaningful results. In such situations, expert knowledge can help to improve the quality of alignments. Results Herein, we describe a semi-automatic version of the alignment program DIALIGN that can take pre-defined constraints into account. It is possible for the user to specify parts of the sequences that are assumed to be homologous and should therefore be aligned to each other. Our software program can use these sites as anchor points by creating a multiple alignment respecting these constraints. This way, our alignment method can produce alignments that are biologically more meaningful than alignments produced by fully automated procedures. As a demonstration of how our method works, we apply our approach to genomic sequences around the Hox gene cluster and to a set of DNA-binding proteins. As a by-product, we obtain insights about the performance of the greedy algorithm that our program uses for multiple alignment and about the underlying objective function. This information will be useful for the further development of DIALIGN. The described alignment approach has been integrated into the TRACKER software system. PMID:16722533

  16. MSA-PAD: DNA multiple sequence alignment framework based on PFAM accessed domain information.

    PubMed

    Balech, Bachir; Vicario, Saverio; Donvito, Giacinto; Monaco, Alfonso; Notarangelo, Pasquale; Pesole, Graziano

    2015-08-01

    Here we present the MSA-PAD application, a DNA multiple sequence alignment framework that uses PFAM protein domain information to align DNA sequences encoding either single or multiple protein domains. MSA-PAD has two alignment options: gene and genome mode.

  17. IP-MSA: Independent order of progressive multiple sequence alignments using different substitution matrices

    NASA Astrophysics Data System (ADS)

    Boraik, Aziz Nasser; Abdullah, Rosni; Venkat, Ibrahim

    2014-12-01

    Multiple sequence alignment (MSA) is an essential process for many biological sequence analyses. There are many algorithms developed to solve MSA, but an efficient computation method with very high accuracy is still a challenge. Progressive alignment is the most widely used approach to compute the final MSA. In this paper, we present a simple and effective progressive approach. Based on the independent order of sequences progressive alignment which proposed in QOMA, this method has been modified to align the whole sequences to maximize the score of MSA. Moreover, in order to further improve the accuracy of the method, we estimate the similarity of any pair of input sequences by using their percent identity, and based on this measure, we choose different substitution matrices during the progressive alignment. In addition, we have included horizontal information to alignment by adjusting the weights of amino acid residues based on their neighboring residues. The experimental results have been tested on popular benchmark of global protein sequences BAliBASE 3.0 and local protein sequences IRMBASE 2.0. The results of the proposed approach outperform the original method in QOMA in terms of sum-of-pair score and column score by up to 14% and 7% respectively.

  18. Multiple sequence alignment in HTML: colored, possibly hyperlinked, compact representations.

    PubMed

    Campagne, F; Maigret, B

    1998-02-01

    Protein sequence alignments are widely used in protein structure prediction, protein engineering, modeling of proteins, etc. This type of representation is useful at different stages of scientific activity: looking at previous results, working on a research project, and presenting the results. There is a need to make it available through a network (intranet or WWW), in a way that allows biologists, chemists, and noncomputer specialists to look at the data and carry on research--possibly in a collaborative research. Previous methods (text-based, Java-based) are reported and their advantages are discussed. We have developed two novel approaches to represent the alignments as colored, hyper-linked HTML pages. The first method creates an HTML page that uses efficiently the image cache mechanism of a WWW browser, thereby allowing the user to browse different alignments without waiting for the images to be loaded through the network, but only for the first viewed alignment. The generated pages can be browsed with any HTML2.0-compliant browser. The second method that we propose uses W3C-CSS1-style sheets to render alignments. This new method generates pages that require recent browsers to be viewed. We implemented these methods in the Viseur program and made a WWW service available that allows a user to convert an MSF alignment file in HTML for WWW publishing. The latter service is available at http:@www.lctn.u-nancy.fr/viseur/services.htm l.

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

    PubMed

    Sudha Sadasivam, G; Baktavatchalam, G

    2010-01-01

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

  20. The impact of single substitutions on multiple sequence alignments.

    PubMed

    Klaere, Steffen; Gesell, Tanja; von Haeseler, Arndt

    2008-12-27

    We introduce another view of sequence evolution. Contrary to other approaches, we model the substitution process in two steps. First we assume (arbitrary) scaled branch lengths on a given phylogenetic tree. Second we allocate a Poisson distributed number of substitutions on the branches. The probability to place a mutation on a branch is proportional to its relative branch length. More importantly, the action of a single mutation on an alignment column is described by a doubly stochastic matrix, the so-called one-step mutation matrix. This matrix leads to analytical formulae for the posterior probability distribution of the number of substitutions for an alignment column.

  1. A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives

    PubMed Central

    Thompson, Julie D.; Linard, Benjamin; Lecompte, Odile; Poch, Olivier

    2011-01-01

    Multiple comparison or alignmentof protein sequences has become a fundamental tool in many different domains in modern molecular biology, from evolutionary studies to prediction of 2D/3D structure, molecular function and inter-molecular interactions etc. By placing the sequence in the framework of the overall family, multiple alignments can be used to identify conserved features and to highlight differences or specificities. In this paper, we describe a comprehensive evaluation of many of the most popular methods for multiple sequence alignment (MSA), based on a new benchmark test set. The benchmark is designed to represent typical problems encountered when aligning the large protein sequence sets that result from today's high throughput biotechnologies. We show that alignmentmethods have significantly progressed and can now identify most of the shared sequence features that determine the broad molecular function(s) of a protein family, even for divergent sequences. However,we have identified a number of important challenges. First, the locally conserved regions, that reflect functional specificities or that modulate a protein's function in a given cellular context,are less well aligned. Second, motifs in natively disordered regions are often misaligned. Third, the badly predicted or fragmentary protein sequences, which make up a large proportion of today's databases, lead to a significant number of alignment errors. Based on this study, we demonstrate that the existing MSA methods can be exploited in combination to improve alignment accuracy, although novel approaches will still be needed to fully explore the most difficult regions. We then propose knowledge-enabled, dynamic solutions that will hopefully pave the way to enhanced alignment construction and exploitation in future evolutionary systems biology studies. PMID:21483869

  2. PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences.

    PubMed

    Mirarab, Siavash; Nguyen, Nam; Guo, Sheng; Wang, Li-San; Kim, Junhyong; Warnow, Tandy

    2015-05-01

    We introduce PASTA, a new multiple sequence alignment algorithm. PASTA uses a new technique to produce an alignment given a guide tree that enables it to be both highly scalable and very accurate. We present a study on biological and simulated data with up to 200,000 sequences, showing that PASTA produces highly accurate alignments, improving on the accuracy and scalability of the leading alignment methods (including SATé). We also show that trees estimated on PASTA alignments are highly accurate--slightly better than SATé trees, but with substantial improvements relative to other methods. Finally, PASTA is faster than SATé, highly parallelizable, and requires relatively little memory.

  3. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

    PubMed Central

    Sievers, Fabian; Wilm, Andreas; Dineen, David; Gibson, Toby J; Karplus, Kevin; Li, Weizhong; Lopez, Rodrigo; McWilliam, Hamish; Remmert, Michael; Söding, Johannes; Thompson, Julie D; Higgins, Desmond G

    2011-01-01

    Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets of the size of many thousands of sequences. Some methods allow computation of larger data sets while sacrificing quality, and others produce high-quality alignments, but scale badly with the number of sequences. In this paper, we describe a new program called Clustal Omega, which can align virtually any number of protein sequences quickly and that delivers accurate alignments. The accuracy of the package on smaller test cases is similar to that of the high-quality aligners. On larger data sets, Clustal Omega outperforms other packages in terms of execution time and quality. Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam. PMID:21988835

  4. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.

    PubMed

    Sievers, Fabian; Wilm, Andreas; Dineen, David; Gibson, Toby J; Karplus, Kevin; Li, Weizhong; Lopez, Rodrigo; McWilliam, Hamish; Remmert, Michael; Söding, Johannes; Thompson, Julie D; Higgins, Desmond G

    2011-10-11

    Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets of the size of many thousands of sequences. Some methods allow computation of larger data sets while sacrificing quality, and others produce high-quality alignments, but scale badly with the number of sequences. In this paper, we describe a new program called Clustal Omega, which can align virtually any number of protein sequences quickly and that delivers accurate alignments. The accuracy of the package on smaller test cases is similar to that of the high-quality aligners. On larger data sets, Clustal Omega outperforms other packages in terms of execution time and quality. Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam.

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

    PubMed

    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.

  6. Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments

    PubMed Central

    Jabado, Omar J.; Palacios, Gustavo; Kapoor, Vishal; Hui, Jeffrey; Renwick, Neil; Zhai, Junhui; Briese, Thomas; Lipkin, W. Ian

    2006-01-01

    Polymerase chain reaction (PCR) is widely applied in clinical and environmental microbiology. Primer design is key to the development of successful assays and is often performed manually by using multiple nucleic acid alignments. Few public software tools exist that allow comprehensive design of degenerate primers for large groups of related targets based on complex multiple sequence alignments. Here we present a method for designing such primers based on tree building followed by application of a set covering algorithm, and demonstrate its utility in compiling Multiplex PCR primer panels for detection and differentiation of viral pathogens. PMID:17135211

  7. AlexSys: a knowledge-based expert system for multiple sequence alignment construction and analysis.

    PubMed

    Aniba, Mohamed Radhouene; Poch, Olivier; Marchler-Bauer, Aron; Thompson, Julie Dawn

    2010-10-01

    Multiple sequence alignment (MSA) is a cornerstone of modern molecular biology and represents a unique means of investigating the patterns of conservation and diversity in complex biological systems. Many different algorithms have been developed to construct MSAs, but previous studies have shown that no single aligner consistently outperforms the rest. This has led to the development of a number of 'meta-methods' that systematically run several aligners and merge the output into one single solution. Although these methods generally produce more accurate alignments, they are inefficient because all the aligners need to be run first and the choice of the best solution is made a posteriori. Here, we describe the development of a new expert system, AlexSys, for the multiple alignment of protein sequences. AlexSys incorporates an intelligent inference engine to automatically select an appropriate aligner a priori, depending only on the nature of the input sequences. The inference engine was trained on a large set of reference multiple alignments, using a novel machine learning approach. Applying AlexSys to a test set of 178 alignments, we show that the expert system represents a good compromise between alignment quality and running time, making it suitable for high throughput projects. AlexSys is freely available from http://alnitak.u-strasbg.fr/∼aniba/alexsys.

  8. Multiple sequence alignment with arbitrary gap costs: computing an optimal solution using polyhedral combinatorics.

    PubMed

    Althaus, Ernst; Caprara, Alberto; Lenhof, Hans-Peter; Reinert, Knut

    2002-01-01

    Multiple sequence alignment is one of the dominant problems in computational molecular biology. Numerous scoring functions and methods have been proposed, most of which result in NP-hard problems. In this paper we propose for the first time a general formulation for multiple alignment with arbitrary gap-costs based on an integer linear program (ILP). In addition we describe a branch-and-cut algorithm to effectively solve the ILP to optimality. We evaluate the performances of our approach in terms of running time and quality of the alignments using the BAliBase database of reference alignments. The results show that our implementation ranks amongst the best programs developed so far.

  9. R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server

    PubMed Central

    Cannone, Jamie J.; Sweeney, Blake A.; Petrov, Anton I.; Gutell, Robin R.; Zirbel, Craig L.; Leontis, Neocles

    2015-01-01

    The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3D structures. A web-based front end is available for manual entry and an Application Program Interface for programmatic access. Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at http://rna.bgsu.edu/r3d-2-msa. PMID:26048960

  10. R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.

    PubMed

    Cannone, Jamie J; Sweeney, Blake A; Petrov, Anton I; Gutell, Robin R; Zirbel, Craig L; Leontis, Neocles

    2015-07-01

    The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3D structures. A web-based front end is available for manual entry and an Application Program Interface for programmatic access. Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at http://rna.bgsu.edu/r3d-2-msa.

  11. Open-Phylo: a customizable crowd-computing platform for multiple sequence alignment

    PubMed Central

    2013-01-01

    Citizen science games such as Galaxy Zoo, Foldit, and Phylo aim to harness the intelligence and processing power generated by crowds of online gamers to solve scientific problems. However, the selection of the data to be analyzed through these games is under the exclusive control of the game designers, and so are the results produced by gamers. Here, we introduce Open-Phylo, a freely accessible crowd-computing platform that enables any scientist to enter our system and use crowds of gamers to assist computer programs in solving one of the most fundamental problems in genomics: the multiple sequence alignment problem. PMID:24148814

  12. Open-Phylo: a customizable crowd-computing platform for multiple sequence alignment.

    PubMed

    Kwak, Daniel; Kam, Alfred; Becerra, David; Zhou, Qikuan; Hops, Adam; Zarour, Eleyine; Kam, Arthur; Sarmenta, Luis; Blanchette, Mathieu; Waldispühl, Jérôme

    2013-01-01

    Citizen science games such as Galaxy Zoo, Foldit, and Phylo aim to harness the intelligence and processing power generated by crowds of online gamers to solve scientific problems. However, the selection of the data to be analyzed through these games is under the exclusive control of the game designers, and so are the results produced by gamers. Here, we introduce Open-Phylo, a freely accessible crowd-computing platform that enables any scientist to enter our system and use crowds of gamers to assist computer programs in solving one of the most fundamental problems in genomics: the multiple sequence alignment problem.

  13. SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction.

    PubMed

    Hagopian, Raffi; Davidson, John R; Datta, Ruchira S; Samad, Bushra; Jarvis, Glen R; Sjölander, Kimmen

    2010-07-01

    We present the jump-start simultaneous alignment and tree construction using hidden Markov models (SATCHMO-JS) web server for simultaneous estimation of protein multiple sequence alignments (MSAs) and phylogenetic trees. The server takes as input a set of sequences in FASTA format, and outputs a phylogenetic tree and MSA; these can be viewed online or downloaded from the website. SATCHMO-JS is an extension of the SATCHMO algorithm, and employs a divide-and-conquer strategy to jump-start SATCHMO at a higher point in the phylogenetic tree, reducing the computational complexity of the progressive all-versus-all HMM-HMM scoring and alignment. Results on a benchmark dataset of 983 structurally aligned pairs from the PREFAB benchmark dataset show that SATCHMO-JS provides a statistically significant improvement in alignment accuracy over MUSCLE, Multiple Alignment using Fast Fourier Transform (MAFFT), ClustalW and the original SATCHMO algorithm. The SATCHMO-JS webserver is available at http://phylogenomics.berkeley.edu/satchmo-js. The datasets used in these experiments are available for download at http://phylogenomics.berkeley.edu/satchmo-js/supplementary/.

  14. MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems.

    PubMed

    González-Domínguez, Jorge; Liu, Yongchao; Touriño, Juan; Schmidt, Bertil

    2016-12-15

    MSAProbs is a state-of-the-art protein multiple sequence alignment tool based on hidden Markov models. It can achieve high alignment accuracy at the expense of relatively long runtimes for large-scale input datasets. In this work we present MSAProbs-MPI, a distributed-memory parallel version of the multithreaded MSAProbs tool that is able to reduce runtimes by exploiting the compute capabilities of common multicore CPU clusters. Our performance evaluation on a cluster with 32 nodes (each containing two Intel Haswell processors) shows reductions in execution time of over one order of magnitude for typical input datasets. Furthermore, MSAProbs-MPI using eight nodes is faster than the GPU-accelerated QuickProbs running on a Tesla K20. Another strong point is that MSAProbs-MPI can deal with large datasets for which MSAProbs and QuickProbs might fail due to time and memory constraints, respectively.

  15. EvalMSA: A Program to Evaluate Multiple Sequence Alignments and Detect Outliers.

    PubMed

    Chiner-Oms, Alvaro; González-Candelas, Fernando

    2016-01-01

    We present EvalMSA, a software tool for evaluating and detecting outliers in multiple sequence alignments (MSAs). This tool allows the identification of divergent sequences in MSAs by scoring the contribution of each row in the alignment to its quality using a sum-of-pair-based method and additional analyses. Our main goal is to provide users with objective data in order to take informed decisions about the relevance and/or pertinence of including/retaining a particular sequence in an MSA. EvalMSA is written in standard Perl and also uses some routines from the statistical language R. Therefore, it is necessary to install the R-base package in order to get full functionality. Binary packages are freely available from http://sourceforge.net/projects/evalmsa/for Linux and Windows.

  16. EvalMSA: A Program to Evaluate Multiple Sequence Alignments and Detect Outliers

    PubMed Central

    Chiner-Oms, Alvaro; González-Candelas, Fernando

    2016-01-01

    We present EvalMSA, a software tool for evaluating and detecting outliers in multiple sequence alignments (MSAs). This tool allows the identification of divergent sequences in MSAs by scoring the contribution of each row in the alignment to its quality using a sum-of-pair-based method and additional analyses. Our main goal is to provide users with objective data in order to take informed decisions about the relevance and/or pertinence of including/retaining a particular sequence in an MSA. EvalMSA is written in standard Perl and also uses some routines from the statistical language R. Therefore, it is necessary to install the R-base package in order to get full functionality. Binary packages are freely available from http://sourceforge.net/projects/evalmsa/for Linux and Windows. PMID:27920488

  17. A probabilistic coding based quantum genetic algorithm for multiple sequence alignment.

    PubMed

    Huo, Hongwei; Xie, Qiaoluan; Shen, Xubang; Stojkovic, Vojislav

    2008-01-01

    This paper presents an original Quantum Genetic algorithm for Multiple sequence ALIGNment (QGMALIGN) that combines a genetic algorithm and a quantum algorithm. A quantum probabilistic coding is designed for representing the multiple sequence alignment. A quantum rotation gate as a mutation operator is used to guide the quantum state evolution. Six genetic operators are designed on the coding basis to improve the solution during the evolutionary process. The features of implicit parallelism and state superposition in quantum mechanics and the global search capability of the genetic algorithm are exploited to get efficient computation. A set of well known test cases from BAliBASE2.0 is used as reference to evaluate the efficiency of the QGMALIGN optimization. The QGMALIGN results have been compared with the most popular methods (CLUSTALX, SAGA, DIALIGN, SB_PIMA, and QGMALIGN) results. The QGMALIGN results show that QGMALIGN performs well on the presenting biological data. The addition of genetic operators to the quantum algorithm lowers the cost of overall running time.

  18. A parallel approach of COFFEE objective function to multiple sequence alignment

    NASA Astrophysics Data System (ADS)

    Zafalon, G. F. D.; Visotaky, J. M. V.; Amorim, A. R.; Valêncio, C. R.; Neves, L. A.; de Souza, R. C. G.; Machado, J. M.

    2015-09-01

    The computational tools to assist genomic analyzes show even more necessary due to fast increasing of data amount available. With high computational costs of deterministic algorithms for sequence alignments, many works concentrate their efforts in the development of heuristic approaches to multiple sequence alignments. However, the selection of an approach, which offers solutions with good biological significance and feasible execution time, is a great challenge. Thus, this work aims to show the parallelization of the processing steps of MSA-GA tool using multithread paradigm in the execution of COFFEE objective function. The standard objective function implemented in the tool is the Weighted Sum of Pairs (WSP), which produces some distortions in the final alignments when sequences sets with low similarity are aligned. Then, in studies previously performed we implemented the COFFEE objective function in the tool to smooth these distortions. Although the nature of COFFEE objective function implies in the increasing of execution time, this approach presents points, which can be executed in parallel. With the improvements implemented in this work, we can verify the execution time of new approach is 24% faster than the sequential approach with COFFEE. Moreover, the COFFEE multithreaded approach is more efficient than WSP, because besides it is slightly fast, its biological results are better.

  19. Multiple sequence alignment using multi-objective based bacterial foraging optimization algorithm.

    PubMed

    Rani, R Ranjani; Ramyachitra, D

    2016-12-01

    Multiple sequence alignment (MSA) is a widespread approach in computational biology and bioinformatics. MSA deals with how the sequences of nucleotides and amino acids are sequenced with possible alignment and minimum number of gaps between them, which directs to the functional, evolutionary and structural relationships among the sequences. Still the computation of MSA is a challenging task to provide an efficient accuracy and statistically significant results of alignments. In this work, the Bacterial Foraging Optimization Algorithm was employed to align the biological sequences which resulted in a non-dominated optimal solution. It employs Multi-objective, such as: Maximization of Similarity, Non-gap percentage, Conserved blocks and Minimization of gap penalty. BAliBASE 3.0 benchmark database was utilized to examine the proposed algorithm against other methods In this paper, two algorithms have been proposed: Hybrid Genetic Algorithm with Artificial Bee Colony (GA-ABC) and Bacterial Foraging Optimization Algorithm. It was found that Hybrid Genetic Algorithm with Artificial Bee Colony performed better than the existing optimization algorithms. But still the conserved blocks were not obtained using GA-ABC. Then BFO was used for the alignment and the conserved blocks were obtained. The proposed Multi-Objective Bacterial Foraging Optimization Algorithm (MO-BFO) was compared with widely used MSA methods Clustal Omega, Kalign, MUSCLE, MAFFT, Genetic Algorithm (GA), Ant Colony Optimization (ACO), Artificial Bee Colony (ABC), Particle Swarm Optimization (PSO) and Hybrid Genetic Algorithm with Artificial Bee Colony (GA-ABC). The final results show that the proposed MO-BFO algorithm yields better alignment than most widely used methods.

  20. IBBOMSA: An Improved Biogeography-based Approach for Multiple Sequence Alignment

    PubMed Central

    Yadav, Rohit Kumar; Banka, Haider

    2016-01-01

    In bioinformatics, multiple sequence alignment (MSA) is an NP-hard problem. Hence, nature-inspired techniques can better approximate the solution. In the current study, a novel biogeography-based optimization (NBBO) is proposed to solve an MSA problem. The biogeography-based optimization (BBO) is a new paradigm for optimization. But, there exists some deficiencies in solving complicated problems such as low population diversity and slow convergence rate. NBBO is an enhanced version of BBO, in which, a new migration operation is proposed to overcome the limitations of BBO. The new migration adopts more information from other habitats, maintains population diversity, and preserves exploitation ability. In the performance analysis, the proposed and existing techniques such as VDGA, MOMSA, and GAPAM are tested on publicly available benchmark datasets (ie, Bali base). It has been observed that the proposed method shows the superiority/competitiveness with the existing techniques. PMID:27812276

  1. A unified statistical model of protein multiple sequence alignment integrating direct coupling and insertions

    PubMed Central

    Kinjo, Akira R.

    2016-01-01

    The multiple sequence alignment (MSA) of a protein family provides a wealth of information in terms of the conservation pattern of amino acid residues not only at each alignment site but also between distant sites. In order to statistically model the MSA incorporating both short-range and long-range correlations as well as insertions, I have derived a lattice gas model of the MSA based on the principle of maximum entropy. The partition function, obtained by the transfer matrix method with a mean-field approximation, accounts for all possible alignments with all possible sequences. The model parameters for short-range and long-range interactions were determined by a self-consistent condition and by a Gaussian approximation, respectively. Using this model with and without long-range interactions, I analyzed the globin and V-set domains by increasing the “temperature” and by “mutating” a site. The correlations between residue conservation and various measures of the system’s stability indicate that the long-range interactions make the conservation pattern more specific to the structure, and increasingly stabilize better conserved residues. PMID:27924257

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

    PubMed

    Martin, Andrew C R

    2014-01-01

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

  3. QuickProbs--a fast multiple sequence alignment algorithm designed for graphics processors.

    PubMed

    Gudyś, Adam; Deorowicz, Sebastian

    2014-01-01

    Multiple sequence alignment is a crucial task in a number of biological analyses like secondary structure prediction, domain searching, phylogeny, etc. MSAProbs is currently the most accurate alignment algorithm, but its effectiveness is obtained at the expense of computational time. In the paper we present QuickProbs, the variant of MSAProbs customised for graphics processors. We selected the two most time consuming stages of MSAProbs to be redesigned for GPU execution: the posterior matrices calculation and the consistency transformation. Experiments on three popular benchmarks (BAliBASE, PREFAB, OXBench-X) on quad-core PC equipped with high-end graphics card show QuickProbs to be 5.7 to 9.7 times faster than original CPU-parallel MSAProbs. Additional tests performed on several protein families from Pfam database give overall speed-up of 6.7. Compared to other algorithms like MAFFT, MUSCLE, or ClustalW, QuickProbs proved to be much more accurate at similar speed. Additionally we introduce a tuned variant of QuickProbs which is significantly more accurate on sets of distantly related sequences than MSAProbs without exceeding its computation time. The GPU part of QuickProbs was implemented in OpenCL, thus the package is suitable for graphics processors produced by all major vendors.

  4. ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments.

    PubMed

    Schwarz, Roland F; Tamuri, Asif U; Kultys, Marek; King, James; Godwin, James; Florescu, Ana M; Schultz, Jörg; Goldman, Nick

    2016-05-05

    Sequence Logos and its variants are the most commonly used method for visualization of multiple sequence alignments (MSAs) and sequence motifs. They provide consensus-based summaries of the sequences in the alignment. Consequently, individual sequences cannot be identified in the visualization and covariant sites are not easily discernible. We recently proposed Sequence Bundles, a motif visualization technique that maintains a one-to-one relationship between sequences and their graphical representation and visualizes covariant sites. We here present Alvis, an open-source platform for the joint explorative analysis of MSAs and phylogenetic trees, employing Sequence Bundles as its main visualization method. Alvis combines the power of the visualization method with an interactive toolkit allowing detection of covariant sites, annotation of trees with synapomorphies and homoplasies, and motif detection. It also offers numerical analysis functionality, such as dimension reduction and classification. Alvis is user-friendly, highly customizable and can export results in publication-quality figures. It is available as a full-featured standalone version (http://www.bitbucket.org/rfs/alvis) and its Sequence Bundles visualization module is further available as a web application (http://science-practice.com/projects/sequence-bundles).

  5. RBT-GA: a novel metaheuristic for solving the multiple sequence alignment problem

    PubMed Central

    Taheri, Javid; Zomaya, Albert Y

    2009-01-01

    Background Multiple Sequence Alignment (MSA) has always been an active area of research in Bioinformatics. MSA is mainly focused on discovering biologically meaningful relationships among different sequences or proteins in order to investigate the underlying main characteristics/functions. This information is also used to generate phylogenetic trees. Results This paper presents a novel approach, namely RBT-GA, to solve the MSA problem using a hybrid solution methodology combining the Rubber Band Technique (RBT) and the Genetic Algorithm (GA) metaheuristic. RBT is inspired by the behavior of an elastic Rubber Band (RB) on a plate with several poles, which is analogues to locations in the input sequences that could potentially be biologically related. A GA attempts to mimic the evolutionary processes of life in order to locate optimal solutions in an often very complex landscape. RBT-GA is a population based optimization algorithm designed to find the optimal alignment for a set of input protein sequences. In this novel technique, each alignment answer is modeled as a chromosome consisting of several poles in the RBT framework. These poles resemble locations in the input sequences that are most likely to be correlated and/or biologically related. A GA-based optimization process improves these chromosomes gradually yielding a set of mostly optimal answers for the MSA problem. Conclusion RBT-GA is tested with one of the well-known benchmarks suites (BALiBASE 2.0) in this area. The obtained results show that the superiority of the proposed technique even in the case of formidable sequences. PMID:19594869

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

    PubMed Central

    2010-01-01

    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 to reliably detect

  7. A quantum-inspired genetic algorithm based on probabilistic coding for multiple sequence alignment.

    PubMed

    Huo, Hong-Wei; Stojkovic, Vojislav; Xie, Qiao-Luan

    2010-02-01

    Quantum parallelism arises from the ability of a quantum memory register to exist in a superposition of base states. Since the number of possible base states is 2(n), where n is the number of qubits in the quantum memory register, one operation on a quantum computer performs what an exponential number of operations on a classical computer performs. The power of quantum algorithms comes from taking advantages of quantum parallelism. Quantum algorithms are exponentially faster than classical algorithms. Genetic optimization algorithms are stochastic search algorithms which are used to search large, nonlinear spaces where expert knowledge is lacking or difficult to encode. QGMALIGN--a probabilistic coding based quantum-inspired genetic algorithm for multiple sequence alignment is presented. A quantum rotation gate as a mutation operator is used to guide the quantum state evolution. Six genetic operators are designed on the coding basis to improve the solution during the evolutionary process. The experimental results show that QGMALIGN can compete with the popular methods, such as CLUSTALX and SAGA, and performs well on the presenting biological data. Moreover, the addition of genetic operators to the quantum-inspired algorithm lowers the cost of overall running time.

  8. CUDA ClustalW: An efficient parallel algorithm for progressive multiple sequence alignment on Multi-GPUs.

    PubMed

    Hung, Che-Lun; Lin, Yu-Shiang; Lin, Chun-Yuan; Chung, Yeh-Ching; Chung, Yi-Fang

    2015-10-01

    For biological applications, sequence alignment is an important strategy to analyze DNA and protein sequences. Multiple sequence alignment is an essential methodology to study biological data, such as homology modeling, phylogenetic reconstruction and etc. However, multiple sequence alignment is a NP-hard problem. In the past decades, progressive approach has been proposed to successfully align multiple sequences by adopting iterative pairwise alignments. Due to rapid growth of the next generation sequencing technologies, a large number of sequences can be produced in a short period of time. When the problem instance is large, progressive alignment will be time consuming. Parallel computing is a suitable solution for such applications, and GPU is one of the important architectures for contemporary parallel computing researches. Therefore, we proposed a GPU version of ClustalW v2.0.11, called CUDA ClustalW v1.0, in this work. From the experiment results, it can be seen that the CUDA ClustalW v1.0 can achieve more than 33× speedups for overall execution time by comparing to ClustalW v2.0.11.

  9. Computational approaches for protein function prediction: a combined strategy from multiple sequence alignment to molecular docking-based virtual screening.

    PubMed

    Pierri, Ciro Leonardo; Parisi, Giovanni; Porcelli, Vito

    2010-09-01

    The functional characterization of proteins represents a daily challenge for biochemical, medical and computational sciences. Although finally proved on the bench, the function of a protein can be successfully predicted by computational approaches that drive the further experimental assays. Current methods for comparative modeling allow the construction of accurate 3D models for proteins of unknown structure, provided that a crystal structure of a homologous protein is available. Binding regions can be proposed by using binding site predictors, data inferred from homologous crystal structures, and data provided from a careful interpretation of the multiple sequence alignment of the investigated protein and its homologs. Once the location of a binding site has been proposed, chemical ligands that have a high likelihood of binding can be identified by using ligand docking and structure-based virtual screening of chemical libraries. Most docking algorithms allow building a list sorted by energy of the lowest energy docking configuration for each ligand of the library. In this review the state-of-the-art of computational approaches in 3D protein comparative modeling and in the study of protein-ligand interactions is provided. Furthermore a possible combined/concerted multistep strategy for protein function prediction, based on multiple sequence alignment, comparative modeling, binding region prediction, and structure-based virtual screening of chemical libraries, is described by using suitable examples. As practical examples, Abl-kinase molecular modeling studies, HPV-E6 protein multiple sequence alignment analysis, and some other model docking-based characterization reports are briefly described to highlight the importance of computational approaches in protein function prediction.

  10. New Challenges of the Computation of Multiple Sequence Alignments in the High-Throughput Era (2010 JGI/ANL HPC Workshop)

    ScienceCinema

    Notredame, Cedric [Centre for Genomic Regulation

    2016-07-12

    Cedric Notredame from the Centre for Genomic Regulation gives a presentation on "New Challenges of the Computation of Multiple Sequence Alignments in the High-Throughput Era" at the JGI/Argonne HPC Workshop on January 26, 2010.

  11. Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search

    NASA Technical Reports Server (NTRS)

    Wheeler, Ward C.

    2003-01-01

    A method to align sequence data based on parsimonious synapomorphy schemes generated by direct optimization (DO; earlier termed optimization alignment) is proposed. DO directly diagnoses sequence data on cladograms without an intervening multiple-alignment step, thereby creating topology-specific, dynamic homology statements. Hence, no multiple-alignment is required to generate cladograms. Unlike general and globally optimal multiple-alignment procedures, the method described here, implied alignment (IA), takes these dynamic homologies and traces them back through a single cladogram, linking the unaligned sequence positions in the terminal taxa via DO transformation series. These "lines of correspondence" link ancestor-descendent states and, when displayed as linearly arrayed columns without hypothetical ancestors, are largely indistinguishable from standard multiple alignment. Since this method is based on synapomorphy, the treatment of certain classes of insertion-deletion (indel) events may be different from that of other alignment procedures. As with all alignment methods, results are dependent on parameter assumptions such as indel cost and transversion:transition ratios. Such an IA could be used as a basis for phylogenetic search, but this would be questionable since the homologies derived from the implied alignment depend on its natal cladogram and any variance, between DO and IA + Search, due to heuristic approach. The utility of this procedure in heuristic cladogram searches using DO and the improvement of heuristic cladogram cost calculations are discussed. c2003 The Willi Hennig Society. Published by Elsevier Science (USA). All rights reserved.

  12. Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search.

    PubMed

    Wheeler, Ward C

    2003-06-01

    A method to align sequence data based on parsimonious synapomorphy schemes generated by direct optimization (DO; earlier termed optimization alignment) is proposed. DO directly diagnoses sequence data on cladograms without an intervening multiple-alignment step, thereby creating topology-specific, dynamic homology statements. Hence, no multiple-alignment is required to generate cladograms. Unlike general and globally optimal multiple-alignment procedures, the method described here, implied alignment (IA), takes these dynamic homologies and traces them back through a single cladogram, linking the unaligned sequence positions in the terminal taxa via DO transformation series. These "lines of correspondence" link ancestor-descendent states and, when displayed as linearly arrayed columns without hypothetical ancestors, are largely indistinguishable from standard multiple alignment. Since this method is based on synapomorphy, the treatment of certain classes of insertion-deletion (indel) events may be different from that of other alignment procedures. As with all alignment methods, results are dependent on parameter assumptions such as indel cost and transversion:transition ratios. Such an IA could be used as a basis for phylogenetic search, but this would be questionable since the homologies derived from the implied alignment depend on its natal cladogram and any variance, between DO and IA + Search, due to heuristic approach. The utility of this procedure in heuristic cladogram searches using DO and the improvement of heuristic cladogram cost calculations are discussed.

  13. PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL

    PubMed Central

    2012-01-01

    Background In recent years, an exponential growing number of tools for protein sequence analysis, editing and modeling tasks have been put at the disposal of the scientific community. Despite the vast majority of these tools have been released as open source software, their deep learning curves often discourages even the most experienced users. Results A simple and intuitive interface, PyMod, between the popular molecular graphics system PyMOL and several other tools (i.e., [PSI-]BLAST, ClustalW, MUSCLE, CEalign and MODELLER) has been developed, to show how the integration of the individual steps required for homology modeling and sequence/structure analysis within the PyMOL framework can hugely simplify these tasks. Sequence similarity searches, multiple sequence and structural alignments generation and editing, and even the possibility to merge sequence and structure alignments have been implemented in PyMod, with the aim of creating a simple, yet powerful tool for sequence and structure analysis and building of homology models. Conclusions PyMod represents a new tool for the analysis and the manipulation of protein sequences and structures. The ease of use, integration with many sequence retrieving and alignment tools and PyMOL, one of the most used molecular visualization system, are the key features of this tool. Source code, installation instructions, video tutorials and a user's guide are freely available at the URL http://schubert.bio.uniroma1.it/pymod/index.html PMID:22536966

  14. PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases

    PubMed Central

    Floden, Evan W.; Tommaso, Paolo D.; Chatzou, Maria; Magis, Cedrik; Notredame, Cedric; Chang, Jia-Ming

    2016-01-01

    The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main novelty of this server is to allow databases of reduced complexity to rapidly perform homology extension. This server also gives the possibility to use transmembrane proteins (TMPs) reference databases to allow even faster homology extension on this important category of proteins. Aside from an MSA, the server also outputs topological prediction of TMPs using the HMMTOP algorithm. Previous benchmarking of the method has shown this approach outperforms the most accurate alignment methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™. The web server is available at http://tcoffee.crg.cat/tmcoffee. PMID:27106060

  15. Liquid-theory analogy of direct-coupling analysis of multiple-sequence alignment and its implications for protein structure prediction

    PubMed Central

    Kinjo, Akira R.

    2015-01-01

    The direct-coupling analysis is a powerful method for protein contact prediction, and enables us to extract “direct” correlations between distant sites that are latent in “indirect” correlations observed in a protein multiple-sequence alignment. I show that the direct correlation can be obtained by using a formulation analogous to the Ornstein-Zernike integral equation in liquid theory. This formulation intuitively illustrates how the indirect or apparent correlation arises from an infinite series of direct correlations, and provides interesting insights into protein structure prediction. PMID:27493860

  16. ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family

    PubMed Central

    Roca, Alberto I; Almada, Albert E; Abajian, Aaron C

    2008-01-01

    Background Multiple sequence alignments are a fundamental tool for the comparative analysis of proteins and nucleic acids. However, large data sets are no longer manageable for visualization and investigation using the traditional stacked sequence alignment representation. Results We introduce ProfileGrids that represent a multiple sequence alignment as a matrix color-coded according to the residue frequency occurring at each column position. JProfileGrid is a Java application for computing and analyzing ProfileGrids. A dynamic interaction with the alignment information is achieved by changing the ProfileGrid color scheme, by extracting sequence subsets at selected residues of interest, and by relating alignment information to residue physical properties. Conserved family motifs can be identified by the overlay of similarity plot calculations on a ProfileGrid. Figures suitable for publication can be generated from the saved spreadsheet output of the colored matrices as well as by the export of conservation information for use in the PyMOL molecular visualization program. We demonstrate the utility of ProfileGrids on 300 bacterial homologs of the RecA family – a universally conserved protein involved in DNA recombination and repair. Careful attention was paid to curating the collected RecA sequences since ProfileGrids allow the easy identification of rare residues in an alignment. We relate the RecA alignment sequence conservation to the following three topics: the recently identified DNA binding residues, the unexplored MAW motif, and a unique Bacillus subtilis RecA homolog sequence feature. Conclusion ProfileGrids allow large protein families to be visualized more effectively than the traditional stacked sequence alignment form. This new graphical representation facilitates the determination of the sequence conservation at residue positions of interest, enables the examination of structural patterns by using residue physical properties, and permits the display

  17. Knowledge-based expert systems and a proof-of-concept case study for multiple sequence alignment construction and analysis.

    PubMed

    Aniba, Mohamed Radhouene; Siguenza, Sophie; Friedrich, Anne; Plewniak, Frédéric; Poch, Olivier; Marchler-Bauer, Aron; Thompson, Julie Dawn

    2009-01-01

    The traditional approach to bioinformatics analyses relies on independent task-specific services and applications, using different input and output formats, often idiosyncratic, and frequently not designed to inter-operate. In general, such analyses were performed by experts who manually verified the results obtained at each step in the process. Today, the amount of bioinformatics information continuously being produced means that handling the various applications used to study this information presents a major data management and analysis challenge to researchers. It is now impossible to manually analyse all this information and new approaches are needed that are capable of processing the large-scale heterogeneous data in order to extract the pertinent information. We review the recent use of integrated expert systems aimed at providing more efficient knowledge extraction for bioinformatics research. A general methodology for building knowledge-based expert systems is described, focusing on the unstructured information management architecture, UIMA, which provides facilities for both data and process management. A case study involving a multiple alignment expert system prototype called AlexSys is also presented.

  18. Inexact Local Alignment Search over Suffix Arrays.

    PubMed

    Ghodsi, Mohammadreza; Pop, Mihai

    2009-11-01

    We describe an algorithm for finding approximate seeds for DNA homology searches. In contrast to previous algorithms that use exact or spaced seeds, our approximate seeds may contain insertions and deletions. We present a generalized heuristic for finding such seeds efficiently and prove that the heuristic does not affect sensitivity. We show how to adapt this algorithm to work over the memory efficient suffix array with provably minimal overhead in running time.We demonstrate the effectiveness of our algorithm on two tasks: whole genome alignment of bacteria and alignment of the DNA sequences of 177 genes that are orthologous in human and mouse. We show our algorithm achieves better sensitivity and uses less memory than other commonly used local alignment tools.

  19. MC64-ClustalWP2: a highly-parallel hybrid strategy to align multiple sequences in many-core architectures.

    PubMed

    Díaz, David; Esteban, Francisco J; Hernández, Pilar; Caballero, Juan Antonio; Guevara, Antonio; Dorado, Gabriel; Gálvez, Sergio

    2014-01-01

    We have developed the MC64-ClustalWP2 as a new implementation of the Clustal W algorithm, integrating a novel parallelization strategy and significantly increasing the performance when aligning long sequences in architectures with many cores. It must be stressed that in such a process, the detailed analysis of both the software and hardware features and peculiarities is of paramount importance to reveal key points to exploit and optimize the full potential of parallelism in many-core CPU systems. The new parallelization approach has focused into the most time-consuming stages of this algorithm. In particular, the so-called progressive alignment has drastically improved the performance, due to a fine-grained approach where the forward and backward loops were unrolled and parallelized. Another key approach has been the implementation of the new algorithm in a hybrid-computing system, integrating both an Intel Xeon multi-core CPU and a Tilera Tile64 many-core card. A comparison with other Clustal W implementations reveals the high-performance of the new algorithm and strategy in many-core CPU architectures, in a scenario where the sequences to align are relatively long (more than 10 kb) and, hence, a many-core GPU hardware cannot be used. Thus, the MC64-ClustalWP2 runs multiple alignments more than 18x than the original Clustal W algorithm, and more than 7x than the best x86 parallel implementation to date, being publicly available through a web service. Besides, these developments have been deployed in cost-effective personal computers and should be useful for life-science researchers, including the identification of identities and differences for mutation/polymorphism analyses, biodiversity and evolutionary studies and for the development of molecular markers for paternity testing, germplasm management and protection, to assist breeding, illegal traffic control, fraud prevention and for the protection of the intellectual property (identification

  20. MC64-ClustalWP2: A Highly-Parallel Hybrid Strategy to Align Multiple Sequences in Many-Core Architectures

    PubMed Central

    Díaz, David; Esteban, Francisco J.; Hernández, Pilar; Caballero, Juan Antonio; Guevara, Antonio

    2014-01-01

    We have developed the MC64-ClustalWP2 as a new implementation of the Clustal W algorithm, integrating a novel parallelization strategy and significantly increasing the performance when aligning long sequences in architectures with many cores. It must be stressed that in such a process, the detailed analysis of both the software and hardware features and peculiarities is of paramount importance to reveal key points to exploit and optimize the full potential of parallelism in many-core CPU systems. The new parallelization approach has focused into the most time-consuming stages of this algorithm. In particular, the so-called progressive alignment has drastically improved the performance, due to a fine-grained approach where the forward and backward loops were unrolled and parallelized. Another key approach has been the implementation of the new algorithm in a hybrid-computing system, integrating both an Intel Xeon multi-core CPU and a Tilera Tile64 many-core card. A comparison with other Clustal W implementations reveals the high-performance of the new algorithm and strategy in many-core CPU architectures, in a scenario where the sequences to align are relatively long (more than 10 kb) and, hence, a many-core GPU hardware cannot be used. Thus, the MC64-ClustalWP2 runs multiple alignments more than 18x than the original Clustal W algorithm, and more than 7x than the best x86 parallel implementation to date, being publicly available through a web service. Besides, these developments have been deployed in cost-effective personal computers and should be useful for life-science researchers, including the identification of identities and differences for mutation/polymorphism analyses, biodiversity and evolutionary studies and for the development of molecular markers for paternity testing, germplasm management and protection, to assist breeding, illegal traffic control, fraud prevention and for the protection of the intellectual property (identification

  1. Differentiated evolutionary relationships among chordates from comparative alignments of multiple sequences of MyoD and MyoG myogenic regulatory factors.

    PubMed

    Oliani, L C; Lidani, K C F; Gabriel, J E

    2015-10-16

    MyoD and MyoG are transcription factors that have essential roles in myogenic lineage determination and muscle differentiation. The purpose of this study was to compare multiple amino acid sequences of myogenic regulatory proteins to infer evolutionary relationships among chordates. Protein sequences from Mus musculus (P10085 and P12979), human Homo sapiens (P15172 and P15173), bovine Bos taurus (Q7YS82 and Q7YS81), wild pig Sus scrofa (P49811 and P49812), quail Coturnix coturnix (P21572 and P34060), chicken Gallus gallus (P16075 and P17920), rat Rattus norvegicus (Q02346 and P20428), domestic water buffalo Bubalus bubalis (D2SP11 and A7L034), and sheep Ovis aries (Q90477 and D3YKV7) were searched from a non-redundant protein sequence database UniProtKB/Swiss-Prot, and subsequently analyzed using the Mega6.0 software. MyoD evolutionary analyses revealed the presence of three main clusters with all mammals branched in one cluster, members of the order Rodentia (mouse and rat) in a second branch linked to the first, and birds of the order Galliformes (chicken and quail) remaining isolated in a third. MyoG evolutionary analyses aligned sequences in two main clusters, all mammalian specimens grouped in different sub-branches, and birds clustered in a second branch. These analyses suggest that the evolution of MyoD and MyoG was driven by different pathways.

  2. Image denoising using local tangent space alignment

    NASA Astrophysics Data System (ADS)

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

    2010-07-01

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

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

    PubMed

    Chen, Jing; Ma, Zhengming; Liu, Yang

    2013-01-01

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

  4. Automatic Parameter Learning for Multiple Local Network Alignment

    PubMed Central

    Novak, Antal; Do, Chuong B.; Srinivasan, Balaji S.; Batzoglou, Serafim

    2009-01-01

    Abstract We developed Græmlin 2.0, a new multiple network aligner with (1) a new multi-stage approach to local network alignment; (2) a novel scoring function that can use arbitrary features of a multiple network alignment, such as protein deletions, protein duplications, protein mutations, and interaction losses; (3) a parameter learning algorithm that uses a training set of known network alignments to learn parameters for our scoring function and thereby adapt it to any set of networks; and (4) an algorithm that uses our scoring function to find approximate multiple network alignments in linear time. We tested Græmlin 2.0's accuracy on protein interaction networks from IntAct, DIP, and the Stanford Network Database. We show that, on each of these datasets, Græmlin 2.0 has higher sensitivity and specificity than existing network aligners. Græmlin 2.0 is available under the GNU public license at http://graemlin.stanford.edu. PMID:19645599

  5. Enforcing Convexity for Improved Alignment with Constrained Local Models

    PubMed Central

    Wang, Yang; Lucey, Simon; Cohn, Jeffrey F.

    2010-01-01

    Constrained local models (CLMs) have recently demonstrated good performance in non-rigid object alignment/tracking in comparison to leading holistic approaches (e.g., AAMs). A major problem hindering the development of CLMs further, for non-rigid object alignment/tracking, is how to jointly optimize the global warp update across all local search responses. Previous methods have either used general purpose optimizers (e.g., simplex methods) or graph based optimization techniques. Unfortunately, problems exist with both these approaches when applied to CLMs. In this paper, we propose a new approach for optimizing the global warp update in an efficient manner by enforcing convexity at each local patch response surface. Furthermore, we show that the classic Lucas-Kanade approach to gradient descent image alignment can be viewed as a special case of our proposed framework. Finally, we demonstrate that our approach receives improved performance for the task of non-rigid face alignment/tracking on the MultiPIE database and the UNBC-McMaster archive. PMID:20622926

  6. Critical thresholds in flocking hydrodynamics with non-local alignment.

    PubMed

    Tadmor, Eitan; Tan, Changhui

    2014-11-13

    We study the large-time behaviour of Eulerian systems augmented with non-local alignment. Such systems arise as hydrodynamic descriptions of agent-based models for self-organized dynamics, e.g. Cucker & Smale (2007 IEEE Trans. Autom. Control 52, 852-862. (doi:10.1109/TAC.2007.895842)) and Motsch & Tadmor (2011 J. Stat. Phys. 144, 923-947. (doi:10.1007/s10955-011-0285-9)) models. We prove that, in analogy with the agent-based models, the presence of non-local alignment enforces strong solutions to self-organize into a macroscopic flock. This then raises the question of existence of such strong solutions. We address this question in one- and two-dimensional set-ups, proving global regularity for subcritical initial data. Indeed, we show that there exist critical thresholds in the phase space of the initial configuration which dictate the global regularity versus a finite-time blow-up. In particular, we explore the regularity of non-local alignment in the presence of vacuum.

  7. Flexible structural protein alignment by a sequence of local transformations

    PubMed Central

    Rocha, Jairo; Segura, Joan; Wilson, Richard C.; Dasgupta, Swagata

    2009-01-01

    Motivation: Throughout evolution, homologous proteins have common regions that stay semi-rigid relative to each other and other parts that vary in a more noticeable way. In order to compare the increasing number of structures in the PDB, flexible geometrical alignments are needed, that are reliable and easy to use. Results: We present a protein structure alignment method whose main feature is the ability to consider different rigid transformations at different sites, allowing for deformations beyond a global rigid transformation. The performance of the method is comparable with that of the best ones from 10 aligners tested, regarding both the quality of the alignments with respect to hand curated ones, and the classification ability. An analysis of some structure pairs from the literature that need to be matched in a flexible fashion are shown. The use of a series of local transformations can be exported to other classifiers, and a future golden protein similarity measure could benefit from it. Availability: A public server for the program is available at http://dmi.uib.es/ProtDeform/. Contact: jairo@uib.es Supplementary information: All data used, results and examples are available at http://dmi.uib.es/people/jairo/bio/ProtDeform.Supplementary data are available at Bioinformatics online. PMID:19417057

  8. Spin Alignment in Analogues of The Local Sheet

    NASA Astrophysics Data System (ADS)

    Conidis, George J.

    2016-10-01

    Tidal torque theory and simulations of large scale structure predict spin vectors of massive galaxies should be coplanar with sheets in the cosmic web. Recently demonstrated, the giants (K s <= -22.5 mag) in the Local Volume beyond the Local Sheet have spin vectors directed close to the plane of the Local Supercluster, supporting the predictions of Tidal Torque Theory. However, the giants in the Local Sheet encircling the Local Group display a distinctly different arrangement, suggesting that the mass asymmetry of the Local Group or its progenitor torqued them from their primordial spin directions. To investigate the origin of the spin alignment of giants locally, analogues of the Local Sheet were identified in the SDSS DR9. Similar to the Local Sheet, analogues have an interacting pair of disk galaxies isolated from the remaining sheet members. Modified sheets in which there is no interacting pair of disk galaxies were identified as a control sample. Galaxies in face-on control sheets do not display axis ratios predominantly weighted toward low values, contrary to the expectation of tidal torque theory. For face-on and edge-on sheets, the distribution of axis ratios for galaxies in analogues is distinct from that in controls with a confidence of 97.6% & 96.9%, respectively. This corroborates the hypothesis that an interacting pair can affect spin directions of neighbouring galaxies.

  9. Heuristic reusable dynamic programming: efficient updates of local sequence alignment.

    PubMed

    Hong, Changjin; Tewfik, Ahmed H

    2009-01-01

    Recomputation of the previously evaluated similarity results between biological sequences becomes inevitable when researchers realize errors in their sequenced data or when the researchers have to compare nearly similar sequences, e.g., in a family of proteins. We present an efficient scheme for updating local sequence alignments with an affine gap model. In principle, using the previous matching result between two amino acid sequences, we perform a forward-backward alignment to generate heuristic searching bands which are bounded by a set of suboptimal paths. Given a correctly updated sequence, we initially predict a new score of the alignment path for each contour to select the best candidates among them. Then, we run the Smith-Waterman algorithm in this confined space. Furthermore, our heuristic alignment for an updated sequence shows that it can be further accelerated by using reusable dynamic programming (rDP), our prior work. In this study, we successfully validate "relative node tolerance bound" (RNTB) in the pruned searching space. Furthermore, we improve the computational performance by quantifying the successful RNTB tolerance probability and switch to rDP on perturbation-resilient columns only. In our searching space derived by a threshold value of 90 percent of the optimal alignment score, we find that 98.3 percent of contours contain correctly updated paths. We also find that our method consumes only 25.36 percent of the runtime cost of sparse dynamic programming (sDP) method, and to only 2.55 percent of that of a normal dynamic programming with the Smith-Waterman algorithm.

  10. Sampling rare events: statistics of local sequence alignments.

    PubMed

    Hartmann, Alexander K

    2002-05-01

    A method to calculate probability distributions in regions where the events are very unlikely (e.g., p approximately 10(-40)) is presented. The basic idea is to map the underlying model on a physical system. The system is simulated at a low temperature, such that preferably configurations with originally low probabilities are generated. Since the distribution of such a physical system is known, the original unbiased distribution can be obtained. As an application, local alignment of protein sequences is studied. The deviation of the distribution p(S) of optimum scores from the extreme-value distribution is quantified. This deviation decreases with growing sequence length.

  11. fMRI alignment based on local functional connectivity patterns

    NASA Astrophysics Data System (ADS)

    Jiang, Di; Du, Yuhui; Cheng, Hewei; Jiang, Tianzi; Fan, Yong

    2012-02-01

    In functional neuroimaging studies, the inter-subject alignment of functional magnetic resonance imaging (fMRI) data is a necessary precursor to improve functional consistency across subjects. Traditional structural MRI based registration methods cannot achieve accurate inter-subject functional consistency in that functional units are not necessarily consistently located relative to anatomical structures due to functional variability across subjects. Although spatial smoothing commonly used in fMRI data preprocessing can reduce the inter-subject functional variability, it may blur the functional signals and thus lose the fine-grained information. In this paper we propose a novel functional signal based fMRI image registration method which aligns local functional connectivity patterns of different subjects to improve the inter-subject functional consistency. Particularly, the functional connectivity is measured using Pearson correlation. For each voxel of an fMRI image, its functional connectivity to every voxel in its local spatial neighborhood, referred to as its local functional connectivity pattern, is characterized by a rotation and shift invariant representation. Based on this representation, the spatial registration of two fMRI images is achieved by minimizing the difference between their corresponding voxels' local functional connectivity patterns using a deformable image registration model. Experiment results based on simulated fMRI data have demonstrated that the proposed method is more robust and reliable than the existing fMRI image registration methods, including maximizing functional correlations and minimizing difference of global connectivity matrices across different subjects. Experiment results based on real resting-state fMRI data have further demonstrated that the proposed fMRI registration method can statistically significantly improve functional consistency across subjects.

  12. Skeleton-based human action recognition using multiple sequence alignment

    NASA Astrophysics Data System (ADS)

    Ding, Wenwen; Liu, Kai; Cheng, Fei; Zhang, Jin; Li, YunSong

    2015-05-01

    Human action recognition and analysis is an active research topic in computer vision for many years. This paper presents a method to represent human actions based on trajectories consisting of 3D joint positions. This method first decompose action into a sequence of meaningful atomic actions (actionlets), and then label actionlets with English alphabets according to the Davies-Bouldin index value. Therefore, an action can be represented using a sequence of actionlet symbols, which will preserve the temporal order of occurrence of each of the actionlets. Finally, we employ sequence comparison to classify multiple actions through using string matching algorithms (Needleman-Wunsch). The effectiveness of the proposed method is evaluated on datasets captured by commodity depth cameras. Experiments of the proposed method on three challenging 3D action datasets show promising results.

  13. Citation Matching in Sanskrit Corpora Using Local Alignment

    NASA Astrophysics Data System (ADS)

    Prasad, Abhinandan S.; Rao, Shrisha

    Citation matching is the problem of finding which citation occurs in a given textual corpus. Most existing citation matching work is done on scientific literature. The goal of this paper is to present methods for performing citation matching on Sanskrit texts. Exact matching and approximate matching are the two methods for performing citation matching. The exact matching method checks for exact occurrence of the citation with respect to the textual corpus. Approximate matching is a fuzzy string-matching method which computes a similarity score between an individual line of the textual corpus and the citation. The Smith-Waterman-Gotoh algorithm for local alignment, which is generally used in bioinformatics, is used here for calculating the similarity score. This similarity score is a measure of the closeness between the text and the citation. The exact- and approximate-matching methods are evaluated and compared. The methods presented can be easily applied to corpora in other Indic languages like Kannada, Tamil, etc. The approximate-matching method can in particular be used in the compilation of critical editions and plagiarism detection in a literary work.

  14. Dark Field Technology - A Practical Approach To Local Alignment

    NASA Astrophysics Data System (ADS)

    Beaulieu, David R.; Hellebrekers, Paul P.

    1987-01-01

    A fully automated direct reticle reference alignment system for use in step and repeat camera systems is described. The technique, first outlined by Janus S. Wilczynski, ("Optical Step and Repeat Camera with Dark Field Alignment", J. Vac. Technol., 16(6), Nov./Dec. 1979), has been implemented on GCA Corporation's DSW Wafer Stepper. Results from various process levels covering the typical CMOS process have shown that better than ±0.2μm alignment accuracy can be obtained with minimal process sensitivity. The technique employs fixed illumination and microscope optics to achieve excellent registration stability and maintenance-free operation. Latent image techniques can be exploited for intra-field, grid and focus characterization.

  15. Swarm intelligence in bioinformatics: methods and implementations for discovering patterns of multiple sequences.

    PubMed

    Cui, Zhihua; Zhang, Yi

    2014-02-01

    As a promising and innovative research field, bioinformatics has attracted increasing attention recently. Beneath the enormous number of open problems in this field, one fundamental issue is about the accurate and efficient computational methodology that can deal with tremendous amounts of data. In this paper, we survey some applications of swarm intelligence to discover patterns of multiple sequences. To provide a deep insight, ant colony optimization, particle swarm optimization, artificial bee colony and artificial fish swarm algorithm are selected, and their applications to multiple sequence alignment and motif detecting problem are discussed.

  16. Alignment of galaxies relative to their local environment in SDSS-DR8

    NASA Astrophysics Data System (ADS)

    Hirv, A.; Pelt, J.; Saar, E.; Tago, E.; Tamm, A.; Tempel, E.; Einasto, M.

    2017-02-01

    Aims: We study the alignment of galaxies relative to their local environment in SDSS-DR8 and, using these data, we discuss evolution scenarios for different types of galaxies. Methods: We defined a vector field of the direction of anisotropy of the local environment of galaxies. We summed the unit direction vectors of all close neighbours of a given galaxy in a particular way to estimate this field. We found the alignment angles between the spin axes of disc galaxies, or the minor axes of elliptical galaxies, and the direction of anisotropy. The distributions of cosines of these angles are compared to the random distributions to analyse the alignment of galaxies. Results: Sab galaxies show perpendicular alignment relative to the direction of anisotropy in a sparse environment, for single galaxies and galaxies of low luminosity. Most of the parallel alignment of Scd galaxies comes from dense regions, from 2...3 member groups and from galaxies with low luminosity. The perpendicular alignment of S0 galaxies does not depend strongly on environmental density nor luminosity; it is detected for single and 2...3 member group galaxies, and for main galaxies of 4...10 member groups. The perpendicular alignment of elliptical galaxies is clearly detected for single galaxies and for members of ≤10 member groups; the alignment increases with environmental density and luminosity. Conclusions: We confirm the existence of fossil tidally induced alignment of Sab galaxies at low z. The alignment of Scd galaxies can be explained via the infall of matter to filaments. S0 galaxies may have encountered relatively massive mergers along the direction of anisotropy. Major mergers along this direction can explain the alignment of elliptical galaxies. Less massive, but repeated mergers are possibly responsible for the formation of elliptical galaxies in sparser areas and for less luminous elliptical galaxies.

  17. Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

    SciTech Connect

    Daily, Jeffrey A.

    2016-02-10

    Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. As a result, a faster intra-sequence pairwise alignment implementation is described and benchmarked. Using a 375 residue query sequence a speed of 136 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon E5-2670 12-core processor system, the highest reported for an implementation based on Farrar’s ’striped’ approach. When using only a single thread, parasail was 1.7 times faster than Rognes’s SWIPE. For many score matrices, parasail is faster than BLAST. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. In conclusion, applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.

  18. Alignments of the galaxies in and around the Virgo cluster with the local velocity shear

    SciTech Connect

    Lee, Jounghun; Rey, Soo Chang; Kim, Suk

    2014-08-10

    Observational evidence is presented for the alignment between the cosmic sheet and the principal axis of the velocity shear field at the position of the Virgo cluster. The galaxies in and around the Virgo cluster from the Extended Virgo Cluster Catalog that was recently constructed by Kim et al. are used to determine the direction of the local sheet. The peculiar velocity field reconstructed from the Sloan Digital Sky Survey Data Release 7 is analyzed to estimate the local velocity shear tensor at the Virgo center. Showing first that the minor principal axis of the local velocity shear tensor is almost parallel to the direction of the line of sight, we detect a clear signal of alignment between the positions of the Virgo satellites and the intermediate principal axis of the local velocity shear projected onto the plane of the sky. Furthermore, the dwarf satellites are found to appear more strongly aligned than their normal counterparts, which is interpreted as an indication of the following. (1) The normal satellites and the dwarf satellites fall in the Virgo cluster preferentially along the local filament and the local sheet, respectively. (2) The local filament is aligned with the minor principal axis of the local velocity shear while the local sheet is parallel to the plane spanned by the minor and intermediate principal axes. Our result is consistent with the recent numerical claim that the velocity shear is a good tracer of the cosmic web.

  19. Localized α4 Integrin Phosphorylation Directs Shear Stress-Induced Endothelial Cell Alignment

    PubMed Central

    Goldfinger, Lawrence E.; Tzima, Eleni; Stockton, Rebecca; Kiosses, William B.; Kinbara, Kayoko; Tkachenko, Eugene; Gutierrez, Edgar; Groisman, Alex; Nguyen, Phu; Chien, Shu; Ginsberg1, Mark H.

    2009-01-01

    Vascular endothelial cells respond to laminar shear stress by aligning in the direction of flow, a process which may contribute to athero-protection. Here we report that localized α4 integrin phosphorylation is a mechanism for establishing the directionality of shear stress-induced alignment in microvascular endothelial cells. Within 5 minutes of exposure to a physiological level of shear stress, endothelial α4 integrins became phosphorylated on Ser988. In wounded monolayers, phosphorylation was enhanced at the downstream edges of cells relative to the source of flow. The shear-induced α4 integrin phosphorylation was blocked by inhibitors of cAMP-dependent protein kinase A (PKA), an enzyme involved in the alignment of endothelial cells under prolonged shear. Moreover, shear-induced localized activation of the small GTPase Rac1, which specifies the directionality of endothelial alignment, was similarly blocked by PKA inhibitors. Furthermore, endothelial cells bearing a non-phosphorylatable α4(S988A) mutation failed to align in response to shear stress, thus establishing α4 as a relevant PKA substrate. We thereby show that shear-induced PKA-dependent α4 integrin phosphorylation at the downstream edge of endothelial cells promotes localized Rac1 activation, which in turn directs cytoskeletal alignment in response to shear stress. PMID:18583710

  20. Information conveyed by inferior colliculus neurons about stimuli with aligned and misaligned sound localization cues

    PubMed Central

    Young, Eric D.

    2011-01-01

    Previous studies have demonstrated that single neurons in the central nucleus of the inferior colliculus (ICC) are sensitive to multiple sound localization cues. We investigated the hypothesis that ICC neurons are specialized to encode multiple sound localization cues that are aligned in space (as would naturally occur from a single broadband sound source). Sound localization cues including interaural time differences (ITDs), interaural level differences (ILDs), and spectral shapes (SSs) were measured in a marmoset monkey. Virtual space methods were used to generate stimuli with aligned and misaligned combinations of cues while recording in the ICC of the same monkey. Mutual information (MI) between spike rates and stimuli for aligned versus misaligned cues were compared. Neurons with best frequencies (BFs) less than ∼11 kHz mostly encoded information about a single sound localization cue, ITD or ILD depending on frequency, consistent with the dominance of ear acoustics by either ITD or ILD at those frequencies. Most neurons with BFs >11 kHz encoded information about multiple sound localization cues, usually ILD and SS, and were sensitive to their alignment. In some neurons MI between stimuli and spike responses was greater for aligned cues, while in others it was greater for misaligned cues. If SS cues were shifted to lower frequencies in the virtual space stimuli, a similar result was found for neurons with BFs <11 kHz, showing that the cue interaction reflects the spectra of the stimuli and not a specialization for representing SS cues. In general the results show that ICC neurons are sensitive to multiple localization cues if they are simultaneously present in the frequency response area of the neuron. However, the representation is diffuse in that there is not a specialization in the ICC for encoding aligned sound localization cues. PMID:21653729

  1. Seeds of Locally Aligned Motion and Stress Coordinate a Collective Cell Migration

    PubMed Central

    Zaritsky, Assaf; Welf, Erik S.; Tseng, Yun-Yu; Angeles Rabadán, M.; Serra-Picamal, Xavier; Trepat, Xavier; Danuser, Gaudenz

    2015-01-01

    We find how collective migration emerges from mechanical information transfer between cells. Local alignment of cell velocity and mechanical stress orientation—a phenomenon dubbed “plithotaxis”—plays a crucial role in inducing coordinated migration. Leader cells at the monolayer edge better align velocity and stress to migrate faster toward the open space. Local seeds of enhanced motion then generate stress on neighboring cells to guide their migration. Stress-induced motion propagates into the monolayer as well as along the monolayer boundary to generate increasingly larger clusters of coordinately migrating cells that move faster with enhanced alignment of velocity and stress. Together, our analysis provides a model of long-range mechanical communication between cells, in which plithotaxis translates local mechanical fluctuations into globally collective migration of entire tissues. PMID:26682808

  2. Local alignment vectors reveal cancer cell-induced ECM fiber remodeling dynamics.

    PubMed

    Lee, Byoungkoo; Konen, Jessica; Wilkinson, Scott; Marcus, Adam I; Jiang, Yi

    2017-01-03

    Invasive cancer cells interact with the surrounding extracellular matrix (ECM), remodeling ECM fiber network structure by condensing, degrading, and aligning these fibers. We developed a novel local alignment vector analysis method to quantitatively measure collagen fiber alignment as a vector field using Circular Statistics. This method was applied to human non-small cell lung carcinoma (NSCLC) cell lines, embedded as spheroids in a collagen gel. Collagen remodeling was monitored using second harmonic generation imaging under normal conditions and when the LKB1-MARK1 pathway was disrupted through RNAi-based approaches. The results showed that inhibiting LKB1 or MARK1 in NSCLC increases the collagen fiber alignment and captures outward alignment vectors from the tumor spheroid, corresponding to high invasiveness of LKB1 mutant cancer cells. With time-lapse imaging of ECM micro-fiber morphology, the local alignment vector can measure the dynamic signature of invasive cancer cell activity and cell-migration-induced ECM and collagen remodeling and realigning dynamics.

  3. Local alignment vectors reveal cancer cell-induced ECM fiber remodeling dynamics

    PubMed Central

    Lee, Byoungkoo; Konen, Jessica; Wilkinson, Scott; Marcus, Adam I.; Jiang, Yi

    2017-01-01

    Invasive cancer cells interact with the surrounding extracellular matrix (ECM), remodeling ECM fiber network structure by condensing, degrading, and aligning these fibers. We developed a novel local alignment vector analysis method to quantitatively measure collagen fiber alignment as a vector field using Circular Statistics. This method was applied to human non-small cell lung carcinoma (NSCLC) cell lines, embedded as spheroids in a collagen gel. Collagen remodeling was monitored using second harmonic generation imaging under normal conditions and when the LKB1-MARK1 pathway was disrupted through RNAi-based approaches. The results showed that inhibiting LKB1 or MARK1 in NSCLC increases the collagen fiber alignment and captures outward alignment vectors from the tumor spheroid, corresponding to high invasiveness of LKB1 mutant cancer cells. With time-lapse imaging of ECM micro-fiber morphology, the local alignment vector can measure the dynamic signature of invasive cancer cell activity and cell-migration-induced ECM and collagen remodeling and realigning dynamics. PMID:28045069

  4. Ligand Binding Site Detection by Local Structure Alignment and Its Performance Complementarity

    PubMed Central

    Lee, Hui Sun; Im, Wonpil

    2013-01-01

    Accurate determination of potential ligand binding sites (BS) is a key step for protein function characterization and structure-based drug design. Despite promising results of template-based BS prediction methods using global structure alignment (GSA), there is a room to improve the performance by properly incorporating local structure alignment (LSA) because BS are local structures and often similar for proteins with dissimilar global folds. We present a template-based ligand BS prediction method using G-LoSA, our LSA tool. A large benchmark set validation shows that G-LoSA predicts drug-like ligands’ positions in single-chain protein targets more precisely than TM-align, a GSA-based method, while the overall success rate of TM-align is better. G-LoSA is particularly efficient for accurate detection of local structures conserved across proteins with diverse global topologies. Recognizing the performance complementarity of G-LoSA to TM-align and a non-template geometry-based method, fpocket, a robust consensus scoring method, CMCS-BSP (Complementary Methods and Consensus Scoring for ligand Binding Site Prediction), is developed and shows improvement on prediction accuracy. The G-LoSA source code is freely available at http://im.bioinformatics.ku.edu/GLoSA. PMID:23957286

  5. Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

    DOE PAGES

    Daily, Jeffrey A.

    2016-02-10

    Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. As a result, a faster intra-sequence pairwise alignment implementation is described and benchmarked. Using a 375 residue query sequence a speed of 136 billion cell updates permore » second (GCUPS) was achieved on a dual Intel Xeon E5-2670 12-core processor system, the highest reported for an implementation based on Farrar’s ’striped’ approach. When using only a single thread, parasail was 1.7 times faster than Rognes’s SWIPE. For many score matrices, parasail is faster than BLAST. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. In conclusion, applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.« less

  6. Dust Grain Alignment and Magnetic Field Strength in the Wall of the Local Bubble

    NASA Astrophysics Data System (ADS)

    Andersson, B.-G.; Medan, Ilija

    2017-01-01

    We use archival data on polarization (Berdyugin 2014) and extinction in the wall of the Local Bubble to study the grain alignment efficiency and the magnetic field strength. We find that the grain alignment efficiency variations can be directly tied to the location of the known OB-associations within 200pc from the Sun, strongly supporting modern, radiation-driven dust grain alignment. Based on the Davis-Chandrasekhar-Fermi method, we find a bimodal magnetic field-strength distribution, where the locations of the strongest fields correlate with the directions towards the near-by OB associations. We hypothesize that this strengthening is due to compression of the bubble wall by the opposing outflows in the Local Bubble and from the surrounding OB associations.

  7. Use of local alignment tensors for the determination of relative configurations in organic compounds.

    PubMed

    Thiele, Christina M; Maliniak, Arnold; Stevensson, Baltzar

    2009-09-16

    In this proof of principle the use of local alignment tensors for the determination of relative configurations in moderately flexible molecules is demonstrated. These tensors are derived from residual dipolar couplings. Two methods for the analysis of partly linearly dependent RDCs in a rigid molecular fragment are also presented.

  8. Coordination Analysis Using Global Structural Constraints and Alignment-based Local Features

    NASA Astrophysics Data System (ADS)

    Hara, Kazuo; Shimbo, Masashi; Matsumoto, Yuji

    We propose a hybrid approach to coordinate structure analysis that combines a simple grammar to ensure consistent global structure of coordinations in a sentence, and features based on sequence alignment to capture local symmetry of conjuncts. The weight of the alignment-based features, which in turn determines the score of coordinate structures, is optimized by perceptron training on a given corpus. A bottom-up chart parsing algorithm efficiently finds the best scoring structure, taking both nested or non-overlapping flat coordinations into account. We demonstrate that our approach outperforms existing parsers in coordination scope detection on the Genia corpus.

  9. Local-global alignment for finding 3D similarities in protein structures

    DOEpatents

    Zemla, Adam T.

    2011-09-20

    A method of finding 3D similarities in protein structures of a first molecule and a second molecule. The method comprises providing preselected information regarding the first molecule and the second molecule. Comparing the first molecule and the second molecule using Longest Continuous Segments (LCS) analysis. Comparing the first molecule and the second molecule using Global Distance Test (GDT) analysis. Comparing the first molecule and the second molecule using Local Global Alignment Scoring function (LGA_S) analysis. Verifying constructed alignment and repeating the steps to find the regions of 3D similarities in protein structures.

  10. Usp16 regulates kinetochore localization of Plk1 to promote proper chromosome alignment in mitosis

    PubMed Central

    Zhuo, Xiaolong; Guo, Xiao; Zhang, Xiaoyan; Jing, Guihua; Wang, Yao; Chen, Qiang; Jiang, Qing

    2015-01-01

    During the G2 to M phase transition, a portion of mitotic regulator Plk1 localizes to the kinetochores and regulates the initiation of kinetochore–microtubule attachments for proper chromosome alignment. Once kinetochore–microtubule attachment is achieved, this portion of Plk1 is removed from the kinetochores as a result of ubiquitination. However, the crucial molecular mechanism that promotes the localization and the maintenance of Plk1 on the kinetochores until metaphase is still unclear. We report that ubiquitin-specific peptidase 16 (Usp16) plays a key role during this process. Usp16 deubiquitinates Plk1, resulting in an enhanced interaction with kinetochore-localized proteins such as BubR1, and thereby retains Plk1 on the kinetochores to promote proper chromosome alignment in early mitosis. Down-regulation of Usp16 causes increased ubiquitination and decreased kinetochore localization of Plk1. Thus, our data unveil a unique mechanism by which Usp16 promotes the localization and maintenance of Plk1 on the kinetochores for proper chromosome alignment. PMID:26323689

  11. An Efficient Parallel Algorithm for Multiple Sequence Similarities Calculation Using a Low Complexity Method

    PubMed Central

    Marucci, Evandro A.; Neves, Leandro A.; Valêncio, Carlo R.; Pinto, Alex R.; Cansian, Adriano M.; de Souza, Rogeria C. G.; Shiyou, Yang; Machado, José M.

    2014-01-01

    With the advance of genomic researches, the number of sequences involved in comparative methods has grown immensely. Among them, there are methods for similarities calculation, which are used by many bioinformatics applications. Due the huge amount of data, the union of low complexity methods with the use of parallel computing is becoming desirable. The k-mers counting is a very efficient method with good biological results. In this work, the development of a parallel algorithm for multiple sequence similarities calculation using the k-mers counting method is proposed. Tests show that the algorithm presents a very good scalability and a nearly linear speedup. For 14 nodes was obtained 12x speedup. This algorithm can be used in the parallelization of some multiple sequence alignment tools, such as MAFFT and MUSCLE. PMID:25140318

  12. Local Release of Paclitaxel from Aligned, Electrospun Microfibers Promotes Axonal Extension.

    PubMed

    Roman, Jose A; Reucroft, Ian; Martin, Russell A; Hurtado, Andres; Mao, Hai-Quan

    2016-10-01

    Traumatic spinal cord injuries ultimately result in an inhibitory environment that prevents axonal regeneration from occurring. A low concentration administration of paclitaxel has been previously shown to promote axonal extension and attenuate the upregulation of inhibitory molecules after a spinal cord injury. In this study, paclitaxel is incorporated into electrospun poly(l-lactic acid) (PLA) microfibers, and it is established that a local release of paclitaxel from aligned, electrospun microfibers promotes neurite extension in a growth-conducive and inhibitory environment. Isolated dorsal root ganglion cells are cultured for 5 d directly on tissue culture polystyrene surface, PLA film, random, or aligned electrospun PLA microfibers (1.44 ± 0.03 μm) with paclitaxel incorporated at various concentrations (0%-5.0% w/w in reference to fiber weight). To determine the effect of a local release of paclitaxel, paclitaxel-loaded microfibers are placed in CellCrown inserts above cultured neurons. Average neurite extension rate is quantified for each sample. A local release of paclitaxel maintains neuronal survival and neurite extension in a concentration-dependent manner when coupled with aligned microfibers when cultured on laminin or an inhibitory surface of aggrecan. The findings provide a targeted approach to improve axonal extension across the inhibitory environment present after a traumatic injury in the spinal cord.

  13. Local and nonlocal strain rate fields and vorticity alignment in turbulent flows.

    PubMed

    Hamlington, Peter E; Schumacher, Jörg; Dahm, Werner J A

    2008-02-01

    Local and nonlocal contributions to the total strain rate tensor S(ij) at any point x in a flow are formulated from an expansion of the vorticity field in a local spherical neighborhood of radius R centered on x. The resulting exact expression allows the nonlocal (background) strain rate tensor S(ij)(B)(x) to be obtained from S(ij)(x). In turbulent flows, where the vorticity naturally concentrates into relatively compact structures, this allows the local alignment of vorticity with the most extensional principal axis of the background strain rate tensor to be evaluated. In the vicinity of any vortical structure, the required radius R and corresponding order n to which the expansion must be carried are determined by the viscous length scale lambda(nu). We demonstrate the convergence to the background strain rate field with increasing R and n for an equilibrium Burgers vortex, and show that this resolves the anomalous alignment of vorticity with the intermediate eigenvector of the total strain rate tensor. We then evaluate the background strain field S(ij)(B)(x) in direct numerical simulations of homogeneous isotropic turbulence where, even for the limited R and n corresponding to the truncated series expansion, the results show an increase in the expected equilibrium alignment of vorticity with the most extensional principal axis of the background strain rate tensor.

  14. A new method for improving functional-to-structural MRI alignment using local Pearson correlation.

    PubMed

    Saad, Ziad S; Glen, Daniel R; Chen, Gang; Beauchamp, Michael S; Desai, Rutvik; Cox, Robert W

    2009-02-01

    Accurate registration of Functional Magnetic Resonance Imaging (FMRI) T2-weighted volumes to same-subject high-resolution T1-weighted structural volumes is important for Blood Oxygenation Level Dependent (BOLD) FMRI and crucial for applications such as cortical surface-based analyses and pre-surgical planning. Such registration is generally implemented by minimizing a cost functional, which measures the mismatch between two image volumes over the group of proper affine transformations. Widely used cost functionals, such as mutual information (MI) and correlation ratio (CR), appear to yield decent alignments when visually judged by matching outer brain contours. However, close inspection reveals that internal brain structures are often significantly misaligned. Poor registration is most evident in the ventricles and sulcal folds, where CSF is concentrated. This observation motivated our development of an improved modality-specific cost functional which uses a weighted local Pearson coefficient (LPC) to align T2- and T1-weighted images. In the absence of an alignment gold standard, we used three human observers blinded to registration method to provide an independent assessment of the quality of the registration for each cost functional. We found that LPC performed significantly better (p<0.001) than generic cost functionals including MI and CR. Generic cost functionals were very often not minimal near the best alignment, thereby suggesting that optimization is not the cause of their failure. Lastly, we emphasize the importance of precise visual inspection of alignment quality and present an automated method for generating composite images that help capture errors of misalignment.

  15. An effortless procedure to align the local frame of an inertial measurement unit to the local frame of another motion capture system.

    PubMed

    Chardonnens, Julien; Favre, Julien; Aminian, Kamiar

    2012-08-31

    Inertial measurement units (IMUs) offer great opportunities to analyze segmental and joints kinematics. When combined with another motion capture system (MCS), for example, to validate new IMU-based applications or to develop mixed systems, it is necessary to align the local frame of the IMU sensors to the local frame of the MCS. Currently, all alignment methods use landmarks on the IMU's casing. Therefore, they can only be used with well-documented IMUs and they are prone to error when the IMU's casing is small. This study proposes an effortless procedure to align the local frame of any IMU to the local frame of any other MCS able to measure the orientation of its local frame. The general concept of this method is to derive the gyroscopic angles for both devices during an alignment movement, and then to use an optimization algorithm to calculate the alignment matrix between both local frames. The alignment movement consists of rotations around three more or less orthogonal axes and it can easily be performed by hands. To test the alignment procedure, an IMU and a magnetic marker were attached to a plate, and 20 alignment movements were recorded. The maximum errors of alignment (accuracy±precision) were 1.02°±0.32° and simulations showed that the method was robust against noise that typically affect IMUs. In conclusion, this study describes an efficient alignment procedure that is quick and easy to perform, and that does not require any alignment device or any knowledge about the IMU casing.

  16. Hole localization, water dissociation mechanisms, and band alignment at aqueous-titania interfaces

    NASA Astrophysics Data System (ADS)

    Lyons, John L.

    Photocatalytic water splitting is a promising method for generating clean energy, but materials that can efficiently act as photocatalysts are scarce. This is in part due to the fact that exposure to water can strongly alter semiconductor surfaces and therefore photocatalyst performance. Many materials are not stable in aqueous environments; in other cases, local changes in structure may occur, affecting energy-level alignment. Even in the simplest case, dynamic fluctuations modify the organization of interface water. Accounting for such effects requires knowledge of the dominant local structural motifs and also accurate semiconductor band-edge positions, making quantitative prediction of energy-level alignments computationally challenging. Here we employ a combined theoretical approach to study the structure, energy alignment, and hole localization at aqueous-titania interfaces. We calculate the explicit aqueous-semiconductor interface using ab initio molecular dynamics, which provides the fluctuating atomic structure, the extent of water dissociation, and the resulting electrostatic potential. For both anatase and rutile TiO2 we observe spontaneous water dissociation and re-association events that occur via distinct mechanisms. We also find a higher-density water layer occurring on anatase. In both cases, we find that the second monolayer of water plays a crucial role in controlling the extent of water dissociation. Using hybrid functional calculations, we then investigate the propensity for dissociated waters to stabilize photo-excited carriers, and compare the results of rutile and anatase aqueous interfaces. Finally, we use the GW approach from many-body perturbation theory to obtain the position of semiconductor band edges relative to the occupied 1b1 level and thus the redox levels of water, and examine how local structural modifications affect these offsets. This work was performed in collaboration with N. Kharche, M. Z. Ertem, J. T. Muckerman, and M. S

  17. Model of myosin node aggregation into a contractile ring: the effect of local alignment

    NASA Astrophysics Data System (ADS)

    Ojkic, Nikola; Wu, Jian-Qiu; Vavylonis, Dimitrios

    2011-09-01

    Actomyosin bundles frequently form through aggregation of membrane-bound myosin clusters. One such example is the formation of the contractile ring in fission yeast from a broad band of cortical nodes. Nodes are macromolecular complexes containing several dozens of myosin-II molecules and a few formin dimers. The condensation of a broad band of nodes into the contractile ring has been previously described by a search, capture, pull and release (SCPR) model. In SCPR, a random search process mediated by actin filaments nucleated by formins leads to transient actomyosin connections among nodes that pull one another into a ring. The SCPR model reproduces the transport of nodes over long distances and predicts observed clump-formation instabilities in mutants. However, the model does not generate transient linear elements and meshwork structures as observed in some wild-type and mutant cells during ring assembly. As a minimal model of node alignment, we added short-range aligning forces to the SCPR model representing currently unresolved mechanisms that may involve structural components, cross-linking and bundling proteins. We studied the effect of the local node alignment mechanism on ring formation numerically. We varied the new parameters and found viable rings for a realistic range of values. Morphologically, transient structures that form during ring assembly resemble those observed in experiments with wild-type and cdc25-22 cells. Our work supports a hierarchical process of ring self-organization involving components drawn together from distant parts of the cell followed by progressive stabilization.

  18. Co-Orientation: Quantifying Simultaneous Co-Localization and Orientational Alignment of Filaments in Light Microscopy.

    PubMed

    Nieuwenhuizen, Robert P J; Nahidiazar, Leila; Manders, Erik M M; Jalink, Kees; Stallinga, Sjoerd; Rieger, Bernd

    2015-01-01

    Co-localization analysis is a widely used tool to seek evidence for functional interactions between molecules in different color channels in microscopic images. Here we extend the basic co-localization analysis by including the orientations of the structures on which the molecules reside. We refer to the combination of co-localization of molecules and orientational alignment of the structures on which they reside as co-orientation. Because the orientation varies with the length scale at which it is evaluated, we consider this scale as a separate informative dimension in the analysis. Additionally we introduce a data driven method for testing the statistical significance of the co-orientation and provide a method for visualizing the local co-orientation strength in images. We demonstrate our methods on simulated localization microscopy data of filamentous structures, as well as experimental images of similar structures acquired with localization microscopy in different color channels. We also show that in cultured primary HUVEC endothelial cells, filaments of the intermediate filament vimentin run close to and parallel with microtubuli. In contrast, no co-orientation was found between keratin and actin filaments. Co-orientation between vimentin and tubulin was also observed in an endothelial cell line, albeit to a lesser extent, but not in 3T3 fibroblasts. These data therefore suggest that microtubuli functionally interact with the vimentin network in a cell-type specific manner.

  19. Mapping local orientation of aligned fibrous scatterers for cancerous tissues using backscattering Mueller matrix imaging

    NASA Astrophysics Data System (ADS)

    He, Honghui; Sun, Minghao; Zeng, Nan; Du, E.; Liu, Shaoxiong; Guo, Yihong; Wu, Jian; He, Yonghong; Ma, Hui

    2014-10-01

    Polarization measurements are sensitive to the microstructure of tissues and can be used to detect pathological changes. Many tissues contain anisotropic fibrous structures. We obtain the local orientation of aligned fibrous scatterers using different groups of the backscattering Mueller matrix elements. Experiments on concentrically well-aligned silk fibers and unstained human papillary thyroid carcinoma tissues show that the m22, m33, m23, and m32 elements have better contrast but higher degeneracy for the extraction of orientation angles. The m12 and m13 elements show lower contrast, but allow us to determine the orientation angle for the fibrous scatterers along all directions. Moreover, Monte Carlo simulations based on the sphere-cylinder scattering model indicate that the oblique incidence of the illumination beam introduces some errors in the orientation angles obtained by both methods. Mapping the local orientation of anisotropic tissues may not only provide information on pathological changes, but can also give new leads to reduce the orientation dependence of polarization measurements.

  20. Understanding the nanoscale local buckling behavior of vertically aligned MWCNT arrays with van der Waals interactions.

    PubMed

    Li, Yupeng; Kim, Hyung-ick; Wei, Bingqing; Kang, Junmo; Choi, Jae-boong; Nam, Jae-Do; Suhr, Jonghwan

    2015-09-14

    The local buckling behavior of vertically aligned carbon nanotubes (VACNTs) has been investigated and interpreted in the view of a collective nanotube response by taking van der Waals interactions into account. To the best of our knowledge, this is the first report on the case of collective VACNT behavior regarding van der Waals force among nanotubes as a lateral support effect during the buckling process. The local buckling propagation and development of VACNTs were experimentally observed and theoretically analyzed by employing finite element modeling with lateral support from van der Waals interactions among nanotubes. Both experimental and theoretical analyses show that VACNTs buckled in the bottom region with many short waves and almost identical wavelengths, indicating a high mode buckling. Furthermore, the propagation and development mechanism of buckling waves follow the wave damping effect.

  1. Improving the Robustness of Local Network Alignment: Design and Extensive Assessment of a Markov Clustering-Based Approach.

    PubMed

    Mina, Marco; Guzzi, Pietro Hiram

    2014-01-01

    The analysis of protein behavior at the network level had been applied to elucidate the mechanisms of protein interaction that are similar in different species. Published network alignment algorithms proved to be able to recapitulate known conserved modules and protein complexes, and infer new conserved interactions confirmed by wet lab experiments. In the meantime, however, a plethora of continuously evolving protein-protein interaction (PPI) data sets have been developed, each featuring different levels of completeness and reliability. For instance, algorithms performance may vary significantly when changing the data set used in their assessment. Moreover, existing papers did not deeply investigate the robustness of alignment algorithms. For instance, some algorithms performances vary significantly when changing the data set used in their assessment. In this work, we design an extensive assessment of current algorithms discussing the robustness of the results on the basis of input networks. We also present AlignMCL, a local network alignment algorithm based on an improved model of alignment graph and Markov Clustering. AlignMCL performs better than other state-of-the-art local alignment algorithms over different updated data sets. In addition, AlignMCL features high levels of robustness, producing similar results regardless the selected data set.

  2. Understanding the nanoscale local buckling behavior of vertically aligned MWCNT arrays with van der Waals interactions

    NASA Astrophysics Data System (ADS)

    Li, Yupeng; Kim, Hyung-Ick; Wei, Bingqing; Kang, Junmo; Choi, Jae-Boong; Nam, Jae-Do; Suhr, Jonghwan

    2015-08-01

    The local buckling behavior of vertically aligned carbon nanotubes (VACNTs) has been investigated and interpreted in the view of a collective nanotube response by taking van der Waals interactions into account. To the best of our knowledge, this is the first report on the case of collective VACNT behavior regarding van der Waals force among nanotubes as a lateral support effect during the buckling process. The local buckling propagation and development of VACNTs were experimentally observed and theoretically analyzed by employing finite element modeling with lateral support from van der Waals interactions among nanotubes. Both experimental and theoretical analyses show that VACNTs buckled in the bottom region with many short waves and almost identical wavelengths, indicating a high mode buckling. Furthermore, the propagation and development mechanism of buckling waves follow the wave damping effect.The local buckling behavior of vertically aligned carbon nanotubes (VACNTs) has been investigated and interpreted in the view of a collective nanotube response by taking van der Waals interactions into account. To the best of our knowledge, this is the first report on the case of collective VACNT behavior regarding van der Waals force among nanotubes as a lateral support effect during the buckling process. The local buckling propagation and development of VACNTs were experimentally observed and theoretically analyzed by employing finite element modeling with lateral support from van der Waals interactions among nanotubes. Both experimental and theoretical analyses show that VACNTs buckled in the bottom region with many short waves and almost identical wavelengths, indicating a high mode buckling. Furthermore, the propagation and development mechanism of buckling waves follow the wave damping effect. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr03581c

  3. Alignment-free cancelable fingerprint templates based on local minutiae information.

    PubMed

    Lee, Chulhan; Choi, Jeung-Yoon; Toh, Kar-Ann; Lee, Sangyoun; Kim, Jaihie

    2007-08-01

    To replace compromised biometric templates, cancelable biometrics has recently been introduced. The concept is to transform a biometric signal or feature into a new one for enrollment and matching. For making cancelable fingerprint templates, previous approaches used either the relative position of a minutia to a core point or the absolute position of a minutia in a given fingerprint image. Thus, a query fingerprint is required to be accurately aligned to the enrolled fingerprint in order to obtain identically transformed minutiae. In this paper, we propose a new method for making cancelable fingerprint templates that do not require alignment. For each minutia, a rotation and translation invariant value is computed from the orientation information of neighboring local regions around the minutia. The invariant value is used as the input to two changing functions that output two values for the translational and rotational movements of the original minutia, respectively, in the cancelable template. When a template is compromised, it is replaced by a new one generated by different changing functions. Our approach preserves the original geometric relationships (translation and rotation) between the enrolled and query templates after they are transformed. Therefore, the transformed templates can be used to verify a person without requiring alignment of the input fingerprint images. In our experiments, we evaluated the proposed method in terms of two criteria: performance and changeability. When evaluating the performance, we examined how verification accuracy varied as the transformed templates were used for matching. When evaluating the changeability, we measured the dissimilarities between the original and transformed templates, and between two differently transformed templates, which were obtained from the same original fingerprint. The experimental results show that the two criteria mutually affect each other and can be controlled by varying the control parameters of

  4. Global classical solutions of the Vlasov-Fokker-Planck equation with local alignment forces

    NASA Astrophysics Data System (ADS)

    Choi, Young-Pil

    2016-07-01

    In this paper, we are concerned with the global well-posedness and time-asymptotic decay of the Vlasov-Fokker-Planck equation with local alignment forces. The equation can be formally derived from an agent-based model for self-organized dynamics called the Motsch-Tadmor model with noises. We present the global existence and uniqueness of classical solutions to the equation around the global Maxwellian in the whole space. For the large-time behavior, we show the algebraic decay rate of solutions towards the equilibrium under suitable assumptions on the initial data. We also remark that the rate of convergence is exponential when the spatial domain is periodic. The main methods used in this paper are the classical energy estimates combined with hyperbolic-parabolic dissipation arguments.

  5. Identification of Ligand Templates using Local Structure Alignment for Structure-based Drug Design

    PubMed Central

    Lee, Hui Sun; Im, Wonpil

    2012-01-01

    With a rapid increase in the number of high-resolution protein-ligand structures, the known protein-ligand structures can be used to gain insight into ligand-binding modes in a target protein. Based on the fact that the structurally similar binding sites share information about their ligands, we have developed a local structure alignment tool, G-LoSA (Graph-based Local Structure Alignment). In G-LoSA, the known protein-ligand binding-site structure library is searched to detect binding-site structures with similar geometry and physicochemical properties to a query binding-site structure regardless of sequence continuity and protein fold. Then, the ligands in the identified complexes are used as templates (i.e., template ligands) to predict/design a ligand for the target protein. The performance of G-LoSA is validated against 76 benchmark targets from the Astex diverse set. Using the currently available protein-ligand structure library, G-LoSA is able to identify a single template ligand (from a non-homologous protein complex) that is highly similar to the target ligand in more than half of the benchmark targets. In addition, our benchmark analyses show that an assembly of structural fragments from multiple template ligands with partial similarity to the target ligand can be used to design novel ligand structures specific to the target protein. This study clearly indicates that a template-based ligand modeling has potential for de novo ligand design and can be a complementary approach to the receptor structure based methods. PMID:22978550

  6. Localized field-aligned currents in the polar cap associated with airglow patches

    NASA Astrophysics Data System (ADS)

    Zou, Ying; Nishimura, Yukitoshi; Burchill, Johnathan K.; Knudsen, David J.; Lyons, Larry R.; Shiokawa, Kazuo; Buchert, Stephan; Chen, Steve; Nicolls, Michael J.; Ruohoniemi, J. Michael; McWilliams, Kathryn A.; Nishitani, Nozomu

    2016-10-01

    Airglow patches have been recently associated with channels of enhanced antisunward ionospheric flows propagating across the polar cap from the dayside to nightside auroral ovals. However, how these flows maintain their localized nature without diffusing away remains unsolved. We examine whether patches and collocated flows are associated with localized field-aligned currents (FACs) in the polar cap by using coordinated observations of the Swarm spacecraft, a polar cap all-sky imager, and Super Dual Auroral Radar Network (SuperDARN) radars. We commonly (66% of cases) identify substantial FAC enhancements around patches, particularly near the patches' leading edge and center, in contrast to what is seen in the otherwise quiet polar cap. These FACs have densities of 0.1-0.2 μA/m-2 and have a distribution of width peaking at 75 km. They can be approximated as infinite current sheets that are orientated roughly parallel to patches. They usually exhibit a Region 1 sense, i.e., a downward FAC lying eastward of an upward FAC. With the addition of Resolute Bay Incoherent Scatter radar data, we find that the FACs can close through Pedersen currents in the ionosphere, consistent with the locally enhanced dawn-dusk electric field across the patch. Our results suggest that ionospheric polar cap flow channels are imposed by structures in the magnetospheric lobe via FACs, and thus manifest mesoscale magnetosphere-ionosphere coupling embedded in large-scale convection.

  7. Performance evaluation of Warshall algorithm and dynamic programming for Markov chain in local sequence alignment.

    PubMed

    Khan, Mohammad Ibrahim; Kamal, Md Sarwar

    2015-03-01

    Markov Chain is very effective in prediction basically in long data set. In DNA sequencing it is always very important to find the existence of certain nucleotides based on the previous history of the data set. We imposed the Chapman Kolmogorov equation to accomplish the task of Markov Chain. Chapman Kolmogorov equation is the key to help the address the proper places of the DNA chain and this is very powerful tools in mathematics as well as in any other prediction based research. It incorporates the score of DNA sequences calculated by various techniques. Our research utilize the fundamentals of Warshall Algorithm (WA) and Dynamic Programming (DP) to measures the score of DNA segments. The outcomes of the experiment are that Warshall Algorithm is good for small DNA sequences on the other hand Dynamic Programming are good for long DNA sequences. On the top of above findings, it is very important to measure the risk factors of local sequencing during the matching of local sequence alignments whatever the length.

  8. Sheet resistance characterization of locally anisotropic transparent conductive films made of aligned metal-enriched single-walled carbon nanotubes.

    PubMed

    Kang, Hosung; Kim, Duckjong; Baik, Seunghyun

    2014-09-21

    One-dimensional conductive fillers such as single-walled carbon nanotubes (SWNTs) can be aggregated and aligned during transparent conductive film (TCF) formation by the vacuum filtration method. The potential error of analysing the average sheet resistance of these anisotropic films, using the four-point probe in-line method and the conversion formula developed assuming uniform isotropic material properties, was systematically investigated by finite element analysis and experiments. The finite element analysis of anisotropic stripe-patterned TCFs with alternating low (ρ1) and high (ρ2) resistivities revealed that the estimated average sheet resistance approached ρ1/t when the probes were parallel to the aligned nanotubes. The thickness of the film is t. It was more close to ρ2/t when the probes were perpendicular to the aligned tubes. Indeed, TCFs fabricated by the vacuum filtration method using metal-enriched SWNTs exhibited highly anisotropic local regions where tubes were aggregated and aligned. The local sheet resistances of randomly oriented, aligned, and perpendicular tube regions of the TCF at a transmittance of 89.9% were 5000, 2.4, and 12 300 Ω □(-1), respectively. Resistivities of the aggregated and aligned tube region (ρ1 = 1.2 × 10(-5) Ω cm) and the region between tubes (ρ2 = 6.2 × 10(-2) Ω cm) could be approximated with the aid of finite element analysis. This work demonstrates the potential error of characterizing the average sheet resistance of anisotropic TCFs using the four-point probe in-line method since surprisingly high or low values could be obtained depending on the measurement angle. On the other hand, a better control of aggregation and alignment of nanotubes would realize TCFs with a very small anisotropic resistivity and a high transparency.

  9. Local extracellular matrix alignment directs cellular protrusion dynamics and migration through Rac1 and FAK.

    PubMed

    Carey, Shawn P; Goldblatt, Zachary E; Martin, Karen E; Romero, Bethsabe; Williams, Rebecca M; Reinhart-King, Cynthia A

    2016-08-08

    Cell migration within 3D interstitial microenvironments is sensitive to extracellular matrix (ECM) properties, but the mechanisms that regulate migration guidance by 3D matrix features remain unclear. To examine the mechanisms underlying the cell migration response to aligned ECM, which is prevalent at the tumor-stroma interface, we utilized time-lapse microscopy to compare the behavior of MDA-MB-231 breast adenocarcinoma cells within randomly organized and well-aligned 3D collagen ECM. We developed a novel experimental system in which cellular morphodynamics during initial 3D cell spreading served as a reductionist model for the complex process of matrix-directed 3D cell migration. Using this approach, we found that ECM alignment induced spatial anisotropy of cells' matrix probing by promoting protrusion frequency, persistence, and lengthening along the alignment axis and suppressing protrusion dynamics orthogonal to alignment. Preference for on-axis behaviors was dependent upon FAK and Rac1 signaling and translated across length and time scales such that cells within aligned ECM exhibited accelerated elongation, front-rear polarization, and migration relative to cells in random ECM. Together, these findings indicate that adhesive and protrusive signaling allow cells to respond to coordinated physical cues in the ECM, promoting migration efficiency and cell migration guidance by 3D matrix structure.

  10. Foundations of statistical methods for multiple sequence alignment and structure prediction

    SciTech Connect

    Lawrence, C.

    1995-12-31

    Statistical algorithms have proven to be useful in computational molecular biology. Many statistical problems are most easily addressed by pretending that critical missing data are available. For some problems statistical inference in facilitated by creating a set of latent variables, none of whose variables are observed. A key observation is that conditional probabilities for the values of the missing data can be inferred by application of Bayes theorem to the observed data. The statistical framework described in this paper employs Boltzmann like models, permutated data likelihood, EM, and Gibbs sampler algorithms. This tutorial reviews the common statistical framework behind all of these algorithms largely in tabular or graphical terms, illustrates its application, and describes the biological underpinnings of the models used.

  11. Gleaning structural and functional information from correlations in protein multiple sequence alignments.

    PubMed

    Neuwald, Andrew F

    2016-06-01

    The availability of vast amounts of protein sequence data facilitates detection of subtle statistical correlations due to imposed structural and functional constraints. Recent breakthroughs using Direct Coupling Analysis (DCA) and related approaches have tapped into correlations believed to be due to compensatory mutations. This has yielded some remarkable results, including substantially improved prediction of protein intra- and inter-domain 3D contacts, of membrane and globular protein structures, of substrate binding sites, and of protein conformational heterogeneity. A complementary approach is Bayesian Partitioning with Pattern Selection (BPPS), which partitions related proteins into hierarchically-arranged subgroups based on correlated residue patterns. These correlated patterns are presumably due to structural and functional constraints associated with evolutionary divergence rather than to compensatory mutations. Hence joint application of DCA- and BPPS-based approaches should help sort out the structural and functional constraints contributing to sequence correlations.

  12. Interim Report on Multiple Sequence Alignments and TaqMan Signature Mapping to Phylogenetic Trees

    SciTech Connect

    Gardner, S; Jaing, C

    2012-03-27

    The goal of this project is to develop forensic genotyping assays for select agent viruses, addressing a significant capability gap for the viral bioforensics and law enforcement community. We used a multipronged approach combining bioinformatics analysis, PCR-enriched samples, microarrays and TaqMan assays to develop high resolution and cost effective genotyping methods for strain level forensic discrimination of viruses. We have leveraged substantial experience and efficiency gained through year 1 on software development, SNP discovery, TaqMan signature design and phylogenetic signature mapping to scale up the development of forensics signatures in year 2. In this report, we have summarized the Taqman signature development for South American hemorrhagic fever viruses, tick-borne encephalitis viruses and henipaviruses, Old World Arenaviruses, filoviruses, Crimean-Congo hemorrhagic fever virus, Rift Valley fever virus and Japanese encephalitis virus.

  13. Combining Multiple Pairwise Structure-based Alignments

    SciTech Connect

    2014-11-12

    CombAlign is a new Python code that generates a gapped, one-to-many, multiple structure-based sequence alignment(MSSA) given a set of pairwise structure-based alignments. In order to better define regions of similarity among related protein structures, it is useful to detect the residue-residue correspondences among a set of pairwise structure alignments. Few codes exist for constructing a one-to-many, multiple sequence alignment derived from a set of structure alignments, and we perceived a need for creating a new tool for combing pairwise structure alignments that would allow for insertion of gaps in the reference structure.

  14. HBLAST: Parallelised sequence similarity--A Hadoop MapReducable basic local alignment search tool.

    PubMed

    O'Driscoll, Aisling; Belogrudov, Vladislav; Carroll, John; Kropp, Kai; Walsh, Paul; Ghazal, Peter; Sleator, Roy D

    2015-04-01

    The recent exponential growth of genomic databases has resulted in the common task of sequence alignment becoming one of the major bottlenecks in the field of computational biology. It is typical for these large datasets and complex computations to require cost prohibitive High Performance Computing (HPC) to function. As such, parallelised solutions have been proposed but many exhibit scalability limitations and are incapable of effectively processing "Big Data" - the name attributed to datasets that are extremely large, complex and require rapid processing. The Hadoop framework, comprised of distributed storage and a parallelised programming framework known as MapReduce, is specifically designed to work with such datasets but it is not trivial to efficiently redesign and implement bioinformatics algorithms according to this paradigm. The parallelisation strategy of "divide and conquer" for alignment algorithms can be applied to both data sets and input query sequences. However, scalability is still an issue due to memory constraints or large databases, with very large database segmentation leading to additional performance decline. Herein, we present Hadoop Blast (HBlast), a parallelised BLAST algorithm that proposes a flexible method to partition both databases and input query sequences using "virtual partitioning". HBlast presents improved scalability over existing solutions and well balanced computational work load while keeping database segmentation and recompilation to a minimum. Enhanced BLAST search performance on cheap memory constrained hardware has significant implications for in field clinical diagnostic testing; enabling faster and more accurate identification of pathogenic DNA in human blood or tissue samples.

  15. An efficient algorithm for pairwise local alignment of protein interaction networks

    DOE PAGES

    Chen, Wenbin; Schmidt, Matthew; Tian, Wenhong; ...

    2015-04-01

    Recently, researchers seeking to understand, modify, and create beneficial traits in organisms have looked for evolutionarily conserved patterns of protein interactions. Their conservation likely means that the proteins of these conserved functional modules are important to the trait's expression. In this paper, we formulate the problem of identifying these conserved patterns as a graph optimization problem, and develop a fast heuristic algorithm for this problem. We compare the performance of our network alignment algorithm to that of the MaWISh algorithm [Koyuturk M, Kim Y, Topkara U, Subramaniam S, Szpankowski W, Grama A, Pairwise alignment of protein interaction networks, J Computmore » Biol 13(2): 182-199, 2006.], which bases its search algorithm on a related decision problem formulation. We find that our algorithm discovers conserved modules with a larger number of proteins in an order of magnitude less time. In conclusion, the protein sets found by our algorithm correspond to known conserved functional modules at comparable precision and recall rates as those produced by the MaWISh algorithm.« less

  16. An efficient algorithm for pairwise local alignment of protein interaction networks

    SciTech Connect

    Chen, Wenbin; Schmidt, Matthew; Tian, Wenhong; Samatova, Nagiza F.; Zhang, Shaohong

    2015-04-01

    Recently, researchers seeking to understand, modify, and create beneficial traits in organisms have looked for evolutionarily conserved patterns of protein interactions. Their conservation likely means that the proteins of these conserved functional modules are important to the trait's expression. In this paper, we formulate the problem of identifying these conserved patterns as a graph optimization problem, and develop a fast heuristic algorithm for this problem. We compare the performance of our network alignment algorithm to that of the MaWISh algorithm [Koyuturk M, Kim Y, Topkara U, Subramaniam S, Szpankowski W, Grama A, Pairwise alignment of protein interaction networks, J Comput Biol 13(2): 182-199, 2006.], which bases its search algorithm on a related decision problem formulation. We find that our algorithm discovers conserved modules with a larger number of proteins in an order of magnitude less time. In conclusion, the protein sets found by our algorithm correspond to known conserved functional modules at comparable precision and recall rates as those produced by the MaWISh algorithm.

  17. An Analysis of State and Local Alignment of Teacher Evaluation in Maryland

    ERIC Educational Resources Information Center

    Peterson, Serene N.

    2014-01-01

    This study explored the components of Maryland's newly-implemented teacher evaluation framework and compared state requirements with evaluations to three local school systems' evaluation procedures. The study sought to investigate the relationship between three evaluation protocols in comparison to the state requirements. Three local school…

  18. Local growth of vertical aligned carbon nanotubes by laserinduced surface modification of coated silicon substrates

    NASA Astrophysics Data System (ADS)

    Zimmer, K.; Böhme, R.; Ruthe, D.; Rudolph, Th; Rauschenbach, B.

    2007-04-01

    The stimulation of carbon nanotubes (CNT) growth in a thermal CVD process using an acetylene/nitrogen gas mixture by KrF-excimer laser exposure of iron nitrate coated silicon is described. At moderate laser fluences of ~1 J/cm2 the growth of nanotube bundles up to 100 μm consisting of vertical aligned multi-walled carbon nanotubes (VA-MWCNT) is observed. AFM measurements show the formation of nanoparticles in the laser-exposed areas. At this catalytic sites the nanotubes grow and sustain one another and forming the well-defined bundles. Via the laser exposure the control of the catalytic sites formation and consequently the nanotube growth and properties can be achieved.

  19. Global and local aspects of the surface potential landscape for energy level alignment at organic-ZnO interfaces

    NASA Astrophysics Data System (ADS)

    Stähler, Julia; Rinke, Patrick

    2017-03-01

    Hybrid systems of organic and inorganic semiconductors are a promising route for the development of novel opto-electronic and light-harvesting devices. A key ingredient for achieving a superior functionality by means of a hybrid system is the right relative position of energy levels at the interfaces of the two material classes. In this Perspective, we address the sensitivity of the potential energy landscape at various ZnO surfaces, a key ingredient for interfacial energy level alignment, by combining one- and two-photon photoelectron spectroscopy with density-functional theory calculations (DFT). We show that even very large work function changes (>2.5 eV) do not necessarily have to be accompanied by surface band bending in ZnO. Band bending - if it does occur - may be localized to few Å or extend over hundreds of nanometers with very different results for the surface work function and energy level alignment. Managing the delicate balance of different interface manipulation mechanisms in organic-inorganic hybrid systems will be a major challenge towards future applications.

  20. Robust Eye Center Localization through Face Alignment and Invariant Isocentric Patterns

    PubMed Central

    Teng, Dongdong; Chen, Dihu; Tan, Hongzhou

    2015-01-01

    The localization of eye centers is a very useful cue for numerous applications like face recognition, facial expression recognition, and the early screening of neurological pathologies. Several methods relying on available light for accurate eye-center localization have been exploited. However, despite the considerable improvements that eye-center localization systems have undergone in recent years, only few of these developments deal with the challenges posed by the profile (non-frontal face). In this paper, we first use the explicit shape regression method to obtain the rough location of the eye centers. Because this method extracts global information from the human face, it is robust against any changes in the eye region. We exploit this robustness and utilize it as a constraint. To locate the eye centers accurately, we employ isophote curvature features, the accuracy of which has been demonstrated in a previous study. By applying these features, we obtain a series of eye-center locations which are candidates for the actual position of the eye-center. Among these locations, the estimated locations which minimize the reconstruction error between the two methods mentioned above are taken as the closest approximation for the eye centers locations. Therefore, we combine explicit shape regression and isophote curvature feature analysis to achieve robustness and accuracy, respectively. In practical experiments, we use BioID and FERET datasets to test our approach to obtaining an accurate eye-center location while retaining robustness against changes in scale and pose. In addition, we apply our method to non-frontal faces to test its robustness and accuracy, which are essential in gaze estimation but have seldom been mentioned in previous works. Through extensive experimentation, we show that the proposed method can achieve a significant improvement in accuracy and robustness over state-of-the-art techniques, with our method ranking second in terms of accuracy

  1. Robust Eye Center Localization through Face Alignment and Invariant Isocentric Patterns.

    PubMed

    Pang, Zhiyong; Wei, Chuansheng; Teng, Dongdong; Chen, Dihu; Tan, Hongzhou

    2015-01-01

    The localization of eye centers is a very useful cue for numerous applications like face recognition, facial expression recognition, and the early screening of neurological pathologies. Several methods relying on available light for accurate eye-center localization have been exploited. However, despite the considerable improvements that eye-center localization systems have undergone in recent years, only few of these developments deal with the challenges posed by the profile (non-frontal face). In this paper, we first use the explicit shape regression method to obtain the rough location of the eye centers. Because this method extracts global information from the human face, it is robust against any changes in the eye region. We exploit this robustness and utilize it as a constraint. To locate the eye centers accurately, we employ isophote curvature features, the accuracy of which has been demonstrated in a previous study. By applying these features, we obtain a series of eye-center locations which are candidates for the actual position of the eye-center. Among these locations, the estimated locations which minimize the reconstruction error between the two methods mentioned above are taken as the closest approximation for the eye centers locations. Therefore, we combine explicit shape regression and isophote curvature feature analysis to achieve robustness and accuracy, respectively. In practical experiments, we use BioID and FERET datasets to test our approach to obtaining an accurate eye-center location while retaining robustness against changes in scale and pose. In addition, we apply our method to non-frontal faces to test its robustness and accuracy, which are essential in gaze estimation but have seldom been mentioned in previous works. Through extensive experimentation, we show that the proposed method can achieve a significant improvement in accuracy and robustness over state-of-the-art techniques, with our method ranking second in terms of accuracy

  2. A novel method of aligning molecules by local surface shape similarity.

    PubMed

    Cosgrove, D A; Bayada, D M; Johnson, A P

    2000-08-01

    A novel shape-based method has been developed for overlaying a series of molecule surfaces into a common reference frame. The surfaces are represented by a set of circular patches of approximately constant curvature. Two molecules are overlaid using a clique-detection algorithm to find a set of patches in the two surfaces that correspond, and overlaying the molecules so that the similar patches on the two surfaces are coincident. The method is thus able to detect areas of local, rather than global, similarity. A consensus overlay for a group of molecules is performed by examining the scores of all pairwise overlays and performing a set of overlays with the highest scores. The utility of the method has been examined by comparing the overlaid and experimental configurations of 4 sets of molecules for which there are X-ray crystal structures of the molecules bound to a protein active site. Results for the overlays are generally encouraging. Of particular note is the correct prediction of the 'reverse orientation' for ligands binding to human rhinovirus coat protein HRV14.

  3. A novel method of aligning molecules by local surface shape similarity

    NASA Astrophysics Data System (ADS)

    Cosgrove, D. A.; Bayada, D. M.; Johnson, A. P.

    2000-08-01

    A novel shape-based method has been developed for overlaying a series of molecule surfaces into a common reference frame. The surfaces are represented by a set of circular patches of approximately constant curvature. Two molecules are overlaid using a clique-detection algorithm to find a set of patches in the two surfaces that correspond, and overlaying the molecules so that the similar patches on the two surfaces are coincident. The method is thus able to detect areas of local, rather than global, similarity. A consensus overlay for a group of molecules is performed by examining the scores of all pairwise overlays and performing a set of overlays with the highest scores. The utility of the method has been examined by comparing the overlaid and experimental configurations of 4 sets of molecules for which there are X-ray crystal structures of the molecules bound to a protein active site. Results for the overlays are generally encouraging. Of particular note is the correct prediction of the `reverse orientation' for ligands binding to human rhinovirus coat protein HRV14.

  4. Reconstructing DNA copy number by joint segmentation of multiple sequences

    PubMed Central

    2012-01-01

    Background Variations in DNA copy number carry information on the modalities of genome evolution and mis-regulation of DNA replication in cancer cells. Their study can help localize tumor suppressor genes, distinguish different populations of cancerous cells, and identify genomic variations responsible for disease phenotypes. A number of different high throughput technologies can be used to identify copy number variable sites, and the literature documents multiple effective algorithms. We focus here on the specific problem of detecting regions where variation in copy number is relatively common in the sample at hand. This problem encompasses the cases of copy number polymorphisms, related samples, technical replicates, and cancerous sub-populations from the same individual. Results We present a segmentation method named generalized fused lasso (GFL) to reconstruct copy number variant regions. GFL is based on penalized estimation and is capable of processing multiple signals jointly. Our approach is computationally very attractive and leads to sensitivity and specificity levels comparable to those of state-of-the-art specialized methodologies. We illustrate its applicability with simulated and real data sets. Conclusions The flexibility of our framework makes it applicable to data obtained with a wide range of technology. Its versatility and speed make GFL particularly useful in the initial screening stages of large data sets. PMID:22897923

  5. FASMA: a service to format and analyze sequences in multiple alignments.

    PubMed

    Costantini, Susan; Colonna, Giovanni; Facchiano, Angelo M

    2007-12-01

    Multiple sequence alignments are successfully applied in many studies for under- standing the structural and functional relations among single nucleic acids and protein sequences as well as whole families. Because of the rapid growth of sequence databases, multiple sequence alignments can often be very large and difficult to visualize and analyze. We offer a new service aimed to visualize and analyze the multiple alignments obtained with different external algorithms, with new features useful for the comparison of the aligned sequences as well as for the creation of a final image of the alignment. The service is named FASMA and is available at http://bioinformatica.isa.cnr.it/FASMA/.

  6. Mango: multiple alignment with N gapped oligos.

    PubMed

    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.

  7. Evaluation of global sequence comparison and one-to-one FASTA local alignment in regulatory allergenicity assessment of transgenic proteins in food crops.

    PubMed

    Song, Ping; Herman, Rod A; Kumpatla, Siva

    2014-09-01

    To address the high false positive rate using >35% identity over 80 amino acids in the regulatory assessment of transgenic proteins for potential allergenicity and the change of E-value with database size, the Needleman-Wunsch global sequence alignment and a one-to-one (1:1) local FASTA search (one protein in the target database at a time) using FASTA were evaluated by comparing proteins randomly selected from Arabidopsis, rice, corn, and soybean with known allergens in a peer-reviewed allergen database (http://www.allergenonline.org/). Compared with the approach of searching >35%/80aa+, the false positive rate measured by specificity rate for identification of true allergens was reduced by a 1:1 global sequence alignment with a cut-off threshold of ≧30% identity and a 1:1 FASTA local alignment with a cut-off E-value of ≦1.0E-09 while maintaining the same sensitivity. Hence, a 1:1 sequence comparison, especially using the FASTA local alignment tool with a biological relevant E-value of 1.0E-09 as a threshold, is recommended for the regulatory assessment of sequence identities between transgenic proteins in food crops and known allergens.

  8. ALIGN_MTX--an optimal pairwise textual sequence alignment program, adapted for using in sequence-structure alignment.

    PubMed

    Vishnepolsky, Boris; Pirtskhalava, Malak

    2009-06-01

    The presented program ALIGN_MTX makes alignment of two textual sequences with an opportunity to use any several characters for the designation of sequence elements and arbitrary user substitution matrices. It can be used not only for the alignment of amino acid and nucleotide sequences but also for sequence-structure alignment used in threading, amino acid sequence alignment, using preliminary known PSSM matrix, and in other cases when alignment of biological or non-biological textual sequences is required. This distinguishes it from the majority of similar alignment programs that make, as a rule, alignment only of amino acid or nucleotide sequences represented as a sequence of single alphabetic characters. ALIGN_MTX is presented as downloadable zip archive at http://www.imbbp.org/software/ALIGN_MTX/ and available for free use. As application of using the program, the results of comparison of different types of substitution matrix for alignment quality in distantly related protein pair sets were presented. Threading matrix SORDIS, based on side-chain orientation in relation to hydrophobic core centers with evolutionary change-based substitution matrix BLOSUM and using multiple sequence alignment information position-specific score matrices (PSSM) were taken for test alignment accuracy. The best performance shows PSSM matrix, but in the reduced set with lower sequence similarity threading matrix SORDIS shows the same performance and it was shown that combined potential with SORDIS and PSSM can improve alignment quality in evolutionary distantly related protein pairs.

  9. SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments

    PubMed Central

    Jessen, Leon Eyrich; Hoof, Ilka; Lund, Ole; Nielsen, Morten

    2013-01-01

    Identifying which mutation(s) within a given genotype is responsible for an observable phenotype is important in many aspects of molecular biology. Here, we present SigniSite, an online application for subgroup-free residue-level genotype–phenotype correlation. In contrast to similar methods, SigniSite does not require any pre-definition of subgroups or binary classification. Input is a set of protein sequences where each sequence has an associated real number, quantifying a given phenotype. SigniSite will then identify which amino acid residues are significantly associated with the data set phenotype. As output, SigniSite displays a sequence logo, depicting the strength of the phenotype association of each residue and a heat-map identifying ‘hot’ or ‘cold’ regions. SigniSite was benchmarked against SPEER, a state-of-the-art method for the prediction of specificity determining positions (SDP) using a set of human immunodeficiency virus protease-inhibitor genotype–phenotype data and corresponding resistance mutation scores from the Stanford University HIV Drug Resistance Database, and a data set of protein families with experimentally annotated SDPs. For both data sets, SigniSite was found to outperform SPEER. SigniSite is available at: http://www.cbs.dtu.dk/services/SigniSite/. PMID:23761454

  10. Multiple protein structure alignment.

    PubMed Central

    Taylor, W. R.; Flores, T. P.; Orengo, C. A.

    1994-01-01

    A method was developed to compare protein structures and to combine them into a multiple structure consensus. Previous methods of multiple structure comparison have only concatenated pairwise alignments or produced a consensus structure by averaging coordinate sets. The current method is a fusion of the fast structure comparison program SSAP and the multiple sequence alignment program MULTAL. As in MULTAL, structures are progressively combined, producing intermediate consensus structures that are compared directly to each other and all remaining single structures. This leads to a hierarchic "condensation," continually evaluated in the light of the emerging conserved core regions. Following the SSAP approach, all interatomic vectors were retained with well-conserved regions distinguished by coherent vector bundles (the structural equivalent of a conserved sequence position). Each bundle of vectors is summarized by a resultant, whereas vector coherence is captured in an error term, which is the only distinction between conserved and variable positions. Resultant vectors are used directly in the comparison, which is weighted by their error values, giving greater importance to the matching of conserved positions. The resultant vectors and their errors can also be used directly in molecular modeling. Applications of the method were assessed by the quality of the resulting sequence alignments, phylogenetic tree construction, and databank scanning with the consensus. Visual assessment of the structural superpositions and consensus structure for various well-characterized families confirmed that the consensus had identified a reasonable core. PMID:7849601

  11. Local photoelectric conversion properties of titanyl-phthalocyanine (TiOPc) coated aligned ZnO nanorods.

    PubMed

    Heng, Liping; Tian, Dongliang; Chen, Long; Su, Junxin; Zhai, Jin; Han, Dong; Jiang, Lei

    2010-02-21

    The direct electrical pathway for rapid collection of charge carriers generated in aligned TiOPc/ZnO nanorod is visualized by using photoconductive atomic force microscopy (pc-AFM), which can provide theoretical guidance for preparing high efficiency solar cells.

  12. Imaging Analysis of Collagen Fiber Networks in Cusps of Porcine Aortic Valves: Effect of their Local Distribution and Alignment on Valve Functionality

    PubMed Central

    Mega, Mor; Marom, Gil; Halevi, Rotem; Hamdan, Ashraf; Bluestein, Danny; Haj-Ali, Rami

    2015-01-01

    The cusps of native Aortic Valve (AV) are composed of collagen bundles embedded in soft tissue, creating a heterogenic tissue with asymmetric alignment in each cusp. This study compares native collagen fiber networks (CFNs) with a goal to better understand their influence on stress distribution and valve kinematics. Images of CFNs from five porcine tricuspid AVs are analyzed and fluid-structure interaction models are generated based on them. Although the valves had similar overall kinematics, the CFNs had distinctive influence on local mechanics. The regions with dilute CFN are more prone to damage since they are subjected to higher stress magnitudes. PMID:26406926

  13. webPRC: the Profile Comparer for alignment-based searching of public domain databases.

    PubMed

    Brandt, Bernd W; Heringa, Jaap

    2009-07-01

    Profile-profile methods are well suited to detect remote evolutionary relationships between protein families. Profile Comparer (PRC) is an existing stand-alone program for scoring and aligning hidden Markov models (HMMs), which are based on multiple sequence alignments. Since PRC compares profile HMMs instead of sequences, it can be used to find distant homologues. For this purpose, PRC is used by, for example, the CATH and Pfam-domain databases. As PRC is a profile comparer, it only reports profile HMM alignments and does not produce multiple sequence alignments. We have developed webPRC server, which makes it straightforward to search for distant homologues or similar alignments in a number of domain databases. In addition, it provides the results both as multiple sequence alignments and aligned HMMs. Furthermore, the user can view the domain annotation, evaluate the PRC hits with the Jalview multiple alignment editor and generate logos from the aligned HMMs or the aligned multiple alignments. Thus, this server assists in detecting distant homologues with PRC as well as in evaluating and using the results. The webPRC interface is available at http://www.ibi.vu.nl/programs/prcwww/.

  14. DNAAlignEditor: DNA alignment editor tool

    PubMed Central

    Sanchez-Villeda, Hector; Schroeder, Steven; Flint-Garcia, Sherry; Guill, Katherine E; Yamasaki, Masanori; McMullen, Michael D

    2008-01-01

    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. PMID:18366684

  15. Multiple Whole Genome Alignments Without a Reference Organism

    SciTech Connect

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

    2009-01-16

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

  16. Multiple whole-genome alignments without a reference organism.

    PubMed

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

    2009-04-01

    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 six Drosophila 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.

  17. Alignment validation

    SciTech Connect

    ALICE; ATLAS; CMS; LHCb; Golling, Tobias

    2008-09-06

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

  18. Applying Agrep to r-NSA to solve multiple sequences approximate matching.

    PubMed

    Ni, Bing; Wong, Man-Hon; Lam, Chi-Fai David; Leung, Kwong-Sak

    2014-01-01

    This paper addresses the approximate matching problem in a database consisting of multiple DNA sequences, where the proposed approach applies Agrep to a new truncated suffix array, r-NSA. The construction time of the structure is linear to the database size, and the computations of indexing a substring in the structure are constant. The number of characters processed in applying Agrep is analysed theoretically, and the theoretical upper-bound can approximate closely the empirical number of characters, which is obtained through enumerating the characters in the actual structure built. Experiments are carried out using (synthetic) random DNA sequences, as well as (real) genome sequences including Hepatitis-B Virus and X-chromosome. Experimental results show that, compared to the straight-forward approach that applies Agrep to multiple sequences individually, the proposed approach solves the matching problem in much shorter time. The speed-up of our approach depends on the sequence patterns, and for highly similar homologous genome sequences, which are the common cases in real-life genomes, it can be up to several orders of magnitude.

  19. An introduction to the Lagan alignment toolkit.

    PubMed

    Brudno, Michael

    2007-01-01

    The Lagan Toolkit is a software package for comparison of genomic sequences. It includes the CHAOS local alignment program, LAGAN global alignment program for two, or more sequences and Shuffle-LAGAN, a "glocal" alignment method that handles genomic rearrangements in a global alignment framework. The alignment programs included in the Lagan Toolkit have been widely used to compare genomes of many organisms, from bacteria to large mammalian genomes. This chapter provides an overview of the algorithms used by the LAGAN programs to construct genomic alignments, explains how to build alignments using either the standalone program or the web server, and discusses some of the common pitfalls users encounter when using the toolkit.

  20. Insight into strain effects on band alignment shifts, carrier localization and recombination kinetics in CdTe/CdS core/shell quantum dots.

    PubMed

    Jing, Lihong; Kershaw, Stephen V; Kipp, Tobias; Kalytchuk, Sergii; Ding, Ke; Zeng, Jianfeng; Jiao, Mingxia; Sun, Xiaoyu; Mews, Alf; Rogach, Andrey L; Gao, Mingyuan

    2015-02-11

    The impact of strain on the optical properties of semiconductor quantum dots (QDs) is fundamentally important while still awaiting detailed investigation. CdTe/CdS core/shell QDs represent a typical strained system due to the substantial lattice mismatch between CdTe and CdS. To probe the strain-related effects, aqueous CdTe/CdS QDs were synthesized by coating different sized CdTe QD cores with CdS shells upon the thermal decomposition of glutathione as a sulfur source under reflux. The shell growth was carefully monitored by both steady-state absorption and fluorescence spectroscopy and transient fluorescence spectroscopy. In combination with structural analysis, the band alignments as a consequence of the strain were modified based on band deformation potential theory. By further taking account of these strain-induced band shifts, the effective mass approximation (EMA) model was modified to simulate the electronic structure, carrier spatial localization, and electron-hole wave function overlap for comparing with experimentally derived results. In particular, the electron/hole eigen energies were predicted for a range of structures with different CdTe core sizes and different CdS shell thicknesses. The overlap of electron and hole wave functions was further simulated to reveal the impact of strain on the electron-hole recombination kinetics as the electron wave function progressively shifts into the CdS shell region while the hole wave function remains heavily localized in CdTe core upon the shell growth. The excellent agreement between the strain-modified EMA model with the experimental data suggests that strain exhibits remarkable effects on the optical properties of mismatched core/shell QDs by altering the electronic structure of the system.

  1. Nova laser alignment control system

    SciTech Connect

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

    1984-03-29

    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.

  2. Field-aligned currents in Saturn's magnetosphere: Local time dependence of southern summer currents in the dawn sector between midnight and noon

    NASA Astrophysics Data System (ADS)

    Hunt, G. J.; Cowley, S. W. H.; Provan, G.; Bunce, E. J.; Alexeev, I. I.; Belenkaya, E. S.; Kalegaev, V. V.; Dougherty, M. K.; Coates, A. J.

    2016-08-01

    We examine and compare the magnetic field perturbations associated with field-aligned ionosphere-magnetosphere coupling currents at Saturn, observed by the Cassini spacecraft during two sequences of highly inclined orbits in 2006/2007 and 2008 under late southern summer conditions. These sequences explore the southern currents in the dawn-noon and midnight sectors, respectively, thus allowing investigation of possible origins of the local time (LT) asymmetry in auroral Saturn kilometric radiation (SKR) emissions, which peak in power at ~8 h LT in the dawn-noon sector. We first show that the dawn-noon field data generally have the same four-sheet current structure as found previously in the midnight data and that both are similarly modulated by "planetary period oscillation" (PPO) currents. We then separate the averaged PPO-independent (e.g., subcorotation) and PPO-related currents for both LT sectors by using the current system symmetry properties. Surprisingly, we find that the PPO-independent currents are essentially identical within uncertainties in the dawn-dusk and midnight sectors, thus providing no explanation for the LT dependence of the SKR emissions. The main PPO-related currents are, however, found to be slightly stronger and narrower in latitudinal width at dawn-noon than at midnight, leading to estimated precipitating electron powers, and hence emissions, that are on average a factor of ~1.3 larger at dawn-noon than at midnight, inadequate to account for the observed LT asymmetry in SKR power by a factor of ~2.7. Some other factors must also be involved, such as a LT asymmetry in the hot magnetospheric auroral source electron population.

  3. Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments

    PubMed Central

    2010-01-01

    Background While the pairwise alignments produced by sequence similarity searches are a powerful tool for identifying homologous proteins - proteins that share a common ancestor and a similar structure; pairwise sequence alignments often fail to represent accurately the structural alignments inferred from three-dimensional coordinates. Since sequence alignment algorithms produce optimal alignments, the best structural alignments must reflect suboptimal sequence alignment scores. Thus, we have examined a range of suboptimal sequence alignments and a range of scoring parameters to understand better which sequence alignments are likely to be more structurally accurate. Results We compared near-optimal protein sequence alignments produced by the Zuker algorithm and a set of probabilistic alignments produced by the probA program with structural alignments produced by four different structure alignment algorithms. There is significant overlap between the solution spaces of structural alignments and both the near-optimal sequence alignments produced by commonly used scoring parameters for sequences that share significant sequence similarity (E-values < 10-5) and the ensemble of probA alignments. We constructed a logistic regression model incorporating three input variables derived from sets of near-optimal alignments: robustness, edge frequency, and maximum bits-per-position. A ROC analysis shows that this model more accurately classifies amino acid pairs (edges in the alignment path graph) according to the likelihood of appearance in structural alignments than the robustness score alone. We investigated various trimming protocols for removing incorrect edges from the optimal sequence alignment; the most effective protocol is to remove matches from the semi-global optimal alignment that are outside the boundaries of the local alignment, although trimming according to the model-generated probabilities achieves a similar level of improvement. The model can also be used to

  4. ALIGNING JIG

    DOEpatents

    Culver, J.S.; Tunnell, W.C.

    1958-08-01

    A jig or device is described for setting or aligning an opening in one member relative to another member or structure, with a predetermined offset, or it may be used for measuring the amount of offset with which the parts have previously been sct. This jig comprises two blocks rabbeted to each other, with means for securing thc upper block to the lower block. The upper block has fingers for contacting one of the members to be a1igmed, the lower block is designed to ride in grooves within the reference member, and calibration marks are provided to determine the amount of offset. This jig is specially designed to align the collimating slits of a mass spectrometer.

  5. Image alignment

    DOEpatents

    Dowell, Larry Jonathan

    2014-04-22

    Disclosed is a method and device for aligning at least two digital images. An embodiment may use frequency-domain transforms of small tiles created from each image to identify substantially similar, "distinguishing" features within each of the images, and then align the images together based on the location of the distinguishing features. To accomplish this, an embodiment may create equal sized tile sub-images for each image. A "key" for each tile may be created by performing a frequency-domain transform calculation on each tile. A information-distance difference between each possible pair of tiles on each image may be calculated to identify distinguishing features. From analysis of the information-distance differences of the pairs of tiles, a subset of tiles with high discrimination metrics in relation to other tiles may be located for each image. The subset of distinguishing tiles for each image may then be compared to locate tiles with substantially similar keys and/or information-distance metrics to other tiles of other images. Once similar tiles are located for each image, the images may be aligned in relation to the identified similar tiles.

  6. Erasing Errors due to Alignment Ambiguity When Estimating Positive Selection

    PubMed Central

    Redelings, Benjamin

    2014-01-01

    Current estimates of diversifying positive selection rely on first having an accurate multiple sequence alignment. Simulation studies have shown that under biologically plausible conditions, relying on a single estimate of the alignment from commonly used alignment software can lead to unacceptably high false-positive rates in detecting diversifying positive selection. We present a novel statistical method that eliminates excess false positives resulting from alignment error by jointly estimating the degree of positive selection and the alignment under an evolutionary model. Our model treats both substitutions and insertions/deletions as sequence changes on a tree and allows site heterogeneity in the substitution process. We conduct inference starting from unaligned sequence data by integrating over all alignments. This approach naturally accounts for ambiguous alignments without requiring ambiguously aligned sites to be identified and removed prior to analysis. We take a Bayesian approach and conduct inference using Markov chain Monte Carlo to integrate over all alignments on a fixed evolutionary tree topology. We introduce a Bayesian version of the branch-site test and assess the evidence for positive selection using Bayes factors. We compare two models of differing dimensionality using a simple alternative to reversible-jump methods. We also describe a more accurate method of estimating the Bayes factor using Rao-Blackwellization. We then show using simulated data that jointly estimating the alignment and the presence of positive selection solves the problem with excessive false positives from erroneous alignments and has nearly the same power to detect positive selection as when the true alignment is known. We also show that samples taken from the posterior alignment distribution using the software BAli-Phy have substantially lower alignment error compared with MUSCLE, MAFFT, PRANK, and FSA alignments. PMID:24866534

  7. A simple and fast approach to prediction of protein secondary structure from multiply aligned sequences with accuracy above 70%.

    PubMed Central

    Mehta, P. K.; Heringa, J.; Argos, P.

    1995-01-01

    To improve secondary structure predictions in protein sequences, the information residing in multiple sequence alignments of substituted but structurally related proteins is exploited. A database comprised of 70 protein families and a total of 2,500 sequences, some of which were aligned by tertiary structural superpositions, was used to calculate residue exchange weight matrices within alpha-helical, beta-strand, and coil substructures, respectively. Secondary structure predictions were made based on the observed residue substitutions in local regions of the multiple alignments and the largest possible associated exchange weights in each of the three matrix types. Comparison of the observed and predicted secondary structure on a per-residue basis yielded a mean accuracy of 72.2%. Individual alpha-helix, beta-strand, and coil states were respectively predicted at 66.7, and 75.8% correctness, representing a well-balanced three-state prediction. The accuracy level, verified by cross-validation through jack-knife tests on all protein families, dropped, on average, to only 70.9%, indicating the rigor of the prediction procedure. On the basis of robustness, conceptual clarity, accuracy, and executable efficiency, the method has considerable advantage, especially with its sole reliance on amino acid substitutions within structurally related proteins. PMID:8580842

  8. SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments

    PubMed Central

    Di Tommaso, Paolo; Bussotti, Giovanni; Kemena, Carsten; Capriotti, Emidio; Chatzou, Maria; Prieto, Pablo; Notredame, Cedric

    2014-01-01

    This article introduces the SARA-Coffee web server; a service allowing the online computation of 3D structure based multiple RNA sequence alignments. The server makes it possible to combine sequences with and without known 3D structures. Given a set of sequences SARA-Coffee outputs a multiple sequence alignment along with a reliability index for every sequence, column and aligned residue. SARA-Coffee combines SARA, a pairwise structural RNA aligner with the R-Coffee multiple RNA aligner in a way that has been shown to improve alignment accuracy over most sequence aligners when enough structural data is available. The server can be accessed from http://tcoffee.crg.cat/apps/tcoffee/do:saracoffee. PMID:24972831

  9. Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees

    PubMed Central

    2010-01-01

    Background Methods of alignment masking, which refers to the technique of excluding alignment blocks prior to tree reconstructions, have been successful in improving the signal-to-noise ratio in sequence alignments. However, the lack of formally well defined methods to identify randomness in sequence alignments has prevented a routine application of alignment masking. In this study, we compared the effects on tree reconstructions of the most commonly used profiling method (GBLOCKS) which uses a predefined set of rules in combination with alignment masking, with a new profiling approach (ALISCORE) based on Monte Carlo resampling within a sliding window, using different data sets and alignment methods. While the GBLOCKS approach excludes variable sections above a certain threshold which choice is left arbitrary, the ALISCORE algorithm is free of a priori rating of parameter space and therefore more objective. Results ALISCORE was successfully extended to amino acids using a proportional model and empirical substitution matrices to score randomness in multiple sequence alignments. A complex bootstrap resampling leads to an even distribution of scores of randomly similar sequences to assess randomness of the observed sequence similarity. Testing performance on real data, both masking methods, GBLOCKS and ALISCORE, helped to improve tree resolution. The sliding window approach was less sensitive to different alignments of identical data sets and performed equally well on all data sets. Concurrently, ALISCORE is capable of dealing with different substitution patterns and heterogeneous base composition. ALISCORE and the most relaxed GBLOCKS gap parameter setting performed best on all data sets. Correspondingly, Neighbor-Net analyses showed the most decrease in conflict. Conclusions Alignment masking improves signal-to-noise ratio in multiple sequence alignments prior to phylogenetic reconstruction. Given the robust performance of alignment profiling, alignment masking

  10. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

    PubMed Central

    Capella-Gutiérrez, Salvador; Silla-Martínez, José M.; Gabaldón, Toni

    2009-01-01

    Summary: Multiple sequence alignments are central to many areas of bioinformatics. It has been shown that the removal of poorly aligned regions from an alignment increases the quality of subsequent analyses. Such an alignment trimming phase is complicated in large-scale phylogenetic analyses that deal with thousands of alignments. Here, we present trimAl, a tool for automated alignment trimming, which is especially suited for large-scale phylogenetic analyses. trimAl can consider several parameters, alone or in multiple combinations, for selecting the most reliable positions in the alignment. These include the proportion of sequences with a gap, the level of amino acid similarity and, if several alignments for the same set of sequences are provided, the level of consistency across different alignments. Moreover, trimAl can automatically select the parameters to be used in each specific alignment so that the signal-to-noise ratio is optimized. Availability: trimAl has been written in C++, it is portable to all platforms. trimAl is freely available for download (http://trimal.cgenomics.org) and can be used online through the Phylemon web server (http://phylemon2.bioinfo.cipf.es/). Supplementary Material is available at http://trimal.cgenomics.org/publications. Contact: tgabaldon@crg.es PMID:19505945

  11. De novo genome assembly of the economically important weed horseweed using integrated data from multiple sequencing platforms.

    PubMed

    Peng, Yanhui; Lai, Zhao; Lane, Thomas; Nageswara-Rao, Madhugiri; Okada, Miki; Jasieniuk, Marie; O'Geen, Henriette; Kim, Ryan W; Sammons, R Douglas; Rieseberg, Loren H; Stewart, C Neal

    2014-11-01

    Horseweed (Conyza canadensis), a member of the Compositae (Asteraceae) family, was the first broadleaf weed to evolve resistance to glyphosate. Horseweed, one of the most problematic weeds in the world, is a true diploid (2n = 2x = 18), with the smallest genome of any known agricultural weed (335 Mb). Thus, it is an appropriate candidate to help us understand the genetic and genomic bases of weediness. We undertook a draft de novo genome assembly of horseweed by combining data from multiple sequencing platforms (454 GS-FLX, Illumina HiSeq 2000, and PacBio RS) using various libraries with different insertion sizes (approximately 350 bp, 600 bp, 3 kb, and 10 kb) of a Tennessee-accessed, glyphosate-resistant horseweed biotype. From 116.3 Gb (approximately 350× coverage) of data, the genome was assembled into 13,966 scaffolds with 50% of the assembly = 33,561 bp. The assembly covered 92.3% of the genome, including the complete chloroplast genome (approximately 153 kb) and a nearly complete mitochondrial genome (approximately 450 kb in 120 scaffolds). The nuclear genome is composed of 44,592 protein-coding genes. Genome resequencing of seven additional horseweed biotypes was performed. These sequence data were assembled and used to analyze genome variation. Simple sequence repeat and single-nucleotide polymorphisms were surveyed. Genomic patterns were detected that associated with glyphosate-resistant or -susceptible biotypes. The draft genome will be useful to better understand weediness and the evolution of herbicide resistance and to devise new management strategies. The genome will also be useful as another reference genome in the Compositae. To our knowledge, this article represents the first published draft genome of an agricultural weed.

  12. MP-Align: alignment of metabolic pathways

    PubMed Central

    2014-01-01

    Background Comparing the metabolic pathways of different species is useful for understanding metabolic functions and can help in studying diseases and engineering drugs. Several comparison techniques for metabolic pathways have been introduced in the literature as a first attempt in this direction. The approaches are based on some simplified representation of metabolic pathways and on a related definition of a similarity score (or distance measure) between two pathways. More recent comparative research focuses on alignment techniques that can identify similar parts between pathways. Results We propose a methodology for the pairwise comparison and alignment of metabolic pathways that aims at providing the largest conserved substructure of the pathways under consideration. The proposed methodology has been implemented in a tool called MP-Align, which has been used to perform several validation tests. The results showed that our similarity score makes it possible to discriminate between different domains and to reconstruct a meaningful phylogeny from metabolic data. The results further demonstrate that our alignment algorithm correctly identifies subpathways sharing a common biological function. Conclusion The results of the validation tests performed with MP-Align are encouraging. A comparison with another proposal in the literature showed that our alignment algorithm is particularly well-suited to finding the largest conserved subpathway of the pathways under examination. PMID:24886436

  13. Girder Alignment Plan

    SciTech Connect

    Wolf, Zackary; Ruland, Robert; LeCocq, Catherine; Lundahl, Eric; Levashov, Yurii; Reese, Ed; Rago, Carl; Poling, Ben; Schafer, Donald; Nuhn, Heinz-Dieter; Wienands, Uli; /SLAC

    2010-11-18

    The girders for the LCLS undulator system contain components which must be aligned with high accuracy relative to each other. The alignment is one of the last steps before the girders go into the tunnel, so the alignment must be done efficiently, on a tight schedule. This note documents the alignment plan which includes efficiency and high accuracy. The motivation for girder alignment involves the following considerations. Using beam based alignment, the girder position will be adjusted until the beam goes through the center of the quadrupole and beam finder wire. For the machine to work properly, the undulator axis must be on this line and the center of the undulator beam pipe must be on this line. The physics reasons for the undulator axis and undulator beam pipe axis to be centered on the beam are different, but the alignment tolerance for both are similar. In addition, the beam position monitor must be centered on the beam to preserve its calibration. Thus, the undulator, undulator beam pipe, quadrupole, beam finder wire, and beam position monitor axes must all be aligned to a common line. All relative alignments are equally important, not just, for example, between quadrupole and undulator. We begin by making the common axis the nominal beam axis in the girder coordinate system. All components will be initially aligned to this axis. A more accurate alignment will then position the components relative to each other, without incorporating the girder itself.

  14. Tidal alignment of galaxies

    SciTech Connect

    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.

  15. Tidal alignment of galaxies

    SciTech Connect

    Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš E-mail: zvlah@stanford.edu

    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.

  16. The GEM Detector projective alignment simulation system

    SciTech Connect

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

    1993-07-09

    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.

  17. Differential Heating of Magnetically Aligned Dust Grains

    NASA Astrophysics Data System (ADS)

    Vaillancourt, John E.; Andersson, B.

    2013-01-01

    We use far-infrared photometric maps from IRAS and Herschel to search for the differential heating of asymmetric dust grains aligned with respect to an interstellar magnetic field and heated by a localized radiation source. The grains are known to be asymmetric and have a net alignment of their axes from observations of background starlight polarization. Modern theories on grain alignment suggest that photons from stars embedded in the foreground cloud are a key ingredient of the physical mechanism responsible for alignment (i.e., radiative torques). This theory predicts a relation between the grain alignment efficiency and the angle between the magnetic field and the direction to the aligning radiation source. This effect has been tentatively observed in a source with a very simple geometry (Andersson et al. 2011): the aligning photons are primarily from a single localized source (i.e., a single star) and the local magnetic field direction is known to be fairly uniform. Such a region also has consequences for the distribution of grain heating. For example, asymmetric grains whose largest cross-sections are normal to the incident stellar radiation will reach warmer equilibrium temperatures compared to grains whose largest cross-section is parallel to that direction. This should be observed as an azimuthal dependence of the dust color temperature. We present evidence of such a dependence using IRAS data at 60 and 100 micron. We expect this effect to be stronger using longer wavelength (i.e., 160 micron) data better coupled to the "big-grain" dust population, grains which are also more efficiently aligned with the local magnetic field. Here we also present the results of our on-going work to search for this signal using Herschel maps towards three candidate stars.

  18. Algorithms for Automatic Alignment of Arrays

    NASA Technical Reports Server (NTRS)

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

    1996-01-01

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

  19. Sparse alignment for robust tensor learning.

    PubMed

    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.

  20. Precision alignment device

    DOEpatents

    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.

  1. Precision alignment device

    DOEpatents

    Jones, Nelson E.

    1990-01-01

    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.

  2. Hybrid vehicle motor alignment

    DOEpatents

    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.

  3. Aligning parallel arrays to reduce communication

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

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

  4. Desktop aligner for fabrication of multilayer microfluidic devices

    PubMed Central

    Li, Xiang; Yu, Zeta Tak For; Geraldo, Dalton; Weng, Shinuo; Alve, Nitesh; Dun, Wu; Kini, Akshay; Patel, Karan; Shu, Roberto; Zhang, Feng; Li, Gang; Jin, Qinghui; Fu, Jianping

    2015-01-01

    Multilayer assembly is a commonly used technique to construct multilayer polydimethylsiloxane (PDMS)-based microfluidic devices with complex 3D architecture and connectivity for large-scale microfluidic integration. Accurate alignment of structure features on different PDMS layers before their permanent bonding is critical in determining the yield and quality of assembled multilayer microfluidic devices. Herein, we report a custom-built desktop aligner capable of both local and global alignments of PDMS layers covering a broad size range. Two digital microscopes were incorporated into the aligner design to allow accurate global alignment of PDMS structures up to 4 in. in diameter. Both local and global alignment accuracies of the desktop aligner were determined to be about 20 μm cm−1. To demonstrate its utility for fabrication of integrated multilayer PDMS microfluidic devices, we applied the desktop aligner to achieve accurate alignment of different functional PDMS layers in multilayer microfluidics including an organs-on-chips device as well as a microfluidic device integrated with vertical passages connecting channels located in different PDMS layers. Owing to its convenient operation, high accuracy, low cost, light weight, and portability, the desktop aligner is useful for microfluidic researchers to achieve rapid and accurate alignment for generating multilayer PDMS microfluidic devices. PMID:26233409

  5. Desktop aligner for fabrication of multilayer microfluidic devices

    NASA Astrophysics Data System (ADS)

    Li, Xiang; Yu, Zeta Tak For; Geraldo, Dalton; Weng, Shinuo; Alve, Nitesh; Dun, Wu; Kini, Akshay; Patel, Karan; Shu, Roberto; Zhang, Feng; Li, Gang; Jin, Qinghui; Fu, Jianping

    2015-07-01

    Multilayer assembly is a commonly used technique to construct multilayer polydimethylsiloxane (PDMS)-based microfluidic devices with complex 3D architecture and connectivity for large-scale microfluidic integration. Accurate alignment of structure features on different PDMS layers before their permanent bonding is critical in determining the yield and quality of assembled multilayer microfluidic devices. Herein, we report a custom-built desktop aligner capable of both local and global alignments of PDMS layers covering a broad size range. Two digital microscopes were incorporated into the aligner design to allow accurate global alignment of PDMS structures up to 4 in. in diameter. Both local and global alignment accuracies of the desktop aligner were determined to be about 20 μm cm-1. To demonstrate its utility for fabrication of integrated multilayer PDMS microfluidic devices, we applied the desktop aligner to achieve accurate alignment of different functional PDMS layers in multilayer microfluidics including an organs-on-chips device as well as a microfluidic device integrated with vertical passages connecting channels located in different PDMS layers. Owing to its convenient operation, high accuracy, low cost, light weight, and portability, the desktop aligner is useful for microfluidic researchers to achieve rapid and accurate alignment for generating multilayer PDMS microfluidic devices.

  6. Alignment of CEBAF cryomodules

    SciTech Connect

    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.

  7. Robust Nonnegative Patch Alignment for Dimensionality Reduction.

    PubMed

    You, Xinge; Ou, Weihua; Chen, Chun Lung Philip; Li, Qiang; Zhu, Ziqi; Tang, Yuanyan

    2015-11-01

    Dimensionality reduction is an important method to analyze high-dimensional data and has many applications in pattern recognition and computer vision. In this paper, we propose a robust nonnegative patch alignment for dimensionality reduction, which includes a reconstruction error term and a whole alignment term. We use correntropy-induced metric to measure the reconstruction error, in which the weight is learned adaptively for each entry. For the whole alignment, we propose locality-preserving robust nonnegative patch alignment (LP-RNA) and sparsity-preserviing robust nonnegative patch alignment (SP-RNA), which are unsupervised and supervised, respectively. In the LP-RNA, we propose a locally sparse graph to encode the local geometric structure of the manifold embedded in high-dimensional space. In particular, we select large p -nearest neighbors for each sample, then obtain the sparse representation with respect to these neighbors. The sparse representation is used to build a graph, which simultaneously enjoys locality, sparseness, and robustness. In the SP-RNA, we simultaneously use local geometric structure and discriminative information, in which the sparse reconstruction coefficient is used to characterize the local geometric structure and weighted distance is used to measure the separability of different classes. For the induced nonconvex objective function, we formulate it into a weighted nonnegative matrix factorization based on half-quadratic optimization. We propose a multiplicative update rule to solve this function and show that the objective function converges to a local optimum. Several experimental results on synthetic and real data sets demonstrate that the learned representation is more discriminative and robust than most existing dimensionality reduction methods.

  8. Pairwise Sequence Alignment Library

    SciTech Connect

    Jeff Daily, PNNL

    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.

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

    ERIC Educational Resources Information Center

    Squires, David

    2012-01-01

    Curriculum alignment research has developed showing the relationship among three alignment categories: the taught curriculum, the tested curriculum and the written curriculum. Each pair (for example, the taught and the written curriculum) shows a positive impact for aligning those results. Following this, alignment results from the Third…

  10. Skip the alignment: degenerate, multiplex primer and probe design using K-mer matching instead of alignments.

    PubMed

    Hysom, David A; Naraghi-Arani, Pejman; Elsheikh, Maher; Carrillo, A Celena; Williams, Peter L; Gardner, Shea N

    2012-01-01

    PriMux is a new software package for selecting multiplex compatible, degenerate primers and probes to detect diverse targets such as viruses. It requires no multiple sequence alignment, instead applying k-mer algorithms, hence it scales well for large target sets and saves user effort from curating sequences into alignable groups. PriMux has the capability to predict degenerate primers as well as probes suitable for TaqMan or other primer/probe triplet assay formats, or simply probes for microarray or other single-oligo assay formats. PriMux employs suffix array methods for efficient calculations on oligos 10-~100 nt in length. TaqMan® primers and probes for each segment of Rift Valley fever virus were designed using PriMux, and lab testing comparing signatures designed using PriMux versus those designed using traditional methods demonstrated equivalent or better sensitivity for the PriMux-designed signatures compared to traditional signatures. In addition, we used PriMux to design TaqMan® primers and probes for unalignable or poorly alignable groups of targets: that is, all segments of Rift Valley fever virus analyzed as a single target set of 198 sequences, or all 2863 Dengue virus genomes for all four serotypes available at the time of our analysis. The PriMux software is available as open source from http://sourceforge.net/projects/PriMux.

  11. Skip the Alignment: Degenerate, Multiplex Primer and Probe Design Using K-mer Matching Instead of Alignments

    PubMed Central

    Hysom, David A.; Naraghi-Arani, Pejman; Elsheikh, Maher; Carrillo, A. Celena; Williams, Peter L.; Gardner, Shea N.

    2012-01-01

    PriMux is a new software package for selecting multiplex compatible, degenerate primers and probes to detect diverse targets such as viruses. It requires no multiple sequence alignment, instead applying k-mer algorithms, hence it scales well for large target sets and saves user effort from curating sequences into alignable groups. PriMux has the capability to predict degenerate primers as well as probes suitable for TaqMan or other primer/probe triplet assay formats, or simply probes for microarray or other single-oligo assay formats. PriMux employs suffix array methods for efficient calculations on oligos 10-∼100 nt in length. TaqMan® primers and probes for each segment of Rift Valley fever virus were designed using PriMux, and lab testing comparing signatures designed using PriMux versus those designed using traditional methods demonstrated equivalent or better sensitivity for the PriMux-designed signatures compared to traditional signatures. In addition, we used PriMux to design TaqMan® primers and probes for unalignable or poorly alignable groups of targets: that is, all segments of Rift Valley fever virus analyzed as a single target set of 198 sequences, or all 2863 Dengue virus genomes for all four serotypes available at the time of our analysis. The PriMux software is available as open source from http://sourceforge.net/projects/PriMux. PMID:22485178

  12. Magnetically Aligned Supramolecular Hydrogels

    PubMed Central

    Wallace, Matthew; Cardoso, Andre Zamith; Frith, William J; Iggo, Jonathan A; Adams, Dave J

    2014-01-01

    The magnetic-field-induced alignment of the fibrillar structures present in an aqueous solution of a dipeptide gelator, and the subsequent retention of this alignment upon transformation to a hydrogel upon the addition of CaCl2 or upon a reduction in solution pH is reported. Utilising the switchable nature of the magnetic field coupled with the slow diffusion of CaCl2, it is possible to precisely control the extent of anisotropy across a hydrogel, something that is generally very difficult to do using alternative methods. The approach is readily extended to other compounds that form viscous solutions at high pH. It is expected that this work will greatly expand the utility of such low-molecular-weight gelators (LMWG) in areas where alignment is key. PMID:25345918

  13. Improved docking alignment system

    NASA Technical Reports Server (NTRS)

    Monford, Leo G. (Inventor)

    1988-01-01

    Improved techniques are provided for the alignment of two objects. The present invention is particularly suited for 3-D translation and 3-D rotational alignment of objects in outer space. A camera is affixed to one object, such as a remote manipulator arm of the spacecraft, while the planar reflective surface is affixed to the other object, such as a grapple fixture. A monitor displays in real-time images from the camera such that the monitor displays both the reflected image of the camera and visible marking on the planar reflective surface when the objects are in proper alignment. The monitor may thus be viewed by the operator and the arm manipulated so that the reflective surface is perpendicular to the optical axis of the camera, the roll of the reflective surface is at a selected angle with respect to the camera, and the camera is spaced a pre-selected distance from the reflective surface.

  14. MUSE optical alignment procedure

    NASA Astrophysics Data System (ADS)

    Laurent, Florence; Renault, Edgard; Loupias, Magali; Kosmalski, Johan; Anwand, Heiko; Bacon, Roland; Boudon, Didier; Caillier, Patrick; Daguisé, Eric; Dubois, Jean-Pierre; Dupuy, Christophe; Kelz, Andreas; Lizon, Jean-Louis; Nicklas, Harald; Parès, Laurent; Remillieux, Alban; Seifert, Walter; Valentin, Hervé; Xu, Wenli

    2012-09-01

    MUSE (Multi Unit Spectroscopic Explorer) is a second generation VLT integral field spectrograph (1x1arcmin² Field of View) developed for the European Southern Observatory (ESO), operating in the visible wavelength range (0.465-0.93 μm). A consortium of seven institutes is currently assembling and testing MUSE in the Integration Hall of the Observatoire de Lyon for the Preliminary Acceptance in Europe, scheduled for 2013. MUSE is composed of several subsystems which are under the responsibility of each institute. The Fore Optics derotates and anamorphoses the image at the focal plane. A Splitting and Relay Optics feed the 24 identical Integral Field Units (IFU), that are mounted within a large monolithic instrument mechanical structure. Each IFU incorporates an image slicer, a fully refractive spectrograph with VPH-grating and a detector system connected to a global vacuum and cryogenic system. During 2011, all MUSE subsystems were integrated, aligned and tested independently in each institute. After validations, the systems were shipped to the P.I. institute at Lyon and were assembled in the Integration Hall This paper describes the end-to-end optical alignment procedure of the MUSE instrument. The design strategy, mixing an optical alignment by manufacturing (plug and play approach) and few adjustments on key components, is presented. We depict the alignment method for identifying the optical axis using several references located in pupil and image planes. All tools required to perform the global alignment between each subsystem are described. The success of this alignment approach is demonstrated by the good results for the MUSE image quality. MUSE commissioning at the VLT (Very Large Telescope) is planned for 2013.

  15. PILOT optical alignment

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  16. Laboratory simulation of field-aligned currents

    NASA Technical Reports Server (NTRS)

    Wessel, Frank J.; Rostoker, Norman

    1993-01-01

    A summary of progress during the period Apr. 1992 to Mar. 1993 is provided. Objectives of the research are (1) to simulate, via laboratory experiments, the three terms of the field-aligned current equation; (2) to simulate auroral-arc formation processes by configuring the boundary conditions of the experimental chamber and plasma parameters to produce highly localized return currents at the end of a field-aligned current system; and (3) to extrapolate these results, using theoretical and computational techniques, to the problem of magnetospheric-ionospheric coupling and to compare them with published literature signatures of auroral-arc phenomena.

  17. Aligned-or Not?

    ERIC Educational Resources Information Center

    Roseman, Jo Ellen; Koppal, Mary

    2015-01-01

    When state leaders and national partners in the development of the Next Generation Science Standards met to consider implementation strategies, states and school districts wanted to know which materials were aligned to the new standards. The answer from the developers was short but not sweet: You won't find much now, and it's going to…

  18. Optically Aligned Drill Press

    NASA Technical Reports Server (NTRS)

    Adderholdt, Bruce M.

    1994-01-01

    Precise drill press equipped with rotary-indexing microscope. Microscope and drill exchange places when turret rotated. Microscope axis first aligned over future hole, then rotated out of way so drill axis assumes its precise position. New procedure takes less time to locate drilling positions and produces more accurate results. Apparatus adapted to such other machine tools as milling and measuring machines.

  19. Curriculum Alignment: Establishing Coherence

    ERIC Educational Resources Information Center

    Gagné, Philippe; Dumont, Laurence; Brunet, Sabine; Boucher, Geneviève

    2013-01-01

    In this paper, we present a step-by-step guide to implement a curricular alignment project, directed at professional development and student support, and developed in a higher education French as a second language department. We outline best practices and preliminary results from our experience and provide ways to adapt our experience to other…

  20. DNA recognition for virus assembly through multiple sequence-independent interactions with a helix-turn-helix motif

    PubMed Central

    Greive, Sandra J.; Fung, Herman K.H.; Chechik, Maria; Jenkins, Huw T.; Weitzel, Stephen E.; Aguiar, Pedro M.; Brentnall, Andrew S.; Glousieau, Matthieu; Gladyshev, Grigory V.; Potts, Jennifer R.; Antson, Alfred A.

    2016-01-01

    The helix-turn-helix (HTH) motif features frequently in protein DNA-binding assemblies. Viral pac site-targeting small terminase proteins possess an unusual architecture in which the HTH motifs are displayed in a ring, distinct from the classical HTH dimer. Here we investigate how such a circular array of HTH motifs enables specific recognition of the viral genome for initiation of DNA packaging during virus assembly. We found, by surface plasmon resonance and analytical ultracentrifugation, that individual HTH motifs of the Bacillus phage SF6 small terminase bind the packaging regions of SF6 and related SPP1 genome weakly, with little local sequence specificity. Nuclear magnetic resonance chemical shift perturbation studies with an arbitrary single-site substrate suggest that the HTH motif contacts DNA similarly to how certain HTH proteins contact DNA non-specifically. Our observations support a model where specificity is generated through conformational selection of an intrinsically bent DNA segment by a ring of HTHs which bind weakly but cooperatively. Such a system would enable viral gene regulation and control of the viral life cycle, with a minimal genome, conferring a major evolutionary advantage for SPP1-like viruses. PMID:26673721

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

    PubMed Central

    Terashi, Genki; Takeda-Shitaka, Mayuko

    2015-01-01

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

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

    PubMed

    Terashi, Genki; Takeda-Shitaka, Mayuko

    2015-01-01

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

  3. MUSE alignment onto VLT

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

  4. Inflation by alignment

    SciTech Connect

    Burgess, C.P.; Roest, Diederik

    2015-06-08

    Pseudo-Goldstone bosons (pGBs) can provide technically natural inflatons, as has been comparatively well-explored in the simplest axion examples. Although inflationary success requires trans-Planckian decay constants, f≳M{sub p}, several mechanisms have been proposed to obtain this, relying on (mis-)alignments between potential and kinetic energies in multiple-field models. We extend these mechanisms to a broader class of inflationary models, including in particular the exponential potentials that arise for pGB potentials based on noncompact groups (and so which might apply to moduli in an extra-dimensional setting). The resulting potentials provide natural large-field inflationary models and can predict a larger primordial tensor signal than is true for simpler single-field versions of these models. In so doing we provide a unified treatment of several alignment mechanisms, showing how each emerges as a limit of the more general setup.

  5. Automatic Word Alignment

    DTIC Science & Technology

    2014-02-18

    strategy was evalu­ ated in the context of English -to-Pashto (E2P) and Pashto-to- English (P2E), a low-resource language pair. For E2P, the training and...improves the quality of automatic word alignment, for example for resource poor language pairs, thus improving Statistical Machine Translation (SMT...example for resource poor language pairs, thus improving Statistical Machine Translation (SMT) performance. 15. SUBJECT TERMS 16. SECURITY

  6. Orbit IMU alignment: Error analysis

    NASA Technical Reports Server (NTRS)

    Corson, R. W.

    1980-01-01

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

  7. Nuclear reactor alignment plate configuration

    SciTech Connect

    Altman, David A; Forsyth, David R; Smith, Richard E; Singleton, Norman R

    2014-01-28

    An alignment plate that is attached to a core barrel of a pressurized water reactor and fits within slots within a top plate of a lower core shroud and upper core plate to maintain lateral alignment of the reactor internals. The alignment plate is connected to the core barrel through two vertically-spaced dowel pins that extend from the outside surface of the core barrel through a reinforcement pad and into corresponding holes in the alignment plate. Additionally, threaded fasteners are inserted around the perimeter of the reinforcement pad and into the alignment plate to further secure the alignment plate to the core barrel. A fillet weld also is deposited around the perimeter of the reinforcement pad. To accomodate thermal growth between the alignment plate and the core barrel, a gap is left above, below and at both sides of one of the dowel pins in the alignment plate holes through with the dowel pins pass.

  8. Dynamic Alignment at SLS

    SciTech Connect

    Ruland, Robert E.

    2003-04-23

    The relative alignment of components in the storage ring of the Swiss Light Source (SLS) is guaranteed by mechanical means. The magnets are rigidly fixed to 48 girders by means of alignment rails with tolerances of less than {+-}15 {micro}m. The bending magnets, supported by 3 point ball bearings, overlap adjacent girders and thus establish virtual train links between the girders, located near the bending magnet centres. Keeping the distortion of the storage ring geometry within a tolerance of {+-}100 {micro}m in order to guarantee sufficient dynamic apertures, requires continuous monitoring and correction of the girder locations. Two monitoring systems for the horizontal and the vertical direction will be installed to measure displacements of the train link between girders, which are due to ground settings and temperature effects: The hydrostatic levelling system (HLS) gives an absolute vertical reference, while the horizontal positioning system (HPS), which employs low cost linear encoders with sub-micron resolution, measures relative horizontal movements. The girder mover system based on five DC motors per girder allows a dynamic realignment of the storage ring within a working window of more than {+-}1 mm for girder translations and {+-}1 mrad for rotations. We will describe both monitoring systems (HLS and HPS) as well as the applied correction scheme based on the girder movers. We also show simulations indicating that beam based girder alignment takes care of most of the static closed orbit correction.

  9. Method for alignment of microwires

    DOEpatents

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

    2017-01-24

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

  10. Alignment as a Teacher Variable

    ERIC Educational Resources Information Center

    Porter, Andrew C.; Smithson, John; Blank, Rolf; Zeidner, Timothy

    2007-01-01

    With the exception of the procedures developed by Porter and colleagues (Porter, 2002), other methods of defining and measuring alignment are essentially limited to alignment between tests and standards. Porter's procedures have been generalized to investigating the alignment between content standards, tests, textbooks, and even classroom…

  11. Precision alignment and mounting apparatus

    NASA Technical Reports Server (NTRS)

    Preston, Dennis R. (Inventor)

    1993-01-01

    An alignment and mounting apparatus for mounting two modules (10,12) includes a first portion having a cylindrical alignment pin (16) projecting normal to a module surface, a second portion having a three-stage alignment guide (18) including a shoehorn flange (34), a Y-slot (42) and a V-block (22) which sequentially guide the alignment pin (16) with successively finer precision and a third portion in the form of a spring-loaded captive fastener (20) for connecting the two modules after alignment is achieved.

  12. Engineering cell alignment in vitro.

    PubMed

    Li, Yuhui; Huang, Guoyou; Zhang, Xiaohui; Wang, Lin; Du, Yanan; Lu, Tian Jian; Xu, Feng

    2014-01-01

    Cell alignment plays a critical role in various cell behaviors including cytoskeleton reorganization, membrane protein relocation, nucleus gene expression, and ECM remodeling. Cell alignment is also known to exert significant effects on tissue regeneration (e.g., neuron) and modulate mechanical properties of tissues including skeleton, cardiac muscle and tendon. Therefore, it is essential to engineer cell alignment in vitro for biomechanics, cell biology, tissue engineering and regenerative medicine applications. With advances in nano- and micro-scale technologies, a variety of approaches have been developed to engineer cell alignment in vitro, including mechanical loading, topographical patterning, and surface chemical treatment. In this review, we first present alignments of various cell types and their functionality in different tissues in vivo including muscle and nerve tissues. Then, we provide an overview of recent approaches for engineering cell alignment in vitro. Finally, concluding remarks and perspectives are addressed for future improvement of engineering cell alignment.

  13. TSGC and JSC Alignment

    NASA Technical Reports Server (NTRS)

    Sanchez, Humberto

    2013-01-01

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

  14. MRFalign: protein homology detection through alignment of Markov random fields.

    PubMed

    Ma, Jianzhu; Wang, Sheng; Wang, Zhiyong; Xu, Jinbo

    2014-03-01

    Sequence-based protein homology detection has been extensively studied and so far the most sensitive method is based upon comparison of protein sequence profiles, which are derived from multiple sequence alignment (MSA) of sequence homologs in a protein family. A sequence profile is usually represented as a position-specific scoring matrix (PSSM) or an HMM (Hidden Markov Model) and accordingly PSSM-PSSM or HMM-HMM comparison is used for homolog detection. This paper presents a new homology detection method MRFalign, consisting of three key components: 1) a Markov Random Fields (MRF) representation of a protein family; 2) a scoring function measuring similarity of two MRFs; and 3) an efficient ADMM (Alternating Direction Method of Multipliers) algorithm aligning two MRFs. Compared to HMM that can only model very short-range residue correlation, MRFs can model long-range residue interaction pattern and thus, encode information for the global 3D structure of a protein family. Consequently, MRF-MRF comparison for remote homology detection shall be much more sensitive than HMM-HMM or PSSM-PSSM comparison. Experiments confirm that MRFalign outperforms several popular HMM or PSSM-based methods in terms of both alignment accuracy and remote homology detection and that MRFalign works particularly well for mainly beta proteins. For example, tested on the benchmark SCOP40 (8353 proteins) for homology detection, PSSM-PSSM and HMM-HMM succeed on 48% and 52% of proteins, respectively, at superfamily level, and on 15% and 27% of proteins, respectively, at fold level. In contrast, MRFalign succeeds on 57.3% and 42.5% of proteins at superfamily and fold level, respectively. This study implies that long-range residue interaction patterns are very helpful for sequence-based homology detection. The software is available for download at http://raptorx.uchicago.edu/download/. A summary of this paper appears in the proceedings of the RECOMB 2014 conference, April 2-5.

  15. OBSERVATIONS OF ENHANCED RADIATIVE GRAIN ALIGNMENT NEAR HD 97300

    SciTech Connect

    Andersson, B-G; Potter, S. B. E-mail: sbp@saao.ac.z

    2010-09-10

    We have obtained optical multi-band polarimetry toward sightlines through the Chamaeleon I cloud, particularly in the vicinity of the young B9/A0 star HD 97300. We show, in agreement with earlier studies, that the radiation field impinging on the cloud in the projected vicinity of the star is dominated by the flux from the star, as evidenced by a local enhancement in the grain heating. By comparing the differential grain heating with the differential change in the location of the peak of the polarization curve, we show that the grain alignment is enhanced by the increase in the radiation field. We also find a weak, but measurable, variation in the grain alignment with the relative angle between the radiation field anisotropy and the magnetic field direction. Such an anisotropy in the grain alignment is consistent with a unique prediction of modern radiative alignment torque theory and provides direct support for radiatively driven grain alignment.

  16. Protein Secondary Structure Prediction Using Local Adaptive Techniques in Training Neural Networks

    NASA Astrophysics Data System (ADS)

    Aik, Lim Eng; Zainuddin, Zarita; Joseph, Annie

    2008-01-01

    One of the most significant problems in computer molecular biology today is how to predict a protein's three-dimensional structure from its one-dimensional amino acid sequence or generally call the protein folding problem and difficult to determine the corresponding protein functions. Thus, this paper involves protein secondary structure prediction using neural network in order to solve the protein folding problem. The neural network used for protein secondary structure prediction is multilayer perceptron (MLP) of the feed-forward variety. The training set are taken from the protein data bank which are 120 proteins while 60 testing set is the proteins which were chosen randomly from the protein data bank. Multiple sequence alignment (MSA) is used to get the protein similar sequence and Position Specific Scoring matrix (PSSM) is used for network input. The training process of the neural network involves local adaptive techniques. Local adaptive techniques used in this paper comprises Learning rate by sign changes, SuperSAB, Quickprop and RPROP. From the simulation, the performance for learning rate by Rprop and Quickprop are superior to all other algorithms with respect to the convergence time. However, the best result was obtained using Rprop algorithm.

  17. Onorbit IMU alignment error budget

    NASA Technical Reports Server (NTRS)

    Corson, R. W.

    1980-01-01

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

  18. Nuclear reactor internals alignment configuration

    DOEpatents

    Gilmore, Charles B.; Singleton, Norman R.

    2009-11-10

    An alignment system that employs jacking block assemblies and alignment posts around the periphery of the top plate of a nuclear reactor lower internals core shroud to align an upper core plate with the lower internals and the core shroud with the core barrel. The distal ends of the alignment posts are chamfered and are closely received within notches machined in the upper core plate at spaced locations around the outer circumference of the upper core plate. The jacking block assemblies are used to center the core shroud in the core barrel and the alignment posts assure the proper orientation of the upper core plate. The alignment posts may alternately be formed in the upper core plate and the notches may be formed in top plate.

  19. Aligned Defrosting Dunes

    NASA Technical Reports Server (NTRS)

    2004-01-01

    17 August 2004 This July 2004 Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image shows a group of aligned barchan sand dunes in the martian north polar region. At the time, the dunes were covered with seasonal frost, but the frost had begun to sublime away, leaving dark spots and dark outlines around the dunes. The surrounding plains exhibit small, diffuse spots that are also the result of subliming seasonal frost. This northern spring image, acquired on a descending ground track (as MGS was moving north to south on the 'night' side of Mars) is located near 78.8oN, 34.8oW. The image covers an area about 3 km (1.9 mi) across and sunlight illuminates the scene from the upper left.

  20. Lunar Alignments - Identification and Analysis

    NASA Astrophysics Data System (ADS)

    González-García, A. César

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

  1. The alignment strategy of HADES

    NASA Astrophysics Data System (ADS)

    Pechenova, O.; Pechenov, V.; Galatyuk, T.; Hennino, T.; Holzmann, R.; Kornakov, G.; Markert, J.; Müntz, C.; Salabura, P.; Schmah, A.; Schwab, E.; Stroth, J.

    2015-06-01

    The global as well as intrinsic alignment of any spectrometer impacts directly on its performance and the quality of the achievable physics results. An overview of the current alignment procedure of the DiElectron Spectrometer HADES is presented with an emphasis on its main features and its accuracy. The sequence of all steps and procedures is given, including details on photogrammetric and track-based alignment.

  2. Alignment of Helical Membrane Protein Sequences Using AlignMe

    PubMed Central

    Khafizov, Kamil; Forrest, Lucy R.

    2013-01-01

    Few sequence alignment methods have been designed specifically for integral membrane proteins, even though these important proteins have distinct evolutionary and structural properties that might affect their alignments. Existing approaches typically consider membrane-related information either by using membrane-specific substitution matrices or by assigning distinct penalties for gap creation in transmembrane and non-transmembrane regions. Here, we ask whether favoring matching of predicted transmembrane segments within a standard dynamic programming algorithm can improve the accuracy of pairwise membrane protein sequence alignments. We tested various strategies using a specifically designed program called AlignMe. An updated set of homologous membrane protein structures, called HOMEP2, was used as a reference for optimizing the gap penalties. The best of the membrane-protein optimized approaches were then tested on an independent reference set of membrane protein sequence alignments from the BAliBASE collection. When secondary structure (S) matching was combined with evolutionary information (using a position-specific substitution matrix (P)), in an approach we called AlignMePS, the resultant pairwise alignments were typically among the most accurate over a broad range of sequence similarities when compared to available methods. Matching transmembrane predictions (T), in addition to evolutionary information, and secondary-structure predictions, in an approach called AlignMePST, generally reduces the accuracy of the alignments of closely-related proteins in the BAliBASE set relative to AlignMePS, but may be useful in cases of extremely distantly related proteins for which sequence information is less informative. The open source AlignMe code is available at https://sourceforge.net/projects/alignme/, and at http://www.forrestlab.org, along with an online server and the HOMEP2 data set. PMID:23469223

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

    SciTech Connect

    Chisari, Nora Elisa; Dvorkin, Cora E-mail: cdvorkin@ias.edu

    2013-12-01

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

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

    SciTech Connect

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

    2005-08-16

    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.

  5. GS-align for glycan structure alignment and similarity measurement

    PubMed Central

    Lee, Hui Sun; Jo, Sunhwan; Mukherjee, Srayanta; Park, Sang-Jun; Skolnick, Jeffrey; Lee, Jooyoung; Im, Wonpil

    2015-01-01

    Motivation: Glycans play critical roles in many biological processes, and their structural diversity is key for specific protein-glycan recognition. Comparative structural studies of biological molecules provide useful insight into their biological relationships. However, most computational tools are designed for protein structure, and despite their importance, there is no currently available tool for comparing glycan structures in a sequence order- and size-independent manner. Results: A novel method, GS-align, is developed for glycan structure alignment and similarity measurement. GS-align generates possible alignments between two glycan structures through iterative maximum clique search and fragment superposition. The optimal alignment is then determined by the maximum structural similarity score, GS-score, which is size-independent. Benchmark tests against the Protein Data Bank (PDB) N-linked glycan library and PDB homologous/non-homologous N-glycoprotein sets indicate that GS-align is a robust computational tool to align glycan structures and quantify their structural similarity. GS-align is also applied to template-based glycan structure prediction and monosaccharide substitution matrix generation to illustrate its utility. Availability and implementation: http://www.glycanstructure.org/gsalign. Contact: wonpil@ku.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25857669

  6. Optical alignment of oval graphene flakes.

    PubMed

    Mobini, E; Rahimzadegan, A; Alaee, R; Rockstuhl, C

    2017-03-15

    Patterned graphene, as an atomically thin layer, supports localized surface plasmon polaritons at mid-infrared or far-infrared frequencies. This provides a pronounced optical force/torque in addition to large optical cross sections and will make it an ideal candidate for optical manipulation. Here, we study the optical force and torque exerted by a linearly polarized plane wave on circular and oval graphene flakes (single layers of graphene). While the torque vanishes for circular flakes, the finite torque allows rotating and orienting oval flakes relative to the electric field polarization. Depending on the wavelength, the alignment is either parallel or perpendicular to the electric field vector. In our contribution, we rely on a full-wave numerical simulation and also on an analytical model that treats the graphene flakes in a dipole approximation. The presented results reveal a good level of control on the spatial alignment of graphene flakes subjected to far-infrared illumination.

  7. QuickProbs 2: Towards rapid construction of high-quality alignments of large protein families

    PubMed Central

    Gudyś, Adam; Deorowicz, Sebastian

    2017-01-01

    The ever-increasing size of sequence databases caused by the development of high throughput sequencing, poses to multiple alignment algorithms one of the greatest challenges yet. As we show, well-established techniques employed for increasing alignment quality, i.e., refinement and consistency, are ineffective when large protein families are investigated. We present QuickProbs 2, an algorithm for multiple sequence alignment. Based on probabilistic models, equipped with novel column-oriented refinement and selective consistency, it offers outstanding accuracy. When analysing hundreds of sequences, Quick-Probs 2 is noticeably better than ClustalΩ and MAFFT, the previous leaders for processing numerous protein families. In the case of smaller sets, for which consistency-based methods are the best performing, QuickProbs 2 is also superior to the competitors. Due to low computational requirements of selective consistency and utilization of massively parallel architectures, presented algorithm has similar execution times to ClustalΩ, and is orders of magnitude faster than full consistency approaches, like MSAProbs or PicXAA. All these make QuickProbs 2 an excellent tool for aligning families ranging from few, to hundreds of proteins. PMID:28139687

  8. Mask alignment system for semiconductor processing

    DOEpatents

    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.

  9. De Novo Genome Assembly of the Economically Important Weed Horseweed Using Integrated Data from Multiple Sequencing Platforms1[C][W][OPEN

    PubMed Central

    Peng, Yanhui; Lai, Zhao; Lane, Thomas; Nageswara-Rao, Madhugiri; Okada, Miki; Jasieniuk, Marie; O’Geen, Henriette; Kim, Ryan W.; Sammons, R. Douglas; Rieseberg, Loren H.; Stewart, C. Neal

    2014-01-01

    Horseweed (Conyza canadensis), a member of the Compositae (Asteraceae) family, was the first broadleaf weed to evolve resistance to glyphosate. Horseweed, one of the most problematic weeds in the world, is a true diploid (2n = 2x = 18), with the smallest genome of any known agricultural weed (335 Mb). Thus, it is an appropriate candidate to help us understand the genetic and genomic bases of weediness. We undertook a draft de novo genome assembly of horseweed by combining data from multiple sequencing platforms (454 GS-FLX, Illumina HiSeq 2000, and PacBio RS) using various libraries with different insertion sizes (approximately 350 bp, 600 bp, 3 kb, and 10 kb) of a Tennessee-accessed, glyphosate-resistant horseweed biotype. From 116.3 Gb (approximately 350× coverage) of data, the genome was assembled into 13,966 scaffolds with 50% of the assembly = 33,561 bp. The assembly covered 92.3% of the genome, including the complete chloroplast genome (approximately 153 kb) and a nearly complete mitochondrial genome (approximately 450 kb in 120 scaffolds). The nuclear genome is composed of 44,592 protein-coding genes. Genome resequencing of seven additional horseweed biotypes was performed. These sequence data were assembled and used to analyze genome variation. Simple sequence repeat and single-nucleotide polymorphisms were surveyed. Genomic patterns were detected that associated with glyphosate-resistant or -susceptible biotypes. The draft genome will be useful to better understand weediness and the evolution of herbicide resistance and to devise new management strategies. The genome will also be useful as another reference genome in the Compositae. To our knowledge, this article represents the first published draft genome of an agricultural weed. PMID:25209985

  10. Lexical alignment in triadic communication

    PubMed Central

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

    2015-01-01

    Lexical alignment refers to the adoption of one’s interlocutor’s lexical items. Accounts of the mechanisms underlying such lexical alignment differ (among other aspects) in the role assigned to addressee-centered behavior. In this study, we used a triadic communicative situation to test which factors may modulate the extent to which participants’ lexical alignment reflects addressee-centered behavior. Pairs of naïve participants played a picture matching game and received information about the order in which pictures were to be matched from a voice over headphones. On critical trials, participants did or did not hear a name for the picture to be matched next over headphones. Importantly, when the voice over headphones provided a name, it did not match the name that the interlocutor had previously used to describe the object. Participants overwhelmingly used the word that the voice over headphones provided. This result points to non-addressee-centered behavior and is discussed in terms of disrupting alignment with the interlocutor as well as in terms of establishing alignment with the voice over headphones. In addition, the type of picture (line drawing vs. tangram shape) independently modulated lexical alignment, such that participants showed more lexical alignment to their interlocutor for (more ambiguous) tangram shapes compared to line drawings. Overall, the results point to a rather large role for non-addressee-centered behavior during lexical alignment. PMID:25762955

  11. Well-pump alignment system

    DOEpatents

    Drumheller, Douglas S.

    1998-01-01

    An improved well-pump for geothermal wells, an alignment system for a well-pump, and to a method for aligning a rotor and stator within a well-pump, wherein the well-pump has a whistle assembly formed at a bottom portion thereof, such that variations in the frequency of the whistle, indicating misalignment, may be monitored during pumping.

  12. CATO: The Clone Alignment Tool.

    PubMed

    Henstock, Peter V; LaPan, Peter

    2016-01-01

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

  13. Drive alignment pays maintenance dividends

    SciTech Connect

    Fedder, R.

    2008-12-15

    Proper alignment of the motor and gear drive on conveying and processing equipment will result in longer bearing and coupling life, along with lower maintenance costs. Selecting an alignment free drive package instead of a traditional foot mounted drive and motor is a major advancement toward these goals. 4 photos.

  14. Alignment of the MINOS FD

    SciTech Connect

    Becker, B.; Boehnlein, D.; /Fermilab

    2004-11-01

    The results and procedure of the alignment of the MINOS Far Detector are presented. The far detector has independent alignments of SM1 and SM2. The misalignments have an estimated uncertainty of {approx}850 {micro}m for SM1 and {approx}750 {micro}m for SM2. The alignment has as inputs the average rotations of U and V as determined by optical survey and strip positions within modules measured from the module mapper. The output of this is a module-module correction for transverse mis-alignments. These results were verified by examining an independent set of data. These alignment constants on average contribute much less then 1% to the total uncertainty in the transverse strip position.

  15. Magnetic alignment and the Poisson alignment reference system

    NASA Astrophysics Data System (ADS)

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

    1990-08-01

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

  16. Testing the tidal alignment model of galaxy intrinsic alignment

    SciTech Connect

    Blazek, Jonathan; Seljak, Uroš; McQuinn, Matthew E-mail: mmcquinn@berkeley.edu

    2011-05-01

    Weak gravitational lensing has become a powerful probe of large-scale structure and cosmological parameters. Precision weak lensing measurements require an understanding of the intrinsic alignment of galaxy ellipticities, which can in turn inform models of galaxy formation. It is hypothesized that elliptical galaxies align with the background tidal field and that this alignment mechanism dominates the correlation between ellipticities on cosmological scales (in the absence of lensing). We use recent large-scale structure measurements from the Sloan Digital Sky Survey to test this picture with several statistics: (1) the correlation between ellipticity and galaxy overdensity, w{sub g+}; (2) the intrinsic alignment auto-correlation functions; (3) the correlation functions of curl-free, E, and divergence-free, B, modes, the latter of which is zero in the linear tidal alignment theory; (4) the alignment correlation function, w{sub g}(r{sub p},θ), a recently developed statistic that generalizes the galaxy correlation function to account for the angle between the galaxy separation vector and the principle axis of ellipticity. We show that recent measurements are largely consistent with the tidal alignment model and discuss dependence on galaxy luminosity. In addition, we show that at linear order the tidal alignment model predicts that the angular dependence of w{sub g}(r{sub p},θ) is simply w{sub g+}(r{sub p})cos (2θ) and that this dependence is consistent with recent measurements. We also study how stochastic nonlinear contributions to galaxy ellipticity impact these statistics. We find that a significant fraction of the observed LRG ellipticity can be explained by alignment with the tidal field on scales ∼> 10 \\hMpc. These considerations are relevant to galaxy formation and evolution.

  17. Multi-Harmony: detecting functional specificity from sequence alignment.

    PubMed

    Brandt, Bernd W; Feenstra, K Anton; Heringa, Jaap

    2010-07-01

    Many protein families contain sub-families with functional specialization, such as binding different ligands or being involved in different protein-protein interactions. A small number of amino acids generally determine functional specificity. The identification of these residues can aid the understanding of protein function and help finding targets for experimental analysis. Here, we present multi-Harmony, an interactive web sever for detecting sub-type-specific sites in proteins starting from a multiple sequence alignment. Combining our Sequence Harmony (SH) and multi-Relief (mR) methods in one web server allows simultaneous analysis and comparison of specificity residues; furthermore, both methods have been significantly improved and extended. SH has been extended to cope with more than two sub-groups. mR has been changed from a sampling implementation to a deterministic one, making it more consistent and user friendly. For both methods Z-scores are reported. The multi-Harmony web server produces a dynamic output page, which includes interactive connections to the Jalview and Jmol applets, thereby allowing interactive analysis of the results. Multi-Harmony is available at http://www.ibi.vu.nl/ programs/shmrwww.

  18. BAYESIAN PROTEIN STRUCTURE ALIGNMENT1

    PubMed Central

    RODRIGUEZ, ABEL; SCHMIDLER, SCOTT C.

    2015-01-01

    The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over evolutionary timescales. A key challenge is the identification and evaluation of structural similarity between proteins; such analysis can aid in understanding the role of newly discovered proteins and help elucidate evolutionary relationships between organisms. Computational biologists have developed many clever algorithmic techniques for comparing protein structures, however, all are based on heuristic optimization criteria, making statistical interpretation somewhat difficult. Here we present a fully probabilistic framework for pairwise structural alignment of proteins. Our approach has several advantages, including the ability to capture alignment uncertainty and to estimate key “gap” parameters which critically affect the quality of the alignment. We show that several existing alignment methods arise as maximum a posteriori estimates under specific choices of prior distributions and error models. Our probabilistic framework is also easily extended to incorporate additional information, which we demonstrate by including primary sequence information to generate simultaneous sequence–structure alignments that can resolve ambiguities obtained using structure alone. This combined model also provides a natural approach for the difficult task of estimating evolutionary distance based on structural alignments. The model is illustrated by comparison with well-established methods on several challenging protein alignment examples. PMID:26925188

  19. Recursive dynamic programming for adaptive sequence and structure alignment

    SciTech Connect

    Thiele, R.; Zimmer, R.; Lengauer, T.

    1995-12-31

    We propose a new alignment procedure that is capable of aligning protein sequences and structures in a unified manner. Recursive dynamic programming (RDP) is a hierarchical method which, on each level of the hierarchy, identifies locally optimal solutions and assembles them into partial alignments of sequences and/or structures. In contrast to classical dynamic programming, RDP can also handle alignment problems that use objective functions not obeying the principle of prefix optimality, e.g. scoring schemes derived from energy potentials of mean force. For such alignment problems, RDP aims at computing solutions that are near-optimal with respect to the involved cost function and biologically meaningful at the same time. Towards this goal, RDP maintains a dynamic balance between different factors governing alignment fitness such as evolutionary relationships and structural preferences. As in the RDP method gaps are not scored explicitly, the problematic assignment of gap cost parameters is circumvented. In order to evaluate the RDP approach we analyse whether known and accepted multiple alignments based on structural information can be reproduced with the RDP method.

  20. Aligning for Innovation - Alignment Strategy to Drive Innovation

    NASA Technical Reports Server (NTRS)

    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.

  1. Fusion bonding and alignment fixture

    DOEpatents

    Ackler, Harold D.; Swierkowski, Stefan P.; Tarte, Lisa A.; Hicks, Randall K.

    2000-01-01

    An improved vacuum fusion bonding structure and process for aligned bonding of large area glass plates, patterned with microchannels and access holes and slots, for elevated glass fusion temperatures. Vacuum pumpout of all the components is through the bottom platform which yields an untouched, defect free top surface which greatly improves optical access through this smooth surface. Also, a completely non-adherent interlayer, such as graphite, with alignment and location features is located between the main steel platform and the glass plate pair, which makes large improvements in quality, yield, and ease of use, and enables aligned bonding of very large glass structures.

  2. Magnetic axis alignment and the Poisson alignment reference system

    NASA Astrophysics Data System (ADS)

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

    1989-01-01

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

  3. Progressive alignment of genomic signals by multiple dynamic time warping.

    PubMed

    Skutkova, Helena; Vitek, Martin; Sedlar, Karel; Provaznik, Ivo

    2015-11-21

    This paper presents the utilization of progressive alignment principle for positional adjustment of a set of genomic signals with different lengths. The new method of multiple alignment of signals based on dynamic time warping is tested for the purpose of evaluating the similarity of different length genes in phylogenetic studies. Two sets of phylogenetic markers were used to demonstrate the effectiveness of the evaluation of intraspecies and interspecies genetic variability. The part of the proposed method is modification of pairwise alignment of two signals by dynamic time warping with using correlation in a sliding window. The correlation based dynamic time warping allows more accurate alignment dependent on local homologies in sequences without the need of scoring matrix or evolutionary models, because mutual similarities of residues are included in the numerical code of signals.

  4. Laser beam alignment apparatus and method

    DOEpatents

    Gruhn, C.R.; Hammond, R.B.

    The disclosure related to an apparatus and method for laser beam alignment. Thermoelectric properties of a disc in a laser beam path are used to provide an indication of beam alignment and/or automatic laser alignment.

  5. Laser beam alignment apparatus and method

    DOEpatents

    Gruhn, Charles R.; Hammond, Robert B.

    1981-01-01

    The disclosure relates to an apparatus and method for laser beam alignment. Thermoelectric properties of a disc in a laser beam path are used to provide an indication of beam alignment and/or automatic laser alignment.

  6. Theory of grain alignment in molecular clouds

    NASA Technical Reports Server (NTRS)

    Roberge, Wayne G.

    1993-01-01

    Research accomplishments are presented and include the following: (1) mathematical theory of grain alignment; (2) super-paramagnetic alignment of molecular cloud grains; and (3) theory of grain alignment by ambipolar diffusion.

  7. Net2Align: An Algorithm For Pairwise Global Alignment of Biological Networks

    PubMed Central

    Wadhwab, Gulshan; Upadhyayaa, K. C.

    2016-01-01

    The amount of data on molecular interactions is growing at an enormous pace, whereas the progress of methods for analysing this data is still lacking behind. Particularly, in the area of comparative analysis of biological networks, where one wishes to explore the similarity between two biological networks, this holds a potential problem. In consideration that the functionality primarily runs at the network level, it advocates the need for robust comparison methods. In this paper, we describe Net2Align, an algorithm for pairwise global alignment that can perform node-to-node correspondences as well as edge-to-edge correspondences into consideration. The uniqueness of our algorithm is in the fact that it is also able to detect the type of interaction, which is essential in case of directed graphs. The existing algorithm is only able to identify the common nodes but not the common edges. Another striking feature of the algorithm is that it is able to remove duplicate entries in case of variable datasets being aligned. This is achieved through creation of a local database which helps exclude duplicate links. In a pervasive computational study on gene regulatory network, we establish that our algorithm surpasses its counterparts in its results. Net2Align has been implemented in Java 7 and the source code is available as supplementary files. PMID:28356678

  8. Fixture for aligning motor assembly

    SciTech Connect

    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.

  9. Stellar Alignments - Identification and Analysis

    NASA Astrophysics Data System (ADS)

    Ruggles, Clive L. N.

    Fortuitous stellar alignments can be fitted to structural orientations with relative ease by the unwary. Nonetheless, cautious approaches taking into account a broader range of cultural evidence, as well as paying due attention to potential methodological pitfalls, have been successful in identifying credible stellar alignments—and constructing plausible assessments of their cultural significance—in a variety of circumstances. These range from single instances of alignments upon particular asterisms where the corroborating historical or ethnographic evidence is strong to repeated instances of oriented structures with only limited independent cultural information but where systematic, data-driven approaches can be productive. In the majority of cases, the identification and interpretation of putative stellar alignments relates to groups of similar monuments or complex single sites and involves a balance between systematic studies of the alignments themselves, backed up by statistical analysis where appropriate, and the consideration of a range of contextual evidence, either derived from the archaeological record alone or from other relevant sources.

  10. RF Jitter Modulation Alignment Sensing

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

  11. Well-pump alignment system

    DOEpatents

    Drumheller, D.S.

    1998-10-20

    An improved well-pump for geothermal wells, an alignment system for a well-pump, and to a method for aligning a rotor and stator within a well-pump are disclosed, wherein the well-pump has a whistle assembly formed at a bottom portion thereof, such that variations in the frequency of the whistle, indicating misalignment, may be monitored during pumping. 6 figs.

  12. The Rigors of Aligning Performance

    DTIC Science & Technology

    2015-06-01

    bearing in mind customer perceptions. Recommendations include employee training centered on goal alignment, which is vital to highlight the...appeared to be lacking in some areas when bearing in mind customer perceptions. Recommendations include employee training centered on goal alignment...through the strategic plan and CONOPS. However, the extent of goal accomplishment appears to be lacking in some areas when bearing in mind the

  13. National Ignition Facility system alignment.

    PubMed

    Burkhart, S C; Bliss, E; Di Nicola, P; Kalantar, D; Lowe-Webb, R; McCarville, T; Nelson, D; Salmon, T; Schindler, T; Villanueva, J; Wilhelmsen, K

    2011-03-10

    The National Ignition Facility (NIF) is the world's largest optical instrument, comprising 192 37 cm square beams, each generating up to 9.6 kJ of 351 nm laser light in a 20 ns beam precisely tailored in time and spectrum. The Facility houses a massive (10 m diameter) target chamber within which the beams converge onto an ∼1 cm size target for the purpose of creating the conditions needed for deuterium/tritium nuclear fusion in a laboratory setting. A formidable challenge was building NIF to the precise requirements for beam propagation, commissioning the beam lines, and engineering systems to reliably and safely align 192 beams within the confines of a multihour shot cycle. Designing the facility to minimize drift and vibration, placing the optical components in their design locations, commissioning beam alignment, and performing precise system alignment are the key alignment accomplishments over the decade of work described herein. The design and positioning phases placed more than 3000 large (2.5 m×2 m×1 m) line-replaceable optics assemblies to within ±1 mm of design requirement. The commissioning and alignment phases validated clear apertures (no clipping) for all beam lines, and demonstrated automated laser alignment within 10 min and alignment to target chamber center within 44 min. Pointing validation system shots to flat gold-plated x-ray emitting targets showed NIF met its design requirement of ±50 μm rms beam pointing to target chamber. Finally, this paper describes the major alignment challenges faced by the NIF Project from inception to present, and how these challenges were met and solved by the NIF design and commissioning teams.

  14. Automated whole-genome multiple alignment of rat, mouse, and human

    SciTech Connect

    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. ConBind: motif-aware cross-species alignment for the identification of functional transcription factor binding sites

    PubMed Central

    Lelieveld, Stefan H.; Schütte, Judith; Dijkstra, Maurits J.J.; Bawono, Punto; Kinston, Sarah J.; Göttgens, Berthold; Heringa, Jaap; Bonzanni, Nicola

    2016-01-01

    Eukaryotic gene expression is regulated by transcription factors (TFs) binding to promoter as well as distal enhancers. TFs recognize short, but specific binding sites (TFBSs) that are located within the promoter and enhancer regions. Functionally relevant TFBSs are often highly conserved during evolution leaving a strong phylogenetic signal. While multiple sequence alignment (MSA) is a potent tool to detect the phylogenetic signal, the current MSA implementations are optimized to align the maximum number of identical nucleotides. This approach might result in the omission of conserved motifs that contain interchangeable nucleotides such as the ETS motif (IUPAC code: GGAW). Here, we introduce ConBind, a novel method to enhance alignment of short motifs, even if their mutual sequence similarity is only partial. ConBind improves the identification of conserved TFBSs by improving the alignment accuracy of TFBS families within orthologous DNA sequences. Functional validation of the Gfi1b + 13 enhancer reveals that ConBind identifies additional functionally important ETS binding sites that were missed by all other tested alignment tools. In addition to the analysis of known regulatory regions, our web tool is useful for the analysis of TFBSs on so far unknown DNA regions identified through ChIP-sequencing. PMID:26721389

  16. Binocular collimation vs conditional alignment

    NASA Astrophysics Data System (ADS)

    Cook, William J.

    2012-10-01

    As binocular enthusiasts share their passion, topics related to collimation abound. Typically, we find how observers, armed only with a jeweler's screwdriver, can "perfectly collimate" his or her binocular, make it "spot on," or other verbiage of similar connotation. Unfortunately, what most are addressing is a form of pseudo-collimation I have referred to since the mid-1970s as "Conditional Alignment." Ignoring the importance of the mechanical axis (hinge) in the alignment process, this "condition," while having the potential to make alignment serviceable, or even outstanding—within a small range of IPD (Interpupillary Distance) settings relative to the user's spatial accommodation (the ability to accept small errors in parallelism of the optical axes)—may take the instrument farther from the 3-axis collimation conscientious manufacturers seek to implement. Becoming more optically savvy—and especially with so many mechanically inferior binoculars entering the marketplace— the consumer contemplating self-repair and alignment has a need to understand the difference between clinical, 3-axis "collimation" (meaning both optical axes are parallel with the axis of the hinge) and "conditional alignment," as differentiated in this paper. Furthermore, I believe there has been a long-standing need for the term "Conditional Alignment," or some equivalent, to be accepted as part of the vernacular of those who use binoculars extensively, whether for professional or recreational activities. Achieving that acceptance is the aim of this paper.

  17. Projection-Based Volume Alignment

    PubMed Central

    Yu, Lingbo; Snapp, Robert R.; Ruiz, Teresa; Radermacher, Michael

    2013-01-01

    When heterogeneous samples of macromolecular assemblies are being examined by 3D electron microscopy (3DEM), often multiple reconstructions are obtained. For example, subtomograms of individual particles can be acquired from tomography, or volumes of multiple 2D classes can be obtained by random conical tilt reconstruction. Of these, similar volumes can be averaged to achieve higher resolution. Volume alignment is an essential step before 3D classification and averaging. Here we present a projection-based volume alignment (PBVA) algorithm. We select a set of projections to represent the reference volume and align them to a second volume. Projection alignment is achieved by maximizing the cross-correlation function with respect to rotation and translation parameters. If data are missing, the cross-correlation functions are normalized accordingly. Accurate alignments are obtained by averaging and quadratic interpolation of the cross-correlation maximum. Comparisons of the computation time between PBVA and traditional 3D cross-correlation methods demonstrate that PBVA outperforms the traditional methods. Performance tests were carried out with different signal-to-noise ratios using modeled noise and with different percentages of missing data using a cryo-EM dataset. All tests show that the algorithm is robust and highly accurate. PBVA was applied to align the reconstructions of a subcomplex of the NADH: ubiquinone oxidoreductase (Complex I) from the yeast Yarrowia lipolytica, followed by classification and averaging. PMID:23410725

  18. Cavity alignment using fringe scanning

    NASA Astrophysics Data System (ADS)

    Sinkunaite, Laura Paulina; Kawabe, Keita; Landry, Michael

    2017-01-01

    LIGO employs two 4-km long Fabry-Pérot arm cavities, which need to be aligned in order for an interferometer to be locked on a TEM00 mode. Once the cavity is locked, alignment signals can be derived from wave-front sensors which measure the TEM01 mode content. However, the alignment state is not always good enough for locking on TEM00. Even when this is the case, the alignment can be evaluated using a free swinging cavity, that shows flashes when higher-order modes become resonant. By moving test masses, small changes are made to the mirror orientation, and hence the TEM00 mode can be optimized iteratively. Currently, this is a manual procedure, and thus it is very time-consuming. Therefore, this project is aimed to study another possible way to lock the cavity on the TEM00 mode. Misalignment information can also be extracted from the power of the higher-order modes transmitted through the cavity. This talk will present an algorithm for this alternative and faster way to derive the alignment state of the arm cavities. Supported by APS FIP, NSF, and Caltech SFP.

  19. Direct numerical simulation of particle alignment in viscoelastic fluids

    NASA Astrophysics Data System (ADS)

    Hulsen, Martien; Jaensson, Nick; Anderson, Patrick

    2016-11-01

    Rigid particles suspended in viscoelastic fluids under shear can align in string-like structures in flow direction. To unravel this phenomenon, we present 3D direct numerical simulations of the alignment of two and three rigid, non-Brownian particles in a shear flow of a viscoelastic fluid. The equations are solved on moving, boundary-fitted meshes, which are locally refined to accurately describe the polymer stresses around and in between the particles. A small minimal gap size between the particles is introduced. The Giesekus model is used and the effect of the Weissenberg number, shear thinning and solvent viscosity is investigated. Alignment of two and three particles is observed. Morphology plots have been created for various combinations of fluid parameters. Alignment is mainly governed by the value of the elasticity parameter S, defined as half of the ratio between the first normal stress difference and shear stress of the suspending fluid. Alignment appears to occur above a critical value of S, which decreases with increasing shear thinning. This result, together with simulations of a shear-thinning Carreau fluid, leads us to the conclusion that normal stress differences are essential for particle alignment to occur, but it is also strongly promoted by shear thinning.

  20. A two-stage approach to automatic face alignment

    NASA Astrophysics Data System (ADS)

    Wang, Tong; Ai, Haizhou; Huang, Gaofeng

    2003-09-01

    Face alignment is very important in face recognition, modeling and synthesis. Many approaches have been developed for this purpose, such as ASM, AAM, DAM and TC-ASM. After a brief review of all those methods, it is pointed out that these approaches all require a manual initialization to the positions of the landmarks and are very sensitive to it, and despite of all those devoted works the outline of a human face remains a difficult task to be localized precisely. In this paper, a two-stage method to achieve frontal face alignment fully automatically is introduced. The first stage is landmarks' initialization called coarse face alignment. In this stage, after a face is detected by an Adaboost cascade face detector, we use Simple Direct Appearance Model (SDAM) to locate a few key points of human face from the texture according which all the initial landmarks are setup as the coarse alignment. The second stage is fine face alignment that uses a variant of AAM method in which shape variation is predicted from texture reconstruction error together with an embedded ASM refinement for the outline landmarks of the face to achieve the fine alignment. Experiments on a face database of 500 people show that this method is very effective for practical applications.

  1. Optimizing a global alignment of protein interaction networks

    PubMed Central

    Chindelevitch, Leonid; Ma, Cheng-Yu; Liao, Chung-Shou; Berger, Bonnie

    2013-01-01

    Motivation: The global alignment of protein interaction networks is a widely studied problem. It is an important first step in understanding the relationship between the proteins in different species and identifying functional orthologs. Furthermore, it can provide useful insights into the species’ evolution. Results: We propose a novel algorithm, PISwap, for optimizing global pairwise alignments of protein interaction networks, based on a local optimization heuristic that has previously demonstrated its effectiveness for a variety of other intractable problems. PISwap can begin with different types of network alignment approaches and then iteratively adjust the initial alignments by incorporating network topology information, trading it off for sequence information. In practice, our algorithm efficiently refines other well-studied alignment techniques with almost no additional time cost. We also show the robustness of the algorithm to noise in protein interaction data. In addition, the flexible nature of this algorithm makes it suitable for different applications of network alignment. This algorithm can yield interesting insights into the evolutionary dynamics of related species. Availability: Our software is freely available for non-commercial purposes from our Web site, http://piswap.csail.mit.edu/. Contact: bab@csail.mit.edu or csliao@ie.nthu.edu.tw Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24048352

  2. A Nonlinear Observer for Gyro Alignment Estimation

    NASA Technical Reports Server (NTRS)

    Thienel, J.; Sanner, R. M.

    2003-01-01

    A nonlinear observer for gyro alignment estimation is presented. The observer is composed of two error terms, an attitude error and an alignment error. The observer is globally stable with exponential convergence of the attitude errors. The gyro alignment estimate converges to the true alignment when the system is completely observable.

  3. Alignment method for parabolic trough solar concentrators

    DOEpatents

    Diver, Richard B.

    2010-02-23

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

  4. Common Core-Aligned Teaching Resources. State Implementation of Common Core State Standards

    ERIC Educational Resources Information Center

    Anderson, Kimberly; Mira, Mary Elizabeth

    2014-01-01

    The following profiles address how the state departments of education are supporting local educators in classroom implementation of the Common Core by providing and/or facilitating the development of instructional resources and materials aligned to the new standards. In order for instructional resources and materials to be aligned to the Common…

  5. The alignment-distribution graph

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

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

  6. The alignment-distribution graph

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

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

  7. Alignment Tool For Inertia Welding

    NASA Technical Reports Server (NTRS)

    Snyder, Gary L.

    1991-01-01

    Compact, easy-to-use tool aligns drive bar of inertia welder over hole in stub. Ensures drive bar concentric to hole within 0.002 in. (0.051 mm.). Holds two batteries and light bulb. Electrical circuit completed, providing current to bulb when pin in contact with post. When pin centered in post hole, it does not touch post, and lamp turns off. Built for use in making repair welds on liquid-oxygen-injector posts in Space Shuttle main engine. Version having suitably modified dimensions used to facilitate alignment in other forests of post.

  8. XUV ionization of aligned molecules

    SciTech Connect

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

    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.

  9. Measurements of magnetic field alignment

    SciTech Connect

    Kuchnir, M.; Schmidt, E.E.

    1987-11-06

    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.

  10. PhyPA: Phylogenetic method with pairwise sequence alignment outperforms likelihood methods in phylogenetics involving highly diverged sequences.

    PubMed

    Xia, Xuhua

    2016-09-01

    While pairwise sequence alignment (PSA) by dynamic programming is guaranteed to generate one of the optimal alignments, multiple sequence alignment (MSA) of highly divergent sequences often results in poorly aligned sequences, plaguing all subsequent phylogenetic analysis. One way to avoid this problem is to use only PSA to reconstruct phylogenetic trees, which can only be done with distance-based methods. I compared the accuracy of this new computational approach (named PhyPA for phylogenetics by pairwise alignment) against the maximum likelihood method using MSA (the ML+MSA approach), based on nucleotide, amino acid and codon sequences simulated with different topologies and tree lengths. I present a surprising discovery that the fast PhyPA method consistently outperforms the slow ML+MSA approach for highly diverged sequences even when all optimization options were turned on for the ML+MSA approach. Only when sequences are not highly diverged (i.e., when a reliable MSA can be obtained) does the ML+MSA approach outperforms PhyPA. The true topologies are always recovered by ML with the true alignment from the simulation. However, with MSA derived from alignment programs such as MAFFT or MUSCLE, the recovered topology consistently has higher likelihood than that for the true topology. Thus, the failure to recover the true topology by the ML+MSA is not because of insufficient search of tree space, but by the distortion of phylogenetic signal by MSA methods. I have implemented in DAMBE PhyPA and two approaches making use of multi-gene data sets to derive phylogenetic support for subtrees equivalent to resampling techniques such as bootstrapping and jackknifing.

  11. Using Variable-Length Aligned Fragment Pairs and an Improved Transition Function for Flexible Protein Structure Alignment.

    PubMed

    Cao, Hu; Lu, Yonggang

    2017-01-01

    With the rapid growth of known protein 3D structures in number, how to efficiently compare protein structures becomes an essential and challenging problem in computational structural biology. At present, many protein structure alignment methods have been developed. Among all these methods, flexible structure alignment methods are shown to be superior to rigid structure alignment methods in identifying structure similarities between proteins, which have gone through conformational changes. It is also found that the methods based on aligned fragment pairs (AFPs) have a special advantage over other approaches in balancing global structure similarities and local structure similarities. Accordingly, we propose a new flexible protein structure alignment method based on variable-length AFPs. Compared with other methods, the proposed method possesses three main advantages. First, it is based on variable-length AFPs. The length of each AFP is separately determined to maximally represent a local similar structure fragment, which reduces the number of AFPs. Second, it uses local coordinate systems, which simplify the computation at each step of the expansion of AFPs during the AFP identification. Third, it decreases the number of twists by rewarding the situation where nonconsecutive AFPs share the same transformation in the alignment, which is realized by dynamic programming with an improved transition function. The experimental data show that compared with FlexProt, FATCAT, and FlexSnap, the proposed method can achieve comparable results by introducing fewer twists. Meanwhile, it can generate results similar to those of the FATCAT method in much less running time due to the reduced number of AFPs.

  12. Analysing the performance of personal computers based on Intel microprocessors for sequence aligning bioinformatics applications.

    PubMed

    Nair, Pradeep S; John, Eugene B

    2007-01-01

    Aligning specific sequences against a very large number of other sequences is a central aspect of bioinformatics. With the widespread availability of personal computers in biology laboratories, sequence alignment is now often performed locally. This makes it necessary to analyse the performance of personal computers for sequence aligning bioinformatics benchmarks. In this paper, we analyse the performance of a personal computer for the popular BLAST and FASTA sequence alignment suites. Results indicate that these benchmarks have a large number of recurring operations and use memory operations extensively. It seems that the performance can be improved with a bigger L1-cache.

  13. Tonal Alignment in Irish Dialects

    ERIC Educational Resources Information Center

    Dalton, Martha; Ni Chasaide, Ailbhe

    2005-01-01

    A comparison of the contour alignment of nuclear and initial prenuclear accents was carried out for the Irish dialects of Gaoth Dobhair in Ulster (GD-U) and Cois Fharraige in Connaught (CF-C). This was done across conditions where the number of unstressed syllables following the nuclear and preceding the initial prenuclear accents was varied from…

  14. Alignment in Second Language Dialogue

    ERIC Educational Resources Information Center

    Costa, Albert; Pickering, Martin; Sorace, Antonella

    2008-01-01

    This paper considers the nature of second language dialogues, involving at least one non-native (L2) speaker. We assume that dialogue is characterised by a process in which interlocutors develop similar mental states to each other (Pickering & Garrod, 2004). We first consider various means in which interlocutors align their mental states, and…

  15. Aligning Assessments for COSMA Accreditation

    ERIC Educational Resources Information Center

    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…

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

    PubMed

    Li, Yan; Gu, Leon; Kanade, Takeo

    2011-09-01

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

  17. Laser-optic instruments improve machinery alignment

    SciTech Connect

    Bloch, H.P.

    1987-10-12

    Laser-optic alignment systems are fast becoming cost-effective devices that improve the accuracy and speed of machinery shaft alignment. Because of the difficulty, if not impossibility, of aligning operating machinery, cold alignment specifications must be determined to compensate for thermal growth so that the shaft alignment remains within tolerances when the machine reaches normal operating temperature. Some methods for accomplishing this are reviewed here. Three years' field experience with laser-optic alignment systems shows that many of these limitations can be eliminated, resulting in a more accurate alignment in less time. Some actual field alignments are given as examples of the improvement achieved by the use of laser equipment, and a procedure is given that shows how the laser-optic system may be used to determine running alignment changes caused by thermal growth.

  18. Normalized entropy measure for multimodality image alignment

    NASA Astrophysics Data System (ADS)

    Studholme, Colin; Hawkes, David J.; Hill, Derek L.

    1998-06-01

    Automated multi-modality 3D medical image alignment has been an active area of research for many years. There have been a number of recent papers proposing and investigating the use of entropy derived measures of brain image alignment. Any registration measure must allow us to choose between transformation estimates based on the similarity of images within their volume of overlap. Since 3D medical images often have a limited extent and overlap, the similarity measure for the two transformation estimates may be derived from two very different regions within the images. Direct measures of information such as the joint entropy and mutual information will therefore be a function of, not only image similarity in the region of overlap, but also of the local image content within the overlap. In this paper we present a new measure, normalized mutual information, which is simply the ratio of the sum of the marginal entropies and the joint entropy. The effect of changing overlap on current entropy measures and this normalized measure are compared using a simple image model and experiments on clinical MR-PET and MR-CT image data. Results indicate that the normalized entropy measure provides significantly improved behavior over a range of imaged fields of view.

  19. Parallel sequence alignment in limited space.

    PubMed

    Grice, J A; Hughey, R; Speck, D

    1995-01-01

    Sequence comparison with affine gap costs is a problem that is readily parallelizable on simple single-instruction, multiple-data stream (SIMD) parallel processors using only constant space per processing element. Unfortunately, the twin problem of sequence alignment, finding the optimal character-by-character correspondence between two sequences, is more complicated. While the innovative O(n2)-time and O(n)-space serial algorithm has been parallelized for multiple-instruction, multiple-data stream (MIMD) computers with only a communication-time slowdown, typically O(log n), it is not suitable for hardware-efficient SIMD parallel processors with only local communication. This paper proposes several methods of computing sequence alignments with limited memory per processing element. The algorithms are also well-suited to serial implementation. The simpler algorithms feature, for an arbitrary integer L, a factor of L slowdown in exchange for reducing space requirements from O(n) to O(L square root of n) per processing element. Using this result, we describe an O(n log n) parallel time algorithm that requires O(log n) space per processing element on O(n) SIMD processing elements with only a mesh or linear interconnection network.

  20. Bokeh mirror alignment for Cherenkov telescopes

    NASA Astrophysics Data System (ADS)

    Mueller, S. A.; Adam, J.; Ahnen, M. L.; Baack, D.; Balbo, M.; Bergmann, M.; Biland, A.; Blank, M.; Bretz, T.; Bruegge, K. A.; Buss, J.; Dmytriiev, A.; Dorner, D.; Einecke, S.; Hempfling, C.; Hildebrand, D.; Hughes, G.; Linhoff, L.; Mannheim, K.; Neise, D.; Neronov, A.; Noethe, M.; Paravac, A.; Pauss, F.; Rhode, W.; Shukla, A.; Temme, F.; Thaele, J.; Walter, R.

    2016-08-01

    Segmented imaging reflectors are a great choice for Imaging Atmospheric Cherenkov Telescopes (IACTs). However, the alignment of the individual mirror facets is challenging. We align a segmented reflector by observing and optimizing its Bokeh function. Bokeh alignment can already be done with very little resources and little preparation time. Further, Bokeh alignment can be done anytime, even during the day. We present a first usage of Bokeh alignment on FACT, a 4m IACT on Canary Island La Palma, Spain and further a first Bokeh alignment test on the CTA MST IACT prototype in Brelin Adlershof.

  1. Simultaneous particle and field observations of field-aligned currents

    NASA Technical Reports Server (NTRS)

    Berko, F. W.; Hoffman, R. A.; Burton, R. K.; Holzer, R. E.

    1973-01-01

    Simultaneous measurements of low energy precipitating electrons and magnetic fluctuations from the low altitude polar orbiting satellite OGO-4 have been compared. Analysis of the two sets of experimental data for isolated events led to the classification of high latitude field-aligned currents as purely temporal or purely spatial variations. Magnetic field disturbances calculated using these simple current models and the measured particle fluxes were in good agreement with measured field values. While fluxes of greater than 1 keV electrons are detected primarily on the nightside, magnetometer disturbances indicative of field-aligned currents were seen at all local times, both in the visual auroral regions and dayside polar cusp. Thus electrons with energies less than approximately 1 keV are the prime charge carriers in high latitude dayside field-aligned currents. The satellite measurements are in good agreement with previously measured field-aligned current values and with values predicted from several models involving magnetospheric field-aligned currents.

  2. Daniel K. Inouye Solar Telescope optical alignment plan

    NASA Astrophysics Data System (ADS)

    Sekulic, Predrag; Liang, Chen; Gonzales, Kerry; Hubbard, Robert P.; Craig, Simon C.

    2016-07-01

    The Daniel K. Inouye Solar Telescope (DKIST) is a 4-meter solar telescope under construction at Haleakala, Hawaii. The challenge of the DKIST optical alignment is the off-axis Gregorian configuration based on an Altitude-Azimuth mount, the independently-rotating Coudé platform and the large number of relay mirrors. This paper describes the optical alignment plan of the complete telescope, including the primary 4.24-m diameter off-axis secondary mirror, the secondary 620 mm diameter off-axis mirror, the transfer optics and the Coudé optics feeding the wavefront correction system and the science instruments. A number of accurate metrology instruments will be used to align the telescope and to reach the performances, including a laser tracker for initial positioning, a theodolite for accurate tilt alignment, a Coordinate Measurement Machine (CMM) arm for local alignment in the Coudé laboratory, and a Shack-Hartmann wavefront sensor to characterize the aberrations by measuring selected target stars. The wavefront will be characterized at the primary focus, the Gregorian focus, the intermediate focus and at the telescope focal plane. The laser tracker will serve also to measure the mirrors positions as function of Altitude angle due to the Telescope Mount Assembly (TMA) structure deflection. This paper describes also the method that will be used to compute the compensating mirrors shift and tilt needed to correct the residual aberrations and position of the focal plane.

  3. Shuttle onboard IMU alignment methods

    NASA Technical Reports Server (NTRS)

    Henderson, D. M.

    1976-01-01

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

  4. Prism Window for Optical Alignment

    NASA Technical Reports Server (NTRS)

    Tang, Hong

    2008-01-01

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

  5. Aligned mesoporous architectures and devices.

    SciTech Connect

    Brinker, C. Jeffrey; Lu, Yunfeng

    2011-03-01

    This is the final report for the Presidential Early Career Award for Science and Engineering - PECASE (LDRD projects 93369 and 118841) awarded to Professor Yunfeng Lu (Tulane University and University of California-Los Angeles). During the last decade, mesoporous materials with tunable periodic pores have been synthesized using surfactant liquid crystalline as templates, opening a new avenue for a wide spectrum of applications. However, the applications are somewhat limited by the unfavorabe pore orientation of these materials. Although substantial effort has been devoted to align the pore channels, fabrication of mesoporous materials with perpendicular pore channels remains challenging. This project focused on fabrication of mesoporous materials with perpendicularly aligned pore channels. We demonstrated structures for use in water purification, separation, sensors, templated synthesis, microelectronics, optics, controlled release, and highly selective catalysts.

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

    SciTech Connect

    Suh, Y; Crane, C; Krishnan, S; Das, P; Koay, E; Beddar, S

    2015-06-15

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

  7. Local alignment tool based on Hadoop framework and GPU architecture.

    PubMed

    Hung, Che-Lun; Hua, Guan-Jie

    2014-01-01

    With the rapid growth of next generation sequencing technologies, such as Slex, more and more data have been discovered and published. To analyze such huge data the computational performance is an important issue. Recently, many tools, such as SOAP, have been implemented on Hadoop and GPU parallel computing architectures. BLASTP is an important tool, implemented on GPU architectures, for biologists to compare protein sequences. To deal with the big biology data, it is hard to rely on single GPU. Therefore, we implement a distributed BLASTP by combining Hadoop and multi-GPUs. The experimental results present that the proposed method can improve the performance of BLASTP on single GPU, and also it can achieve high availability and fault tolerance.

  8. Aligning incentives in supply chains.

    PubMed

    Narayanan, V G; Raman, Ananth

    2004-11-01

    Most companies don't worry about the behavior of their supply chain partners. Instead, they expect the supply chain to work efficiently without interference, as if guided by Adam Smith's famed invisible hand. In their study of more than 50 supply networks, V.G. Narayanan and Ananth Raman found that companies often looked out for their own interests and ignored those of their network partners. Consequently, supply chains performed poorly. Those results aren't shocking when you consider that supply chains extend across several functions and many companies, each with its own priorities and goals. Yet all those functions and firms must pull in the same direction for a chain to deliver goods and services to consumers quickly and cost-effectively. According to the authors, a supply chain works well only if the risks, costs, and rewards of doing business are distributed fairly across the network. In fact, misaligned incentives are often the cause of excess inventory, stock-outs, incorrect forecasts, inadequate sales efforts, and even poor customer service. The fates of all supply chain partners are interlinked: If the firms work together to serve consumers, they will all win. However, they can do that only if incentives are aligned. Companies must acknowledge that the problem of incentive misalignment exists and then determine its root cause and align or redesign incentives. They can improve alignment by, for instance, adopting revenue-sharing contracts, using technology to track previously hidden information, or working with intermediaries to build trust among network partners. It's also important to periodically reassess incentives, because even top-performing networks find that changes in technology or business conditions alter the alignment of incentives.

  9. Fiber alignment apparatus and method

    DOEpatents

    Kravitz, S.H.; Warren, M.E.; Snipes, M.B. Jr.; Armendariz, M.G.; Word, J.C. V

    1997-08-19

    A fiber alignment apparatus includes a micro-machined nickel spring that captures and locks arrays of single mode fibers into position. The design consists of a movable nickel leaf shaped spring and a fixed pocket where fibers are held. The fiber is slid between the spring and a fixed block, which tensions the spring. When the fiber reaches the pocket, it automatically falls into the pocket and is held by the pressure of the leaf spring. 8 figs.

  10. Fiber alignment apparatus and method

    DOEpatents

    Kravitz, Stanley H.; Warren, Mial Evans; Snipes, Jr., Morris Burton; Armendariz, Marcelino Guadalupe; Word, V., James Cole

    1997-01-01

    A fiber alignment apparatus includes a micro-machined nickel spring that captures and locks arrays of single mode fibers into position. The design consists of a movable nickel leaf shaped spring and a fixed pocket where fibers are held. The fiber is slid between the spring and a fixed block, which tensions the spring. When the fiber reaches the pocket, it automatically falls into the pocket and is held by the pressure of the leaf spring.

  11. Threaded pilot insures cutting tool alignment

    NASA Technical Reports Server (NTRS)

    Goldman, R.; Schneider, W. E.

    1966-01-01

    Threaded pilot allows machining of a port component, or boss, after the reciprocating hole has been threaded. It is used to align cutting surfaces with the boss threads, thus insuring precision alignment.

  12. Aligning Plasma-Arc Welding Oscillations

    NASA Technical Reports Server (NTRS)

    Norris, Jeff; Fairley, Mike

    1989-01-01

    Tool aids in alignment of oscillator probe on variable-polarity plasma-arc welding torch. Probe magnetically pulls arc from side to side as it moves along joint. Tensile strength of joint depends on alignment of weld bead and on alignment of probe. Operator installs new tool on front of torch body, levels it with built-in bubble glass, inserts probe in slot on tool, and locks probe in place. Procedure faster and easier and resulting alignment more accurate and repeatable.

  13. Use laser-optics for machinery alignment

    SciTech Connect

    Bloch, H.P.

    1987-10-01

    Many sources attribute most bearing overload and destructive vibration in industrial machinery to shaft misalignment. There is considerable disagreement as to the alignment quality required. There is also little agreement on suitable calculation methods and achievable accuracy for anticipated thermal growth of machinery (necessary if running alignment is to remain acceptable). This article examines existing alignment quality guidelines for relevance and consistency, and reviews the application of laser-optic alignment systems based on three years of field experience.

  14. Vertically aligned nanostructure scanning probe microscope tips

    DOEpatents

    Guillorn, Michael A.; Ilic, Bojan; Melechko, Anatoli V.; Merkulov, Vladimir I.; Lowndes, Douglas H.; Simpson, Michael L.

    2006-12-19

    Methods and apparatus are described for cantilever structures that include a vertically aligned nanostructure, especially vertically aligned carbon nanofiber scanning probe microscope tips. An apparatus includes a cantilever structure including a substrate including a cantilever body, that optionally includes a doped layer, and a vertically aligned nanostructure coupled to the cantilever body.

  15. Ultrafast electron diffraction from aligned molecules

    SciTech Connect

    Centurion, Martin

    2015-08-17

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

  16. AdoMet radical proteins—from structure to evolution—alignment of divergent protein sequences reveals strong secondary structure element conservation

    PubMed Central

    Nicolet, Yvain; Drennan, Catherine L.

    2004-01-01

    Eighteen subclasses of S-adenosyl-l-methionine (AdoMet) radical proteins have been aligned in the first bioinformatics study of the AdoMet radical superfamily to utilize crystallographic information. The recently resolved X-ray structure of biotin synthase (BioB) was used to guide the multiple sequence alignment, and the recently resolved X-ray structure of coproporphyrinogen III oxidase (HemN) was used as the control. Despite the low 9% sequence identity between BioB and HemN, the multiple sequence alignment correctly predicted all but one of the core helices in HemN, and correctly predicted the residues in the enzyme active site. This alignment further suggests that the AdoMet radical proteins may have evolved from half-barrel structures (αβ)4 to three-quarter-barrel structures (αβ)6 to full-barrel structures (αβ)8. It predicts that anaerobic ribonucleotide reductase (RNR) activase, an ancient enzyme that, it has been suggested, serves as a link between the RNA and DNA worlds, will have a half-barrel structure, whereas the three-quarter barrel, exemplified by HemN, will be the most common architecture for AdoMet radical enzymes, and fewer members of the superfamily will join BioB in using a complete (αβ)8 TIM-barrel fold to perform radical chemistry. These differences in barrel architecture also explain how AdoMet radical enzymes can act on substrates that range in size from 10 atoms to 608 residue proteins. PMID:15289575

  17. Coval: Improving Alignment Quality and Variant Calling Accuracy for Next-Generation Sequencing Data

    PubMed Central

    Kosugi, Shunichi; Natsume, Satoshi; Yoshida, Kentaro; MacLean, Daniel; Cano, Liliana; Kamoun, Sophien; Terauchi, Ryohei

    2013-01-01

    Accurate identification of DNA polymorphisms using next-generation sequencing technology is challenging because of a high rate of sequencing error and incorrect mapping of reads to reference genomes. Currently available short read aligners and DNA variant callers suffer from these problems. We developed the Coval software to improve the quality of short read alignments. Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads. The error correction is executed based on the base quality and allele frequency at the non-reference positions for an individual or pooled sample. We demonstrated the utility of Coval by applying it to simulated genomes and experimentally obtained short-read data of rice, nematode, and mouse. Moreover, we found an unexpectedly large number of incorrectly mapped reads in ‘targeted’ alignments, where the whole genome sequencing reads had been aligned to a local genomic segment, and showed that Coval effectively eliminated such spurious alignments. We conclude that Coval significantly improves the quality of short-read sequence alignments, thereby increasing the calling accuracy of currently available tools for SNP and indel identification. Coval is available at http://sourceforge.net/projects/coval105/. PMID:24116042

  18. Aligning Two Genomic Sequences That Contain Duplications

    NASA Astrophysics Data System (ADS)

    Hou, Minmei; Riemer, Cathy; Berman, Piotr; Hardison, Ross C.; Miller, Webb

    It is difficult to properly align genomic sequences that contain intra-species duplications. With this goal in mind, we have developed a tool, called TOAST (two-way orthologous alignment selection tool), for predicting whether two aligned regions from different species are orthologous, i.e., separated by a speciation event, as opposed to a duplication event. The advantage of restricting alignment to orthologous pairs is that they constitute the aligning regions that are most likely to share the same biological function, and most easily analyzed for evidence of selection. We evaluate TOAST on 12 human/mouse gene clusters.

  19. Accelerator and transport line survey and alignment

    SciTech Connect

    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.

  20. Antares beam-alignment-system performance

    SciTech Connect

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

    1983-01-01

    The beam alignment system for the 24-beam-sector Antares CO/sub 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/sub 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.

  1. FOGSAA: Fast Optimal Global Sequence Alignment Algorithm

    NASA Astrophysics Data System (ADS)

    Chakraborty, Angana; Bandyopadhyay, Sanghamitra

    2013-04-01

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

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

    NASA Technical Reports Server (NTRS)

    Hagopian, John G.

    2010-01-01

    A technique was created to measure the pupil alignment of instruments in situ by measuring calibrated pupil alignment references (PARs) in instruments. The PAR can also be measured using an alignment telescope or an imaging system. PAR allows the verification of the science instrument (SI) pupil alignment at the integrated science instrument module (ISIM) level of assembly at ambient and cryogenic operating temperature. This will allow verification of the ISIM+SI alignment, and provide feedback to realign the SI if necessary.

  3. Aligned interactions in cosmic rays

    NASA Astrophysics Data System (ADS)

    Kempa, J.

    2015-12-01

    The first clean Centauro was found in cosmic rays years many ago at Mt Chacaltaya experiment. Since that time, many people have tried to find this type of interaction, both in cosmic rays and at accelerators. But no one has found a clean cases of this type of interaction.It happened finally in the last exposure of emulsion at Mt Chacaltaya where the second clean Centauro has been found. The experimental data for both the Centauros and STRANA will be presented and discussed in this paper. We also present our comments to the intriguing question of the existence of a type of nuclear interactions at high energy with alignment.

  4. MEANS FOR DETERMINING CENTRIFUGE ALIGNMENT

    DOEpatents

    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.

  5. Aligned interactions in cosmic rays

    SciTech Connect

    Kempa, J.

    2015-12-15

    The first clean Centauro was found in cosmic rays years many ago at Mt Chacaltaya experiment. Since that time, many people have tried to find this type of interaction, both in cosmic rays and at accelerators. But no one has found a clean cases of this type of interaction.It happened finally in the last exposure of emulsion at Mt Chacaltaya where the second clean Centauro has been found. The experimental data for both the Centauros and STRANA will be presented and discussed in this paper. We also present our comments to the intriguing question of the existence of a type of nuclear interactions at high energy with alignment.

  6. Method for protein structure alignment

    DOEpatents

    Blankenbecler, Richard; Ohlsson, Mattias; Peterson, Carsten; Ringner, Markus

    2005-02-22

    This invention provides a method for protein structure alignment. More particularly, the present invention provides a method for identification, classification and prediction of protein structures. The present invention involves two key ingredients. First, an energy or cost function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. Second, a minimization of the energy or cost function by an iterative method, where in each iteration (1) a mean field method is employed for the assignment variables and (2) exact rotation and/or translation of atomic coordinates is performed, weighted with the corresponding assignment variables.

  7. Comparative Topological Analysis of Neuronal Arbors via Sequence Representation and Alignment

    NASA Astrophysics Data System (ADS)

    Gillette, Todd Aaron

    Neuronal morphology is a key mediator of neuronal function, defining the profile of connectivity and shaping signal integration and propagation. Reconstructing neurite processes is technically challenging and thus data has historically been relatively sparse. Data collection and curation along with more efficient and reliable data production methods provide opportunities for the application of informatics to find new relationships and more effectively explore the field. This dissertation presents a method for aiding the development of data production as well as a novel representation and set of analyses for extracting morphological patterns. The DIADEM Challenge was organized for the purposes of determining the state of the art in automated neuronal reconstruction and what existing challenges remained. As one of the co-organizers of the Challenge, I developed the DIADEM metric, a tool designed to measure the effectiveness of automated reconstruction algorithms by comparing resulting reconstructions to expert-produced gold standards and identifying errors of various types. It has been used in the DIADEM Challenge and in the testing of several algorithms since. Further, this dissertation describes a topological sequence representation of neuronal trees amenable to various forms of sequence analysis, notably motif analysis, global pairwise alignment, clustering, and multiple sequence alignment. Motif analysis of neuronal arbors shows a large difference in bifurcation type proportions between axons and dendrites, but that relatively simple growth mechanisms account for most higher order motifs. Pairwise global alignment of topological sequences, modified from traditional sequence alignment to preserve tree relationships, enabled cluster analysis which displayed strong correspondence with known cell classes by cell type, species, and brain region. Multiple alignment of sequences in selected clusters enabled the extraction of conserved features, revealing mouse

  8. Keeping speed and distance for aligned motion

    NASA Astrophysics Data System (ADS)

    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.

  9. Strategies for active alignment of lenses

    NASA Astrophysics Data System (ADS)

    Langehanenberg, Patrik; Heinisch, Josef; Wilde, Chrisitan; Hahne, Felix; Lüerß, Bernd

    2015-10-01

    Today's optical systems require up-to-date assembly and joining technology. The trend of keeping dimensions as small as possible while maintaining or increasing optical imaging performance leaves little to no room for mechanical lens adjustment equipment that may remain in the final product. In this context active alignment of optical elements opens up possibilities for the fast and cost-economic manufacturing of lenses and lens assemblies with highest optical performance. Active alignment for lens manufacturing is the precise alignment of the optical axis of a lens with respect to an optical or mechanical reference axis (e.g. housing) including subsequent fixation by glue. In this contribution we will describe different approaches for active alignment and outline strengths and limitations of the different methods. Using the SmartAlign principle, highest quality cemented lenses can be manufactured without the need for high precision prealignment, while the reduction to a single alignment step greatly reduces the cycle time. The same strategies can also be applied to bonding processes. Lenses and lens groups can be aligned to both mechanical and optical axes to maximize the optical performance of a given assembly. In hybrid assemblies using both mechanical tolerances and active alignment, SmartAlign can be used to align critical lens elements anywhere inside the system for optimized total performance. Since all geometrical parameters are re-measured before each alignment, this process is especially suited for complex and time-consuming production processes where the stability of the reference axis would otherwise be critical. For highest performance, lenses can be actively aligned using up to five degrees of freedom. In this way, SmartAlign enables the production of ultra-precise mounted lenses with an alignment precision below 1 μm.

  10. Measuring alignment of loading fixture

    DOEpatents

    Scavone, Donald W.

    1989-01-01

    An apparatus and method for measuring the alignment of a clevis and pin type loading fixture for compact tension specimens include a pair of substantially identical flat loading ligaments. Each loading ligament has two apertures for the reception of a respective pin of the loading fixture and a thickness less than one-half of a width of the clevis opening. The pair of loading ligaments are mounted in the clevis openings at respective sides thereof. The loading ligaments are then loaded by the pins of the loading fixture and the strain in each loading ligament is measured. By comparing the relative strain of each loading ligament, the alignment of the loading fixture is determined. Preferably, a suitable strain gage device is located at each longitudinal edge of a respective loading ligament equidistant from the two apertures in order to determine the strain thereat and hence the strain of each ligament. The loading ligaments are made substantially identical by jig grinding the loading ligaments as a matched set. Each loading ligament can also be individually calibrated prior to the measurement.

  11. A Technique for determining the director pretilt angle in cells with hybrid or homeotropic alignment of a nematic liquid crystal

    NASA Astrophysics Data System (ADS)

    Vakulin, D. A.

    2015-12-01

    A new technique for determining the director pretilt angle in cells with hybrid or homeotropic alignment of a nematic liquid crystal has been developed. To use this technique, it is necessary to experimentally determine the transmission of an optical system in parallel polarizers and maximum transmission of a cell in crossed polarizers. The technique makes it possible to locally control the liquid crystal director alignment on an aligning surface.

  12. SDT: a virus classification tool based on pairwise sequence alignment and identity calculation.

    PubMed

    Muhire, Brejnev Muhizi; Varsani, Arvind; Martin, Darren Patrick

    2014-01-01

    The perpetually increasing rate at which viral full-genome sequences are being determined is creating a pressing demand for computational tools that will aid the objective classification of these genome sequences. Taxonomic classification approaches that are based on pairwise genetic identity measures are potentially highly automatable and are progressively gaining favour with the International Committee on Taxonomy of Viruses (ICTV). There are, however, various issues with the calculation of such measures that could potentially undermine the accuracy and consistency with which they can be applied to virus classification. Firstly, pairwise sequence identities computed based on multiple sequence alignments rather than on multiple independent pairwise alignments can lead to the deflation of identity scores with increasing dataset sizes. Also, when gap-characters need to be introduced during sequence alignments to account for insertions and deletions, methodological variations in the way that these characters are introduced and handled during pairwise genetic identity calculations can cause high degrees of inconsistency in the way that different methods classify the same sets of sequences. Here we present Sequence Demarcation Tool (SDT), a free user-friendly computer program that aims to provide a robust and highly reproducible means of objectively using pairwise genetic identity calculations to classify any set of nucleotide or amino acid sequences. SDT can produce publication quality pairwise identity plots and colour-coded distance matrices to further aid the classification of sequences according to ICTV approved taxonomic demarcation criteria. Besides a graphical interface version of the program for Windows computers, command-line versions of the program are available for a variety of different operating systems (including a parallel version for cluster computing platforms).

  13. Terrestrial ionospheric signatures of field-aligned currents

    NASA Technical Reports Server (NTRS)

    Friis-Christensen, E.

    1990-01-01

    The occurrence of traveling field-aligned current filaments and twin-vortex patterns is suggested to be related to sudden changes in solar wind dynamic pressure and/or the IMF. Greenland magnetometer observations of the cleft region magnetic perturbations associated with small-scale twin-vortex patterns show that these events occur on both sides of the magnetic local noon, contradicting Glassmeier at al.'s (1989) statistical analysis of 82 twin-vortex subauroral-latitude events obtained by the Scandinavian Magnetometer Array; the stations are closer to the ionospheric projection of the cleft earlier in magnetic local time, relative to the across-the-cleft-located Greenland stations.

  14. Versatile alignment layer method for new types of liquid crystal photonic devices

    SciTech Connect

    Finnemeyer, V.; Bryant, D.; Lu, L.; Bos, P.; Reich, R.; Clark, H.; Berry, S.; Bozler, C.; Yaroshchuk, O.

    2015-07-21

    Liquid crystal photonic devices are becoming increasingly popular. These devices often present a challenge when it comes to creating a robust alignment layer in pre-assembled cells. In this paper, we describe a method of infusing a dye into a microcavity to produce an effective photo-definable alignment layer. However, previous research on such alignment layers has shown that they have limited stability, particularly against subsequent light exposure. As such, we further describe a method of utilizing a pre-polymer, infused into the microcavity along with the liquid crystal, to provide photostability. We demonstrate that the polymer layer, formed under ultraviolet irradiation of liquid crystal cells, has been effectively localized to a thin region near the substrate surface and provides a significant improvement in the photostability of the liquid crystal alignment. This versatile alignment layer method, capable of being utilized in devices from the described microcavities to displays, offers significant promise for new photonics applications.

  15. GSK3 Regulates Mitotic Chromosomal Alignment through CRMP4

    PubMed Central

    Ong Tone, Stephan; Dayanandan, Bama

    2010-01-01

    Background Glycogen Synthase Kinase 3 (GSK3) has been implicated in regulating chromosomal alignment and mitotic progression but the physiological substrates mediating these GSK3-dependent effects have not been identified. Collapsin Response Mediator Protein 4 (CRMP4) is a cytosolic phosphoprotein known to regulate cytoskeletal dynamics and is a known physiological substrate of GSK3. In this study, we investigate the role of CRMP4 during mitosis. Methodology and Principal Findings Here we demonstrate that during mitosis CRMP4 phosphorylation is regulated in a GSK3-dependent manner. We show that CRMP4 localizes to spindle microtubules during mitosis and loss of CRMP4 disrupts chromosomal alignment and mitotic progression. The effect of CRMP4 on chromosomal alignment is dependent on phosphorylation by GSK3 identifying CRMP4 as a critical GSK3 substrate during mitotic progression. We also provide mechanistic data demonstrating that CRMP4 regulates spindle microtubules consistent with its known role in the regulation of the microtubule cytoskeleton. Conclusion and Significance Our findings identify CRMP4 as a key physiological substrate of GSK3 in regulating chromosomal alignment and mitotic progression through its effect on spindle microtubules. PMID:21179545

  16. Distributed sequence alignment applications for the public computing architecture.

    PubMed

    Pellicer, S; Chen, G; Chan, K C C; Pan, Y

    2008-03-01

    The public computer architecture shows promise as a platform for solving fundamental problems in bioinformatics such as global gene sequence alignment and data mining with tools such as the basic local alignment search tool (BLAST). Our implementation of these two problems on the Berkeley open infrastructure for network computing (BOINC) platform demonstrates a runtime reduction factor of 1.15 for sequence alignment and 16.76 for BLAST. While the runtime reduction factor of the global gene sequence alignment application is modest, this value is based on a theoretical sequential runtime extrapolated from the calculation of a smaller problem. Because this runtime is extrapolated from running the calculation in memory, the theoretical sequential runtime would require 37.3 GB of memory on a single system. With this in mind, the BOINC implementation not only offers the reduced runtime, but also the aggregation of the available memory of all participant nodes. If an actual sequential run of the problem were compared, a more drastic reduction in the runtime would be seen due to an additional secondary storage I/O overhead for a practical system. Despite the limitations of the public computer architecture, most notably in communication overhead, it represents a practical platform for grid- and cluster-scale bioinformatics computations today and shows great potential for future implementations.

  17. Automated interferometric alignment system for paraboloidal mirrors

    DOEpatents

    Maxey, L.C.

    1993-09-28

    A method is described for a systematic method of interpreting interference fringes obtained by using a corner cube retroreflector as an alignment aid when aligning a paraboloid to a spherical wavefront. This is applicable to any general case where such alignment is required, but is specifically applicable in the case of aligning an autocollimating test using a diverging beam wavefront. In addition, the method provides information which can be systematically interpreted such that independent information about pitch, yaw and focus errors can be obtained. Thus, the system lends itself readily to automation. Finally, although the method is developed specifically for paraboloids, it can be seen to be applicable to a variety of other aspheric optics when applied in combination with a wavefront corrector that produces a wavefront which, when reflected from the correctly aligned aspheric surface will produce a collimated wavefront like that obtained from the paraboloid when it is correctly aligned to a spherical wavefront. 14 figures.

  18. The Alignment of Galaxy Structures

    NASA Astrophysics Data System (ADS)

    Biernacka, M.; Panko, E.; Bajan, K.; Godłowski, W.; Flin, P.

    2015-11-01

    We analyzed the orientation of the sample of ACO galaxy clusters. We examined the alignment in a subsample of 1056 galaxy structures taken from the Panko-Flin (2006) Catalog with known BM morphological types. We were looking for a correlation between the orientation of the cluster and the positions of neighboring clusters. The Binggeli effect (the excess of small values of the Δθ angles between the direction toward neighboring clusters and the cluster position angle) is observed, having a range up to about 45 h-1 Mpc. The strongest effect was found for elongated BM type I clusters. This is probably connected with the origins of the supergiant galaxy and with cluster formation along a long filament or plane in a supercluster.

  19. AIMFAST: Alignment Implementation for Manufacturing

    SciTech Connect

    2012-09-13

    AIMFAST is a software code used to align facets on a dish concentrator to a specific aimpoint strategy to minimize peak fluxes and maximize system optical performance. AIMFAST uses a large monitor or projections screen to display fringe patterns, and a machine vision camera to image the reflection of these patterns in the subject dish mirrors. From these images, a detailed map of surface normals can be generated and compared to design or fitted mirror shapes. This fitted comparison is then used to develop a single vector representing the orientation of the facets relative to the design orientation, and provide near-real-time adjustment information to a communicating computer. The communicating computer can display adjustments or directly interface with adjustment tools. The software for the communicating computer is specific to the implementation and is not a part of AIMFAST.

  20. IAIMFAST: Alignment Implementation for Manufacturing

    SciTech Connect

    Andraka, Charles E.

    2013-08-29

    AIMFAST is a software code used to align facets on a dish concentrator to a specific aimpoint strategy to minimize peak fluxes and maximize system optical performance. AIM FAST uses a large monitor to display fringe patterns, and a machine vision camera to image the reflection of these patterns in the subject dish mirrors. From these images, a detailed map of surface normals can be generated and compared to design or fitted mirror shapes. This fitted comparison is then used to develop a single vector representing the orientation of the facets relative to the design orientation, and provide near-real-time adjustment information to a communicating computer. The communicating computer can display adjustments or directly interface with adjustment tools.

  1. Tonal alignment in Irish dialects.

    PubMed

    Dalton, Martha; Chasaide, Ailbhe Ní

    2005-01-01

    A comparison of the contour alignment of nuclear and initial prenuclear accents was carried out for the Irish dialects of Gaoth Dobhair in Ulster (GD-U) and Cois Fharraige in Connaught (CF-C). This was done across conditions where the number of unstressed syllables following the nuclear and preceding the initial prenuclear accents was varied from 2-0. This tests a variable peak hypothesis prompted by findings for other languages, that peak timing drifts as a function of the number of syllables preceding (the prenuclear) and following (the nuclear) accent. These data also test a second hypothesis that the L*+H dominant accent of GD-U might be viewed as being underlyingly the same as the dominant H* or H*+L accent of the CF-C dialect. According to this realignment hypothesis, the difference between these Ulster and Connaught dialects lies in the way that the melodic tier is aligned to the segmental tier: GD-U would be viewed as having a delayed realization of the peak relative to the Connaught dialect. Results do not support the variable peak hypothesis for Irish, as in either dialect, the peak appeared to be rather fixed across the three conditions examined (though not necessarily identical for prenuclear and nuclear positions). The results also militate against the realignment hypothesis, which rather than providing a more simple unifying account, would greatly complicate it. One reason is that there is a peak timing difference between the nuclear and prenuclear accents of CF-C, not mirrored in GD-U. Furthermore, even if one were to limit consideration to a single (e.g., prenuclear) context, a simple realignment of the accents in one dialect does not generate the appropriate contour in the other.

  2. Free-space optical communication alignment system

    NASA Astrophysics Data System (ADS)

    Mariola, M.; Petruccione, F.

    2016-10-01

    Optical communication systems in free space require a coarse and fine alignment system to align the receiver and transmitter. In general a coarse alignment is not entirely accurate to transmit the laser beacon in the exact direction of the visible field of the camera. During this process, some algorithms such as the raster, spiral and raster spiral scan algorithm can be used to find the spot of the laser beacon. Applications that require to transmit data in form of polarization signals, such as quantum cryptography, requires a polarisation bases alignment system to transmit and receive the photons. In this paper we present a fine alignment system using a polarised laser beacon. The system proposed was subdivided into a coarse and fine alignment system. The coarse alignment was implemented by using the GPS to acquire the geographical position of the transmitter, receiver and a reference point. The fine alignment was achieved by using a polarised laser beacon from the receiver to the transmitter and a camera located on the transmitter side. The algorithm presented was capable of excluding the background noise. Furthermore the polarisation of the laser beacon was used to align the polarisation bases of the transmitter and the receiver.

  3. Some aspects of SR beamline alignment

    NASA Astrophysics Data System (ADS)

    Gaponov, Yu. A.; Cerenius, Y.; Nygaard, J.; Ursby, T.; Larsson, K.

    2011-09-01

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

  4. VIRUS spectrograph assembly and alignment procedures

    NASA Astrophysics Data System (ADS)

    Prochaska, Travis; Allen, Richard D.; Boster, Emily; DePoy, D. L.; Herbig, Benjamin; Hill, Gary J.; Lee, Hanshin; Marshall, Jennifer L.; Martin, Emily C.; Meador, William; Rheault, Jean-Philippe; Tuttle, Sarah E.; Vattiat, Brian L.

    2012-09-01

    We describe the mechanical assembly and optical alignment processes used to construct the Visual Integral-Field Replicable Unit Spectrograph (VIRUS) instrument. VIRUS is a set of 150+ optical spectrographs designed to support observations for the Hobby-Eberly Telescope Dark Energy Experiment (HETDEX). To meet the instrument's manufacturing constraints, a production line will be set up to build subassemblies in parallel. To aid in the instrument's assembly and alignment, specialized fixtures and adjustment apparatuses have been developed. We describe the design and operations of the various optics alignment apparatuses, as well as the mirrors' alignment and bonding fixtures.

  5. Optimizing femorotibial alignment in high tibial osteotomy

    PubMed Central

    Rudan, John; Harrison, Mark; Simurda, Michael A

    Objective To study factors that affect femorotibial (F-T) alignment after valgus closing wedge tibial osteotomy. Study design A review of standardized standing radiographs. Femorotibial alignment was measured 1 year postoperatively for over- and under-correction. Changes in F–T alignment and in tibial plateau angle were measured. Setting An urban hospital and orthopedic clinic. Patients Eighty-two patients with osteoarthritis and varus femorotibial alignment underwent valgus closing wedge tibial osteotomy. Patients having a diagnosis of inflammatory arthritis or a prior osteotomy about the knee were excluded. Results A 1° wedge removed from the tibia resulted in an average correction of F–T alignment of 1.2°. A knee that had increased valgus orientation of the distal femur had a greater degree of correction, averaging 1.46° in F–T alignment per degree of tibial wedge. This resulted in excessive postoperative valgus alignment for some patients who had increased valgus tilt of the distal femur. Optimal F–T alignment of 6° to 14° of valgus occurred when the postoperative tibial inclination was 4° to 8° of valgus. Conclusions There was a trend for knees with increased valgus orientation of the distal femur to have greater correction in F–T alignment after tibial osteotomy, likely because of a greater opening up of the medial joint space during stance. Surgeons need to account for this in their preoperative planning. PMID:10526522

  6. Dialogue: Interactive Alignment and Its Implications for Language Learning and Language Change

    NASA Astrophysics Data System (ADS)

    Garrod, Simon; Pickering, Martin J.

    This chapter discusses language processing during conversation. In particular, it considers why taking part in a conversation is more straightforward than speaking or listening in isolation. We argue that conversation is easy because speakers and listeners automatically align with each other at different linguistic levels (e.g., sound, grammar, meaning) which leads to alignment at the level of interpretation. This alignment process is reflected in the repetitiveness of dialogue at different levels and occurs both on the basis of local mechanisms of priming and more global mechanisms of routinization. We argue that the latter process may tell us something about both acquisition of language and historical processes of language change.

  7. Quantum Suppression of Alignment in Ultrasmall Grains: Microwave Emission from Spinning Dust will be Negligibly Polarized

    NASA Astrophysics Data System (ADS)

    Draine, B. T.; Hensley, Brandon S.

    2016-11-01

    The quantization of energy levels in small, cold, free-flying nanoparticles suppresses dissipative processes that convert grain rotational kinetic energy into heat. For interstellar grains small enough to have ˜GHz rotation rates, the suppression of dissipation can be extreme. As a result, alignment of such grains is suppressed. This applies both to alignment of the grain body with its angular momentum {\\boldsymbol{J}}, and to alignment of {\\boldsymbol{J}} with the local magnetic field {\\boldsymbol{B}} 0. If the anomalous microwave emission is rotational emission from spinning grains, then it will be negligibly polarized at GHz frequencies, with P ≲ 10-6 at ν > 10 GHz.

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

    SciTech Connect

    Mohammadi, Shahin; Gleich, David F.; Kolda, Tamara G.; Grama, Ananth

    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.

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

    PubMed

    Jordan, Gregory; Goldman, Nick

    2012-04-01

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

  10. Magnetic alignment in grazing and resting cattle and deer

    PubMed Central

    Begall, Sabine; Červený, Jaroslav; Neef, Julia; Vojtěch, Oldřich; Burda, Hynek

    2008-01-01

    We demonstrate by means of simple, noninvasive methods (analysis of satellite images, field observations, and measuring “deer beds” in snow) that domestic cattle (n = 8,510 in 308 pastures) across the globe, and grazing and resting red and roe deer (n = 2,974 at 241 localities), align their body axes in roughly a north–south direction. Direct observations of roe deer revealed that animals orient their heads northward when grazing or resting. Amazingly, this ubiquitous phenomenon does not seem to have been noticed by herdsmen, ranchers, or hunters. Because wind and light conditions could be excluded as a common denominator determining the body axis orientation, magnetic alignment is the most parsimonious explanation. To test the hypothesis that cattle orient their body axes along the field lines of the Earth's magnetic field, we analyzed the body orientation of cattle from localities with high magnetic declination. Here, magnetic north was a better predictor than geographic north. This study reveals the magnetic alignment in large mammals based on statistically sufficient sample sizes. Our findings open horizons for the study of magnetoreception in general and are of potential significance for applied ethology (husbandry, animal welfare). They challenge neuroscientists and biophysics to explain the proximate mechanisms. PMID:18725629

  11. Magnetic alignment in grazing and resting cattle and deer.

    PubMed

    Begall, Sabine; Cerveny, Jaroslav; Neef, Julia; Vojtech, Oldrich; Burda, Hynek

    2008-09-09

    We demonstrate by means of simple, noninvasive methods (analysis of satellite images, field observations, and measuring "deer beds" in snow) that domestic cattle (n = 8,510 in 308 pastures) across the globe, and grazing and resting red and roe deer (n = 2,974 at 241 localities), align their body axes in roughly a north-south direction. Direct observations of roe deer revealed that animals orient their heads northward when grazing or resting. Amazingly, this ubiquitous phenomenon does not seem to have been noticed by herdsmen, ranchers, or hunters. Because wind and light conditions could be excluded as a common denominator determining the body axis orientation, magnetic alignment is the most parsimonious explanation. To test the hypothesis that cattle orient their body axes along the field lines of the Earth's magnetic field, we analyzed the body orientation of cattle from localities with high magnetic declination. Here, magnetic north was a better predictor than geographic north. This study reveals the magnetic alignment in large mammals based on statistically sufficient sample sizes. Our findings open horizons for the study of magnetoreception in general and are of potential significance for applied ethology (husbandry, animal welfare). They challenge neuroscientists and biophysics to explain the proximate mechanisms.

  12. Learning Deep Sharable and Structural Detectors for Face Alignment.

    PubMed

    Liu, Hao; Lu, Jiwen; Feng, Jianjiang; Zhou, Jie

    2017-04-01

    Face alignment aims at localizing multiple facial landmarks for a given facial image, which usually suffers from large variances of diverse facial expressions, aspect ratios and partial occlusions, especially when face images were captured in wild conditions. Conventional face alignment methods extract local features and then directly concatenate these features for global shape regression. Unlike these methods which cannot explicitly model the correlation of neighbouring landmarks and motivated by the fact that individual landmarks are usually correlated, we propose a deep sharable and structural detectors (DSSD) method for face alignment. To achieve this, we firstly develop a structural feature learning method to explicitly exploit the correlation of neighbouring landmarks, which learns to cover semantic information to disambiguate the neighbouring landmarks. Moreover, our model selectively learns a subset of sharable latent tasks across neighbouring landmarks under the paradigm of the multi-task learning framework, so that the redundancy information of the overlapped patches can be efficiently removed. To better improve the performance, we extend our DSSD to a recurrent DSSD (R-DSSD) architecture by integrating with the complementary information from multi-scale perspectives. Experimental results on the widely used benchmark datasets show that our methods achieve very competitive performance compared to the state-of-the-arts.

  13. Shear alignment of a disordered lamellar mesophase.

    PubMed

    Kumaran, V; Raman, D S S

    2011-03-01

    The shear alignment of an initially disordered lamellar phase is examined using lattice Boltzmann simulations of a mesoscopic model based on a free-energy functional for the concentration modulation. For a small shear cell of width 8λ, the qualitative features of the alignment process are strongly dependent on the Schmidt number Sc=ν/D (ratio of kinematic viscosity and mass diffusion coefficient). Here, λ is the wavelength of the concentration modulation. At low Schmidt number, it is found that there is a significant initial increase in the viscosity, coinciding with the alignment of layers along the extensional axis, followed by a decrease at long times due to the alignment along the flow direction. At high Schmidt number, alignment takes place due to the breakage and reformation of layers because diffusion is slow compared to shear deformation; this results in faster alignment. The system size has a strong effect on the alignment process; perfect alignment takes place for a small systems of width 8λ and 16λ, while a larger system of width 32λ does not align completely even at long times. In the larger system, there appears to be a dynamical steady state in which the layers are not perfectly aligned--where there is a balance between the annealing of defects due to shear and the creation due to an instability of the aligned lamellar phase under shear. We observe two types of defect creation mechanisms: the buckling instability under dilation, which was reported earlier, as well as a second mechanism due to layer compression.

  14. Fitting alignment tensor components to experimental RDCs, CSAs and RQCs.

    PubMed

    Wirz, Lukas N; Allison, Jane R

    2015-05-01

    Residual dipolar couplings, chemical shift anisotropies and quadrupolar couplings provide information about the orientation of inter-spin vectors and the anisotropic contribution of the local environment to the chemical shifts of nuclei, respectively. Structural interpretation of these observables requires parameterization of their angular dependence in terms of an alignment tensor. We compare and evaluate two algorithms for generating the optimal alignment tensor for a given molecular structure and set of experimental data, namely SVD (Losonczi et al. in J Magn Reson 138(2):334-342, 1999), which scales as [Formula: see text], and the linear least squares algorithm (Press et al. in Numerical recipes in C. The art of scientific computing, 2nd edn. Cambridge University Press, Cambridge, 1997), which scales as [Formula: see text].

  15. Reconfigurable systems for sequence alignment and for general dynamic programming.

    PubMed

    Jacobi, Ricardo P; Ayala-Rincón, Mauricio; Carvalho, Luis G A; Llanos, Carlos H; Hartenstein, Reiner W

    2005-09-30

    Reconfigurable systolic arrays can be adapted to efficiently resolve a wide spectrum of computational problems; parallelism is naturally explored in systolic arrays and reconfigurability allows for redefinition of the interconnections and operations even during run time (dynamically). We present a reconfigurable systolic architecture that can be applied for the efficient treatment of several dynamic programming methods for resolving well-known problems, such as global and local sequence alignment, approximate string matching and longest common subsequence. The dynamicity of the reconfigurability was found to be useful for practical applications in the construction of sequence alignments. A VHDL (VHSIC hardware description language) version of this new architecture was implemented on an APEX FPGA (Field programmable gate array). It would be several magnitudes faster than the software algorithm alternatives.

  16. Self-aligning LED-based optical link

    NASA Astrophysics Data System (ADS)

    Shen, Thomas C.; Drost, Robert J.; Rzasa, John R.; Sadler, Brian M.; Davis, Christopher C.

    2016-09-01

    The steady advances in light-emitting diode (LED) technology have motivated the use of LEDs in optical wireless communication (OWC) applications such as indoor local area networks (LANs) and communication between mobile platforms (e.g., robots, vehicles). In contrast to traditional radio frequency (RF) wireless communication, OWC utilizes electromagnetic spectrum that is largely unregulated and unrestricted. OWC communication may be especially useful in RF-denied environments, in which RF communication may be prohibited or undesirable. However, OWC does present some challenges, including the need to maintain alignment between potentially moving nodes. We describe a novel system for link alignment that is composed of a hyperboloidal mirror, camera, and gimbal. The experimental system is able to use the mirror and camera to detect an LED beacon of a neighboring node and estimate its bearing (azimuth and elevation), point the gimbal towards the beacon, and establish an optical link.

  17. A machine-learning approach reveals that alignment properties alone can accurately predict inference of lateral gene transfer from discordant phylogenies.

    PubMed

    Roettger, Mayo; Martin, William; Dagan, Tal

    2009-09-01

    Among the methods currently used in phylogenomic practice to detect the presence of lateral gene transfer (LGT), one of the most frequently employed is the comparison of gene tree topologies for different genes. In cases where the phylogenies for different genes are incompatible, or discordant, for well-supported branches there are three simple interpretations for the result: 1) gene duplications (paralogy) followed by many independent gene losses have occurred, 2) LGT has occurred, or 3) the phylogeny is well supported but for reasons unknown is nonetheless incorrect. Here, we focus on the third possibility by examining the properties of 22,437 published multiple sequence alignments, the Bayesian maximum likelihood trees for which either do or do not suggest the occurrence of LGT by the criterion of discordant branches. The alignments that produce discordant phylogenies differ significantly in several salient alignment properties from those that do not. Using a support vector machine, we were able to predict the inference of discordant tree topologies with up to 80% accuracy from alignment properties alone.

  18. Precise 3D image alignment in micro-axial tomography.

    PubMed

    Matula, P; Kozubek, M; Staier, F; Hausmann, M

    2003-02-01

    Micro (micro-) axial tomography is a challenging technique in microscopy which improves quantitative imaging especially in cytogenetic applications by means of defined sample rotation under the microscope objective. The advantage of micro-axial tomography is an effective improvement of the precision of distance measurements between point-like objects. Under certain circumstances, the effective (3D) resolution can be improved by optimized acquisition depending on subsequent, multi-perspective image recording of the same objects followed by reconstruction methods. This requires, however, a very precise alignment of the tilted views. We present a novel feature-based image alignment method with a precision better than the full width at half maximum of the point spread function. The features are the positions (centres of gravity) of all fluorescent objects observed in the images (e.g. cell nuclei, fluorescent signals inside cell nuclei, fluorescent beads, etc.). Thus, real alignment precision depends on the localization precision of these objects. The method automatically determines the corresponding objects in subsequently tilted perspectives using a weighted bipartite graph. The optimum transformation function is computed in a least squares manner based on the coordinates of the centres of gravity of the matched objects. The theoretically feasible precision of the method was calculated using computer-generated data and confirmed by tests on real image series obtained from data sets of 200 nm fluorescent nano-particles. The advantages of the proposed algorithm are its speed and accuracy, which means that if enough objects are included, the real alignment precision is better than the axial localization precision of a single object. The alignment precision can be assessed directly from the algorithm's output. Thus, the method can be applied not only for image alignment and object matching in tilted view series in order to reconstruct (3D) images, but also to validate the

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

    NASA Astrophysics Data System (ADS)

    Chen, Guan-Jye; Bodoh, D.; Wallace, John P.; Anderson, Paul D.; Reilly, Michael T.; Nachman, Ramez; Cerrina, Franco

    1992-07-01

    We describe the implementation of the two-state alignment system into the CXrL aligner, which is developed at our Center for X-ray Lithography. The CXrL aligner is designed to expose sub 0.25 μm feature size integrated circuits. The aligner consists of a three-axes two-state alignment system for alignment error detection and a piezo based precision mechanical stage for alignment error correction. The wafer is held by a precision vacuum chuck, while the mask is held by three vacuum suction cups located around the glass ring. In the prototype, the mask to wafer relative positioning is achieved by 3 motorized stages (for gap setting) and 3 piezo-actuators (for lateral alignment). Since the optical system is designed to be located outside of the synchrotron radiation path, alignment can be performed during exposure. We present the results of the alignment system performance, such as noise equivalent displacement and alignment signal response time. An alignment signal repeatibility of much better than 3σ = 0.07μm is achieved. We also briefly describe the future evaluation of the system, such as overlay measurement of the system using verniers and SEM inspection of some specially designed patterns.

  20. Phylogenetic Inference From Conserved sites Alignments

    SciTech Connect

    grundy, W.N.; Naylor, G.J.P.

    1999-08-15

    Molecular sequences provide a rich source of data for inferring the phylogenetic relationships among species. However, recent work indicates that even an accurate multiple alignment of a large sequence set may yield an incorrect phylogeny and that the quality of the phylogenetic tree improves when the input consists only of the highly conserved, motif regions of the alignment. This work introduces two methods of producing multiple alignments that include only the conserved regions of the initial alignment. The first method retains conserved motifs, whereas the second retains individual conserved sites in the initial alignment. Using parsimony analysis on a mitochondrial data set containing 19 species among which the phylogenetic relationships are widely accepted, both conserved alignment methods produce better phylogenetic trees than the complete alignment. Unlike any of the 19 inference methods used before to analyze this data, both methods produce trees that are completely consistent with the known phylogeny. The motif-based method employs far fewer alignment sites for comparable error rates. For a larger data set containing mitochondrial sequences from 39 species, the site-based method produces a phylogenetic tree that is largely consistent with known phylogenetic relationships and suggests several novel placements.

  1. Nonvisual Cues for Aligning to Cross Streets

    ERIC Educational Resources Information Center

    Scott, Alan C.; Barlow, Janet M.; Guth, David A.; Bentzen, Billie Louise; Cunningham, Christopher M.; Long, Richard

    2011-01-01

    Accurately aligning to a crosswalk is an important component of safe street crossing for pedestrians who are blind. Six alignment cues were evaluated in a simulated crosswalk environment in which the angle of the crosswalk was not always in line with the slope of the ramp. The effectiveness of each cue is reported and implications are discussed.…

  2. Instructional Alignment under No Child Left Behind

    ERIC Educational Resources Information Center

    Polikoff, Morgan S.

    2012-01-01

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

  3. Probabilistic sequence alignment of stratigraphic records

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

  4. Galaxy Alignments: Observations and Impact on Cosmology

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

    Galaxy shapes are not randomly oriented, rather they are statistically aligned in a way that can depend on formation environment, history and galaxy type. Studying the alignment of galaxies can therefore deliver important information about the physics of galaxy formation and evolution as well as the growth of structure in the Universe. In this review paper we summarise key measurements of galaxy alignments, divided by galaxy type, scale and environment. We also cover the statistics and formalism necessary to understand the observations in the literature. With the emergence of weak gravitational lensing as a precision probe of cosmology, galaxy alignments have taken on an added importance because they can mimic cosmic shear, the effect of gravitational lensing by large-scale structure on observed galaxy shapes. This makes galaxy alignments, commonly referred to as intrinsic alignments, an important systematic effect in weak lensing studies. We quantify the impact of intrinsic alignments on cosmic shear surveys and finish by reviewing practical mitigation techniques which attempt to remove contamination by intrinsic alignments.

  5. Achieving Organisational Change through Values Alignment

    ERIC Educational Resources Information Center

    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…

  6. Overlay improvement by zone alignment strategy

    NASA Astrophysics Data System (ADS)

    Huang, Chun-Yen; Lee, Ai-Yi; Shih, Chiang-Lin; Yang, Richer; Yuan, Michael; Chen, Henry; Chang, Ray

    2008-03-01

    It is evident that DRAM ground rule continues to shrink down to 90nm and beyond, overlay performance has become more and more critical and important. Wafer edge shows different behavior from center by processes, e.g. a tremendous misalignment at wafer edge makes yield loss . When a conventional linear model is used for alignment correction, higher uncorrectable overlay residuals mostly happen at wafer edge. Therefore, it's obviously necessary to introduce an innovational alignment correction methdology to reduce unwanted wafer edge effect. In this study, we demonstrate the achievement of moderating poor overlay in wafer edge area by a novel zone-dependent alignment strategy, the so-called "Zone Alignment (ZA)". The main difference between the conventional linear model and zone alignment strategy is that the latter compensates an improper averaging effect from first modeling through weighting all surrounding marks with a nonlinear model. In addition, the effects of mark quantity and sampling distribution from "Zone Alignment" are also introduced in this paper. The results of this study indicate that ZA can reduce uncorrectable overlay residual and improve wafer-to-wafer variation significantly. Furthermore, obvious yield improvement is verified by ZA strategy. In conclusion, Zone alignment is the noteworthy strategy for overlay improvement. Moreover, suitable alignment map and mark numbers should be taken into consideration carefully when ZA is applied for further technology node.

  7. Alignment of Developments in Higher Education

    ERIC Educational Resources Information Center

    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…

  8. Compositions for directed alignment of conjugated polymers

    DOEpatents

    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).

  9. Optical alignment of a pupil imaging spectrometer

    NASA Technical Reports Server (NTRS)

    Horchem, Stephen D.; Kohrman, Richard J.

    1989-01-01

    The GOES Sounder is a 19-channel discrete filter spectrometer with an additional channel for star sensing. This paper presents the GOES Sounder's instrument optics and compensations, alignment rationale, and alignment mechanism and sensitivities. The results of a line of sight tolerance analysis of the instrument are described, and the prealignment and instrument coregistration are addressed.

  10. Precision aligned split V-block

    DOEpatents

    George, Irwin S.

    1984-01-01

    A precision aligned split V-block for holding a workpiece during a milling operation having an expandable frame for allowing various sized workpieces to be accommodated, is easily secured directly to the mill table and having key lugs in one base of the split V-block that assures constant alignment.

  11. Partial Automated Alignment and Integration System

    NASA Technical Reports Server (NTRS)

    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. Evaluating Content Alignment in Computerized Adaptive Testing

    ERIC Educational Resources Information Center

    Wise, Steven L.; Kingsbury, G. Gage; Webb, Norman L.

    2015-01-01

    The alignment between a test and the content domain it measures represents key evidence for the validation of test score inferences. Although procedures have been developed for evaluating the content alignment of linear tests, these procedures are not readily applicable to computerized adaptive tests (CATs), which require large item pools and do…

  13. Alignment-free phylogenetics and population genetics.

    PubMed

    Haubold, Bernhard

    2014-05-01

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

  14. Vane segment support and alignment device

    DOEpatents

    McLaurin, L.D.; Sizemore, J.D.

    1999-07-13

    A support and alignment assembly for supporting and aligning a vane segment is provided. The support and alignment assembly comprises a torque plate which defines an opening for receiving an eccentric pin and a locking end member for receiving a lock socket member. An eccentric pin adjustably supported by the torque plate opening for supporting and aligning a vane segment is provided. A lock socket member adapted to securely receive the eccentric pin and rotated therewith, and adjustably engage the torque plate locking end is provided. The lock socket member receives the eccentric pin, such that when the eccentric pin is adjusted to align the vane segment, the lock socket member engages the torque plate locking end to secure the vane segment in the desired position. 5 figs.

  15. Vane segment support and alignment device

    SciTech Connect

    McLaurin, Leroy Dixon; Sizemore, John Derek

    1999-01-01

    A support and alignment assembly for supporting and aligning a vane segment is provided. The support and alignment assembly comprises a torque plate which defines an opening for receiving an eccentric pin and a locking end member for receiving a lock socket member. An eccentric pin adjustably supported by the torque plate opening for supporting and aligning a vane segment is provided. A lock socket member adapted to securely receive the eccentric pin and rotated therewith, and adjustably engage the torque plate locking end is provided. The lock socket member receives the eccentric pin, such that when the eccentric pin is adjusted to align the vane segment, the lock socket member engages the torque plate locking end to secure the vane segment in the desired position.

  16. Aligning Greek-English parallel texts

    NASA Astrophysics Data System (ADS)

    Galiotou, Eleni; Koronakis, George; Lazari, Vassiliki

    2015-02-01

    In this paper, we discuss issues concerning the alignment of parallel texts written in languages with different alphabets based on an experiment of aligning texts from the proceedings of the European Parliament in Greek and English. First, we describe our implementation of the k-vec algorithm and its application to the bilingual corpus. Then the output of the algorithm is used as a starting point for an alignment procedure at a sentence level which also takes into account mark-ups of meta-information. The results of the implementation are compared to those of the application of the Church and Gale alignment algorithm on the Europarl corpus. The conclusions of this comparison can give useful insights as for the efficiency of alignment algorithms when applied to the particular bilingual corpus.

  17. Automated interferometric alignment system for paraboloidal mirrors

    DOEpatents

    Maxey, L. Curtis

    1993-01-01

    A method is described for a systematic method of interpreting interference fringes obtained by using a corner cube retroreflector as an alignment aid when aigning a paraboloid to a spherical wavefront. This is applicable to any general case where such alignment is required, but is specifically applicable in the case of aligning an autocollimating test using a diverging beam wavefront. In addition, the method provides information which can be systematically interpreted such that independent information about pitch, yaw and focus errors can be obtained. Thus, the system lends itself readily to automation. Finally, although the method is developed specifically for paraboloids, it can be seen to be applicable to a variety of other aspheric optics when applied in combination with a wavefront corrector that produces a wavefront which, when reflected from the correctly aligned aspheric surface will produce a collimated wavefront like that obtained from the paraboloid when it is correctly aligned to a spherical wavefront.

  18. Array tomography: semiautomated image alignment.

    PubMed

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

    2010-11-01

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

  19. Recursions for statistical multiple alignment

    PubMed Central

    Hein, Jotun; Jensen, Jens Ledet; Pedersen, Christian N. S.

    2003-01-01

    Algorithms are presented that allow the calculation of the probability of a set of sequences related by a binary tree that have evolved according to the Thorne–Kishino–Felsenstein model for a fixed set of parameters. The algorithms are based on a Markov chain generating sequences and their alignment at nodes in a tree. Depending on whether the complete realization of this Markov chain is decomposed into the first transition and the rest of the realization or the last transition and the first part of the realization, two kinds of recursions are obtained that are computationally similar but probabilistically different. The running time of the algorithms is \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} \\begin{equation*}O({\\Pi}_{i}^{d}=1~L_{i})\\end{equation*}\\end{document}, where Li is the length of the ith observed sequences and d is the number of sequences. An alternative recursion is also formulated that uses only a Markov chain involving the inner nodes of a tree. PMID:14657378

  20. GLOBAL PEAK ALIGNMENT FOR COMPREHENSIVE TWO-DIMENSIONAL GAS CHROMATOGRAPHY MASS SPECTROMETRY USING POINT MATCHING ALGORITHMS

    PubMed Central

    Deng, Beichuan; Kim, Seongho; Li, Hengguang; Heath, Elisabeth; Zhang, Xiang

    2016-01-01

    Comprehensive two-dimensional gas chromatography coupled with mass spectrometry (GC×GC-MS) has been used to analyze multiple samples in a metabolomics study. However, due to some uncontrollable experimental conditions, such as the differences in temperature or pressure, matrix effects on samples, and stationary phase degradation, there is always a shift of retention times in the two GC columns between samples. In order to correct the retention time shifts in GC×GC-MS, the peak alignment is a crucial data analysis step to recognize the peaks generated by the same metabolite in different samples. Two approaches have been developed for GC×GC-MS data alignment: profile alignment and peak matching alignment. However, these existing alignment methods are all based on a local alignment, resulting that a peak may not be correctly aligned in a dense chromatographic region where many peaks are present in a small region. False alignment will result in false discovery in the downstream statistical analysis. We, therefore, develop a global comparison based peak alignment method using point matching algorithm (PMA-PA) for both homogeneous and heterogeneous data. The developed algorithm PMA-PA first extracts feature points (peaks) in the chromatography and then searches globally the matching peaks in the consecutive chromatography by adopting the projection of rigid and non-rigid transformation. PMA-PA is further applied to two real experimental data sets, showing that PMA-PA is a promising peak alignment algorithm for both homogenous and heterogeneous data in terms of F1 score, although it uses only peak location information. PMID:27650662

  1. Beam and target alignment at the National Ignition Facility using the Target Alignment Sensor (TAS)

    NASA Astrophysics Data System (ADS)

    Di Nicola, P.; Kalantar, D.; McCarville, T.; Klingmann, J.; Alvarez, S.; Lowe-Webb, R.; Lawson, J.; Datte, P.; Danforth, P.; Schneider, M.; Di Nicola, J.-M.; Jackson, J.; Orth, C.; Azevedo, S.; Tommasini, R.; Manuel, A.; Wallace, R.

    2012-10-01

    The requirements for beam and target alignment for successful ignition experiments on the National Ignition Facility (NIF) are stringent: the average of beams to the target must be within 25 μm. Beam and target alignment are achieved with the Target Alignment Sensor (TAS). The TAS is a precision optical device that is inserted into target chamber center to facilitate both beam and target alignment. It incorporates two camera views (upper/lower and side) mounted on each of two stage assemblies (jaws) to view and align the target. It also incorporates a large mirror on each of the two assemblies to reflect the alignment beams onto the upper/lower cameras for beam alignment. The TAS is located in the chamber using reference features by viewing it with two external telescope views. The two jaws are adjusted in elevation to match the desired beam and target alignment locations. For some shot setups, a sequence of TAS positions is required to achieve the full setup and alignment. In this paper we describe the TAS, the characterization of the TAS coordinates for beam and target alignment, and summarize pointing shots that demonstrate the accuracy of beam-target alignment.

  2. Structure based alignment and clustering of proteins (STRALCP)

    DOEpatents

    Zemla, Adam T.; Zhou, Carol E.; Smith, Jason R.; Lam, Marisa W.

    2013-06-18

    Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a "structural footprint" to the cluster.

  3. An Improved Inertial Frame Alignment Algorithm Based on Horizontal Alignment Information for Marine SINS.

    PubMed

    Che, Yanting; Wang, Qiuying; Gao, Wei; Yu, Fei

    2015-10-05

    In this paper, an improved inertial frame alignment algorithm for a marine SINS under mooring conditions is proposed, which significantly improves accuracy. Since the horizontal alignment is easy to complete, and a characteristic of gravity is that its component in the horizontal plane is zero, we use a clever method to improve the conventional inertial alignment algorithm. Firstly, a large misalignment angle model and a dimensionality reduction Gauss-Hermite filter are employed to establish the fine horizontal reference frame. Based on this, the projection of the gravity in the body inertial coordinate frame can be calculated easily. Then, the initial alignment algorithm is accomplished through an inertial frame alignment algorithm. The simulation and experiment results show that the improved initial alignment algorithm performs better than the conventional inertial alignment algorithm, and meets the accuracy requirements of a medium-accuracy marine SINS.

  4. Proper alignment of the microscope.

    PubMed

    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.

  5. Daily Bone Alignment With Limited Repeat CT Correction Rivals Daily Ultrasound Alignment for Prostate Radiotherapy

    SciTech Connect

    O'Daniel, Jennifer C.; Dong Lei Zhang Lifei; Wang He; Tucker, Susan L.; Kudchadker, Rajat J.; Lee, Andrew K.; Cheung, Rex; Cox, James D.; Kuban, Deborah A.; Mohan, Radhe

    2008-05-01

    Purpose: To compare the effectiveness of daily ultrasound (US)- and computed tomography (CT)-guided alignments with an off-line correction protocol using daily bone alignment plus a correction factor for systematic internal prostate displacement (CF{sub ID}). Methods and Materials: Ten prostate cancer patients underwent CT scans three times weekly using an integrated CT-linear accelerator system, followed by alignment using US for daily radiotherapy. Intensity-modulated radiotherapy plans were designed with our current clinical margins. The treatment plan was copied onto the repeat CT images and aligned using several methods: (1) bone alignment plus CF{sub ID} after three off-line CT scans (bone+3CT), (2) bone alignment plus CF{sub ID} after six off-line CT scans (bone+6CT), (3) US alignment, and (4) CT alignment. The accuracy of the repeated US and CT measurements to determine the CF{sub ID} was compared. The target dosimetric effect was quantified. Results: The CF{sub ID} for internal systematic prostate displacements was more accurately measured with limited repeat CT scans than with US (residual error, 0.0 {+-} 0.7 mm vs. 2.0 {+-} 3.2 mm). Bone+3CT, bone+6CT, and US provided equivalent prostate and seminal vesicle dose coverage, but bone+3CT and bone+6CT produced more precise daily alignments. Daily CT alignment provided the greatest target dose coverage. Conclusion: Daily bone alignment plus CF{sub ID} for internal systematic prostate displacement provided better daily alignment precision and equivalent dose coverage compared with daily US alignment. The CF{sub ID} should be based on at least three repeat CT scans, which could be collected before the start of treatment or during the first 3 treatment days. Daily bone alignment plus CF{sub ID} provides another option for accurate prostate cancer patient positioning.

  6. Scale dependence of the alignment between strain rate and rotation in turbulent shear flow

    NASA Astrophysics Data System (ADS)

    Fiscaletti, D.; Elsinga, G. E.; Attili, A.; Bisetti, F.; Buxton, O. R. H.

    2016-10-01

    The scale dependence of the statistical alignment tendencies of the eigenvectors of the strain-rate tensor ei, with the vorticity vector ω , is examined in the self-preserving region of a planar turbulent mixing layer. Data from a direct numerical simulation are filtered at various length scales and the probability density functions of the magnitude of the alignment cosines between the two unit vectors | ei.ω ̂| are examined. It is observed that the alignment tendencies are insensitive to the concurrent large-scale velocity fluctuations, but are quantitatively affected by the nature of the concurrent large-scale velocity-gradient fluctuations. It is confirmed that the small-scale (local) vorticity vector is preferentially aligned in parallel with the large-scale (background) extensive strain-rate eigenvector e1, in contrast to the global tendency for ω to be aligned in parallel with the intermediate strain-rate eigenvector [Hamlington et al., Phys. Fluids 20, 111703 (2008), 10.1063/1.3021055]. When only data from regions of the flow that exhibit strong swirling are included, the so-called high-enstrophy worms, the alignment tendencies are exaggerated with respect to the global picture. These findings support the notion that the production of enstrophy, responsible for a net cascade of turbulent kinetic energy from large scales to small scales, is driven by vorticity stretching due to the preferential parallel alignment between ω and nonlocal e1 and that the strongly swirling worms are kinematically significant to this process.

  7. iPBA: a tool for protein structure comparison using sequence alignment strategies

    PubMed Central

    Gelly, Jean-Christophe; Joseph, Agnel Praveen; Srinivasan, Narayanaswamy; de Brevern, Alexandre G.

    2011-01-01

    With the immense growth in the number of available protein structures, fast and accurate structure comparison has been essential. We propose an efficient method for structure comparison, based on a structural alphabet. Protein Blocks (PBs) is a widely used structural alphabet with 16 pentapeptide conformations that can fairly approximate a complete protein chain. Thus a 3D structure can be translated into a 1D sequence of PBs. With a simple Needleman–Wunsch approach and a raw PB substitution matrix, PB-based structural alignments were better than many popular methods. iPBA web server presents an improved alignment approach using (i) specialized PB Substitution Matrices (SM) and (ii) anchor-based alignment methodology. With these developments, the quality of ∼88% of alignments was improved. iPBA alignments were also better than DALI, MUSTANG and GANGSTA+ in >80% of the cases. The webserver is designed to for both pairwise comparisons and database searches. Outputs are given as sequence alignment and superposed 3D structures displayed using PyMol and Jmol. A local alignment option for detecting subs-structural similarity is also embedded. As a fast and efficient ‘sequence-based’ structure comparison tool, we believe that it will be quite useful to the scientific community. iPBA can be accessed at http://www.dsimb.inserm.fr/dsimb_tools/ipba/. PMID:21586582

  8. Three discontinuous Galerkin schemes for the anisotropic heat conduction equation on non-aligned grids

    NASA Astrophysics Data System (ADS)

    Held, M.; Wiesenberger, M.; Stegmeir, A.

    2016-02-01

    We present and discuss three discontinuous Galerkin (dG) discretizations for the anisotropic heat conduction equation on non-aligned cylindrical grids. Our non-aligned scheme relies on a self-adjoint local dG (LDG) discretization of the elliptic operator. It conserves the energy exactly and converges with arbitrary order. The pollution by numerical perpendicular heat fluxes decreases with superconvergence rates. We compare this scheme with aligned schemes that are based on the flux-coordinate independent approach for the discretization of parallel derivatives. Here, the dG method provides the necessary interpolation. The first aligned discretization can be used in an explicit time-integrator. However, the scheme violates conservation of energy and shows up stagnating convergence rates for very high resolutions. We overcome this partly by using the adjoint of the parallel derivative operator to construct a second self-adjoint aligned scheme. This scheme preserves energy, but reveals unphysical oscillations in the numerical tests, which result in a decreased order of convergence. Both aligned schemes exhibit low numerical heat fluxes into the perpendicular direction and are superior for flute-modes with finite parallel gradients. We build our argumentation on various numerical experiments on all three schemes for a general axisymmetric magnetic field, which is closed by a comparison to the aligned finite difference (FD) schemes of Stegmeir et al. (2014) and Stegmeir et al. (submitted for publication).

  9. Alignment Cube with One Diffractive Face

    NASA Technical Reports Server (NTRS)

    Ohl, Raymond G.; Sampler, Henry P.; Strojny, Carl R.; Hagopian, John G.; McMann, Joseph C.

    2006-01-01

    An enhanced alignment cube has been invented for use in a confined setting (e.g., a cryogenic chamber) in which optical access may be limited to a single line of sight. Whereas traditional alignment-cube practice entails the use of two theodolites aimed along two lines of sight, the enhanced alignment cube yields complete alignment information through use of a single theodolite aimed along a single line of sight. Typically, an alignment cube is placed in contact with a datum surface or other reference feature on a scientific instrument during assembly or testing of the instrument. The alignment cube is then used in measuring a small angular deviation of the feature from a precise required orientation. Commonly, the deviation is expressed in terms of rotations (Rx,Ry,Rz) of the cube about the corresponding Cartesian axes (x,y,z). In traditional practice, in order to measure all three rotations, it is necessary to use two theodolites aimed at two orthogonal faces of the alignment cube, as shown in the upper part of the figure. To be able to perform such a measurement, one needs optical access to these two faces. In the case of an alignment cube inside a cryogenic chamber or other enclosed space, the optical-access requirement translates to a requirement for two windows located along the corresponding two orthogonal lines of sight into the chamber. In a typical application, it is difficult or impossible to provide two windows. The present enhanced version of the alignment cube makes it possible to measure all three rotations by use of a single line of sight, thereby obviating a second window.

  10. Templating of self-alignment patterns of anisotropic gold nanoparticles on ordered SWNT macrostructures.

    PubMed

    Dan, Budhadipta; Wingfield, Tyler B; Evans, Julian S; Mirri, Francesca; Pint, Cary L; Pasquali, Matteo; Smalyukh, Ivan I

    2011-09-01

    We report a simple and versatile technique for oriented assembly of gold nanorods on aligned single-walled carbon nanotube (SWNT) macrostructures, such as thin nanotube films and nanotube fibers. The deposition and assembly is accomplished via drop drying of dilute gold nanorod suspensions on SWNT macrostructures under ambient conditions. Guided by anisotropic interactions, gold nanorods, and polygonal platelets spontaneously align with SWNTs, resulting in macroscopic arrays of locally ordered nanorods supported on aligned SWNT substrates. SEM reveals that the scalar order parameter of rods relative to the local average SWNT alignment is 0.7 for rods on SWNT films and 0.9 for rods on SWNT fibers. This self-alignment is enabled by anisotropic gold nanoparticle-SWNT interactions and is observed for a wide range of nanoparticles, including nanorods with aspect ratios ranging from 2-35, thin gold triangular and other polygonal platelets. The plasmonic properties of aligned gold nanorods together with superior electronic, chemical and mechanical properties of SWNTs make these hybrid nanocomposites valuable for the design of self-assembled multifunctional optoelectronic materials and optical metamaterials.

  11. Rotational Alignment Altered by Source Position Correlations

    NASA Technical Reports Server (NTRS)

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

    2010-01-01

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

  12. Coelostat and heliostat - Theory of alignment

    NASA Astrophysics Data System (ADS)

    Demianski, M.; Pasachoff, J. M.

    1984-06-01

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

  13. Switchable Fresnel lens based on micropatterned alignment.

    PubMed

    Wang, Xiao-Qian; Srivastava, Abhishek K; Chigrinov, Vladimir G; Kwok, Hoi-Sing

    2013-06-01

    In this Letter we disclose a method to fabricate a liquid crystal (LC) Fresnel zone lens (FZL) with higher efficiency. The LCFZL, based on alternate twisted nematic (TN) and planar aligned (PA) regions, has been prepared by means of a two-step photo-alignment process. The FZL profile for both optical regimes, i.e., in TN and PA alignment domains, generates the same focal length (f). Thus, the proposed LCFZL manifests double light intensity at the focal point and therefore offers double the efficiency of existing FZLs. Moreover, because of lower driving voltage and fast response, these elements could find application in many modern devices.

  14. Self-aligning biaxial load frame

    DOEpatents

    Ward, Michael B.; Epstein, Jonathan S.; Lloyd, W. Randolph

    1994-01-01

    An self-aligning biaxial loading apparatus for use in testing the strength of specimens while maintaining a constant specimen centroid during the loading operation. The self-aligning biaxial loading apparatus consists of a load frame and two load assemblies for imparting two independent perpendicular forces upon a test specimen. The constant test specimen centroid is maintained by providing elements for linear motion of the load frame relative to a fixed crosshead, and by alignment and linear motion elements of one load assembly relative to the load frame.

  15. Self-aligning biaxial load frame

    DOEpatents

    Ward, M.B.; Epstein, J.S.; Lloyd, W.R.

    1994-01-18

    An self-aligning biaxial loading apparatus for use in testing the strength of specimens while maintaining a constant specimen centroid during the loading operation. The self-aligning biaxial loading apparatus consists of a load frame and two load assemblies for imparting two independent perpendicular forces upon a test specimen. The constant test specimen centroid is maintained by providing elements for linear motion of the load frame relative to a fixed cross head, and by alignment and linear motion elements of one load assembly relative to the load frame. 3 figures.

  16. Energy band alignment at the nanoscale

    NASA Astrophysics Data System (ADS)

    Deuermeier, Jonas; Fortunato, Elvira; Martins, Rodrigo; Klein, Andreas

    2017-01-01

    The energy band alignments at interfaces often determine the electrical functionality of a device. Along with the size reduction into the nanoscale, functional coatings become thinner than a nanometer. With the traditional analysis of the energy band alignment by in situ photoelectron spectroscopy, a critical film thickness is needed to determine the valence band offset. By making use of the Auger parameter, it becomes possible to determine the energy band alignment to coatings, which are only a few Ångström thin. This is demonstrated with experimental data of Cu2O on different kinds of substrate materials.

  17. Understanding Beam Alignment in a Coherent Lidar System

    NASA Technical Reports Server (NTRS)

    Prasad, Narasimha S.; Roychoudhari, Chandrasekhar

    2015-01-01

    Optical beam alignment in a coherent lidar (or ladar) receiver system plays a critical role in optimizing its performance. Optical alignment in a coherent lidar system dictates the wavefront curvature (phase front) and Poynting vector) matching of the local oscillator beam with the incoming receiver beam on a detector. However, this alignment is often not easy to achieve and is rarely perfect. Furthermore, optical fibers are being increasingly used in coherent lidar system receivers for transporting radiation to achieve architectural elegance. Single mode fibers also require stringent mode matching for efficient light coupling. The detector response characteristics vary with the misalignment of the two pointing vectors. Misalignment can lead to increase in DC current. Also, a lens in front of the detector may exasperate phase front and Poynting vector mismatch. Non-Interaction of Waves, or the NIW property indicates the light beams do not interfere by themselves in the absence of detecting dipoles. In this paper, we will analyze the extent of misalignment on the detector specifications using pointing vectors of mixing beams in light of the NIW property.

  18. Magnetically aligned H I fibers and the rolling hough transform

    SciTech Connect

    Clark, S. E.; Putman, M. E.; Peek, J. E. G.

    2014-07-01

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

  19. Global multiple protein-protein interaction network alignment by combining pairwise network alignments

    PubMed Central

    2015-01-01

    Background A wealth of protein interaction data has become available in recent years, creating an urgent need for powerful analysis techniques. In this context, the problem of finding biologically meaningful correspondences between different protein-protein interaction networks (PPIN) is of particular interest. The PPIN of a species can be compared with that of other species through the process of PPIN alignment. Such an alignment can provide insight into basic problems like species evolution and network component function determination, as well as translational problems such as target identification and elucidation of mechanisms of disease spread. Furthermore, multiple PPINs can be aligned simultaneously, expanding the analytical implications of the result. While there are several pairwise network alignment algorithms, few methods are capable of multiple network alignment. Results We propose SMAL, a MNA algorithm based on the philosophy of scaffold-based alignment. SMAL is capable of converting results from any global pairwise alignment algorithms into a MNA in linear time. Using this method, we have built multiple network alignments based on combining pairwise alignments from a number of publicly available (pairwise) network aligners. We tested SMAL using PPINs of eight species derived from the IntAct repository and employed a number of measures to evaluate performance. Additionally, as part of our experimental investigations, we compared the effectiveness of SMAL while aligning up to eight input PPINs, and examined the effect of scaffold network choice on the alignments. Conclusions A key advantage of SMAL lies in its ability to create MNAs through the use of pairwise network aligners for which native MNA implementations do not exist. Experiments indicate that the performance of SMAL was comparable to that of the native MNA implementation of established methods such as IsoRankN and SMETANA. However, in terms of computational time, SMAL was significantly faster

  20. Magnetic alignment in carps: evidence from the Czech christmas fish market.

    PubMed

    Hart, Vlastimil; Kušta, Tomáš; Němec, Pavel; Bláhová, Veronika; Ježek, Miloš; Nováková, Petra; Begall, Sabine; Cervený, Jaroslav; Hanzal, Vladimír; Malkemper, Erich Pascal; Stípek, Kamil; Vole, Christiane; Burda, Hynek

    2012-01-01

    While magnetoreception in birds has been studied intensively, the literature on magnetoreception in bony fish, and particularly in non-migratory fish, is quite scarce. We examined alignment of common carps (Cyprinus carpio) at traditional Christmas sale in the Czech Republic. The sample comprised measurements of the directional bearings in 14,537 individual fish, distributed among 80 large circular plastic tubs, at 25 localities in the Czech Republic, during 817 sampling sessions, on seven subsequent days in December 2011. We found that carps displayed a statistically highly significant spontaneous preference to align their bodies along the North-South axis. In the absence of any other common orientation cues which could explain this directional preference, we attribute the alignment of the fish to the geomagnetic field lines. It is apparent that the display of magnetic alignment is a simple experimental paradigm of great heuristic potential.

  1. Multi-subject Manifold Alignment of Functional Network Structures via Joint Diagonalization.

    PubMed

    Nenning, Karl-Heinz; Kollndorfer, Kathrin; Schöpf, Veronika; Prayer, Daniela; Langs, Georg

    2015-01-01

    Functional magnetic resonance imaging group studies rely on the ability to establish correspondence across individuals. This enables location specific comparison of functional brain characteristics. Registration is often based on morphology and does not take variability of functional localization into account. This can lead to a loss of specificity, or confounds when studying diseases. In this paper we propose multi-subject functional registration by manifold alignment via coupled joint diagonalization. The functional network structure of each subject is encoded in a diffusion map, where functional relationships are decoupled from spatial position. Two-step manifold alignment estimates initial correspondences between functionally equivalent regions. Then, coupled joint diagonalization establishes common eigenbases across all individuals, and refines the functional correspondences. We evaluate our approach on fMRI data acquired during a language paradigm. Experiments demonstrate the benefits in matching accuracy achieved by coupled joint diagonalization compared to previously proposed functional alignment approaches, or alignment based on structural correspondences.

  2. Magnetic Alignment in Carps: Evidence from the Czech Christmas Fish Market

    PubMed Central

    Hart, Vlastimil; Kušta, Tomáš; Němec, Pavel; Bláhová, Veronika; Ježek, Miloš; Nováková, Petra; Begall, Sabine; Červený, Jaroslav; Hanzal, Vladimír; Malkemper, Erich Pascal; Štípek, Kamil; Vole, Christiane; Burda, Hynek

    2012-01-01

    While magnetoreception in birds has been studied intensively, the literature on magnetoreception in bony fish, and particularly in non-migratory fish, is quite scarce. We examined alignment of common carps (Cyprinus carpio) at traditional Christmas sale in the Czech Republic. The sample comprised measurements of the directional bearings in 14,537 individual fish, distributed among 80 large circular plastic tubs, at 25 localities in the Czech Republic, during 817 sampling sessions, on seven subsequent days in December 2011. We found that carps displayed a statistically highly significant spontaneous preference to align their bodies along the North-South axis. In the absence of any other common orientation cues which could explain this directional preference, we attribute the alignment of the fish to the geomagnetic field lines. It is apparent that the display of magnetic alignment is a simple experimental paradigm of great heuristic potential. PMID:23227241

  3. Thalamic theta phase alignment predicts human memory formation and anterior thalamic cross-frequency coupling.

    PubMed

    Sweeney-Reed, Catherine M; Zaehle, Tino; Voges, Jürgen; Schmitt, Friedhelm C; Buentjen, Lars; Kopitzki, Klaus; Hinrichs, Hermann; Heinze, Hans-Jochen; Rugg, Michael D; Knight, Robert T; Richardson-Klavehn, Alan

    2015-05-20

    Previously we reported electrophysiological evidence for a role for the anterior thalamic nucleus (ATN) in human memory formation (Sweeney-Reed et al., 2014). Theta-gamma cross-frequency coupling (CFC) predicted successful memory formation, with the involvement of gamma oscillations suggesting memory-relevant local processing in the ATN. The importance of the theta frequency range in memory processing is well-established, and phase alignment of oscillations is considered to be necessary for synaptic plasticity. We hypothesized that theta phase alignment in the ATN would be necessary for memory encoding. Further analysis of the electrophysiological data reveal that phase alignment in the theta rhythm was greater during successful compared with unsuccessful encoding, and that this alignment was correlated with the CFC. These findings support an active processing role for the ATN during memory formation.

  4. Computing posterior probabilities for score-based alignments using ppALIGN.

    PubMed

    Wolfsheimer, Stefan; Hartmann, Alexander; Rabus, Ralf; Nuel, Gregory

    2012-05-16

    Score-based pairwise alignments are widely used in bioinformatics in particular with molecular database search tools, such as the BLAST family. Due to sophisticated heuristics, such algorithms are usually fast but the underlying scoring model unfortunately lacks a statistical description of the reliability of the reported alignments. In particular, close to gaps, in low-score or low-complexity regions, a huge number of alternative alignments arise which results in a decrease of the certainty of the alignment. ppALIGN is a software package that uses hidden Markov Model techniques to compute position-wise reliability of score-based pairwise alignments of DNA or protein sequences. The design of the model allows for a direct connection between the scoring function and the parameters of the probabilistic model. For this reason it is suitable to analyze the outcomes of popular score based aligners and search tools without having to choose a complicated set of parameters. By contrast, our program only requires the classical score parameters (the scoring function and gap costs). The package comes along with a library written in C++, a standalone program for user defined alignments (ppALIGN) and another program (ppBLAST) which can process a complete result set of BLAST. The main algorithms essentially exhibit a linear time complexity (in the alignment lengths), and they are hence suitable for on-line computations. We have also included alternative decoding algorithms to provide alternative alignments. ppALIGN is a fast program/library that helps detect and quantify questionable regions in pairwise alignments. Due to its structure, the input/output interface it can to be connected to other post-processing tools. Empirically, we illustrate its usefulness in terms of correctly predicted reliable regions for sequences generated using the ROSE model for sequence evolution, and identify sensor-specific regions in the denitrifying betaproteobacterium Aromatoleum aromaticum.

  5. Environmental Geometry Aligns the Hippocampal Map during Spatial Reorientation.

    PubMed

    Keinath, Alex T; Julian, Joshua B; Epstein, Russell A; Muzzio, Isabel A

    2017-02-06

    When a navigator's internal sense of direction is disrupted, she must rely on external cues to regain her bearings, a process termed spatial reorientation. Extensive research has demonstrated that the geometric shape of the environment exerts powerful control over reorientation behavior, but the neural and cognitive mechanisms underlying this phenomenon are not well understood. Whereas some theories claim that geometry controls behavior through an allocentric mechanism potentially tied to the hippocampus, others postulate that disoriented navigators reach their goals by using an egocentric view-matching strategy. To resolve this debate, we characterized hippocampal representations during reorientation. We first recorded from CA1 cells as disoriented mice foraged in chambers of various shapes. We found that the alignment of the recovered hippocampal map was determined by the geometry of the chamber, but not by nongeometric cues, even when these cues could be used to disambiguate geometric ambiguities. We then recorded hippocampal activity as disoriented mice performed a classical goal-directed spatial memory task in a rectangular chamber. Again, we found that the recovered hippocampal map aligned solely to the chamber geometry. Critically, we also found a strong correspondence between the hippocampal map alignment and the animal's behavior, making it possible to predict the search location of the animal from neural responses on a trial-by-trial basis. Together, these results demonstrate that spatial reorientation involves the alignment of the hippocampal map to local geometry. We hypothesize that geometry may be an especially salient cue for reorientation because it is an inherently stable aspect of the environment.

  6. Integrated web service for improving alignment quality based on segments comparison

    PubMed Central

    Plewczynski, Dariusz; Rychlewski, Leszek; Ye, Yuzhen; Jaroszewski, Lukasz; Godzik, Adam

    2004-01-01

    Background Defining blocks forming the global protein structure on the basis of local structural regularity is a very fruitful idea, extensively used in description, and prediction of structure from only sequence information. Over many years the secondary structure elements were used as available building blocks with great success. Specially prepared sets of possible structural motifs can be used to describe similarity between very distant, non-homologous proteins. The reason for utilizing the structural information in the description of proteins is straightforward. Structural comparison is able to detect approximately twice as many distant relationships as sequence comparison at the same error rate. Results Here we provide a new fragment library for Local Structure Segment (LSS) prediction called FRAGlib which is integrated with a previously described segment alignment algorithm SEA. A joined FRAGlib/SEA server provides easy access to both algorithms, allowing a one stop alignment service using a novel approach to protein sequence alignment based on a network matching approach. The FRAGlib used as secondary structure prediction achieves only 73% accuracy in Q3 measure, but when combined with the SEA alignment, it achieves a significant improvement in pairwise sequence alignment quality, as compared to previous SEA implementation and other public alignment algorithms. The FRAGlib algorithm takes ~2 min. to search over FRAGlib database for a typical query protein with 500 residues. The SEA service align two typical proteins within circa ~5 min. All supplementary materials (detailed results of all the benchmarks, the list of test proteins and the whole fragments library) are available for download on-line at . Conclusions The joined FRAGlib/SEA server will be a valuable tool both for molecular biologists working on protein sequence analysis and for bioinformaticians developing computational methods of structure prediction and alignment of proteins. PMID:15271224

  7. Automatic alignment method for calibration of hydrometers

    NASA Astrophysics Data System (ADS)

    Lee, Y. J.; Chang, K. H.; Chon, J. C.; Oh, C. Y.

    2004-04-01

    This paper presents a new method to automatically align specific scale-marks for the calibration of hydrometers. A hydrometer calibration system adopting the new method consists of a vision system, a stepping motor, and software to control the system. The vision system is composed of a CCD camera and a frame grabber, and is used to acquire images. The stepping motor moves the camera, which is attached to the vessel containing a reference liquid, along the hydrometer. The operating program has two main functions: to process images from the camera to find the position of the horizontal plane and to control the stepping motor for the alignment of the horizontal plane with a particular scale-mark. Any system adopting this automatic alignment method is a convenient and precise means of calibrating a hydrometer. The performance of the proposed method is illustrated by comparing the calibration results using the automatic alignment method with those obtained using the manual method.

  8. Fiber optics welder having movable aligning mirror

    DOEpatents

    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.

  9. Regionally Aligned Forces: Concept Viability and Implementation

    DTIC Science & Technology

    2015-03-01

    Carlisle Compendia of Collaborative Research United States Army War College Student Publications Regionally Aligned Forces: Concept Viability and...Concept Viability and Implementation 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER...Carlisle Compendia of Collaborative Research United States Army War College Student Publications Regionally Aligned Forces: Concept Viability and

  10. Technology Alignment and Portfolio Prioritization (TAPP)

    NASA Technical Reports Server (NTRS)

    Funaro, Gregory V.; Alexander, Reginald A.

    2015-01-01

    Technology Alignment and Portfolio Prioritization (TAPP) is a method being developed by the Advanced Concepts Office, at NASA Marshall Space Flight Center. The TAPP method expands on current technology assessment methods by incorporating the technological structure underlying technology development, e.g., organizational structures and resources, institutional policy and strategy, and the factors that motivate technological change. This paper discusses the methods ACO is currently developing to better perform technology assessments while taking into consideration Strategic Alignment, Technology Forecasting, and Long Term Planning.

  11. Control rod housing alignment and repair method

    SciTech Connect

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

    1992-04-07

    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.

  12. Molecular focusing and alignment with plasmon fields.

    PubMed

    Artamonov, Maxim; Seideman, Tamar

    2010-12-08

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

  13. A Tracker Alignment Framework for Augmented Reality

    DTIC Science & Technology

    2003-01-01

    A Tracker Alignment Framework for Augmented Reality Yohan Baillot and Simon J. Julier ITT Advanced Engineering & Sciences 2560 Huntington Ave...with as few as three measurements. 1. Introduction Almost all Augmented Reality (AR) systems use a track- ing system to capture motion of objects in...DATES COVERED 00-00-2003 to 00-00-2003 4. TITLE AND SUBTITLE A Tracker Alignment Framework for Augmented Reality 5a. CONTRACT NUMBER 5b. GRANT

  14. Unconventional High Density Vertically Aligned Conducting Polymer

    DTIC Science & Technology

    2014-08-21

    electrodes with unique and controlled nano-morphologies: highly aligned carbon nanotubes (A-CNT) and graphene. This program also developed the...highly aligned carbon nanotubes forests (A-CNTs) and graphene. As synthesized A- CNTs have low volume fraction of CNT (~ 1 %). Traditional method to... nanotubes (A-CNTs). In contract to the electric double layer capacitors (EDLC) which store charges on the surface of the electrodes, conducting

  15. Alignment of photoions far from threshold

    NASA Astrophysics Data System (ADS)

    Das, Romith; Wu, Chuanyong; Mihill, A. G.; Poliakoff, E. D.; Wang, Kwanghsi; McKoy, V.

    1994-09-01

    We present results of measurements and calculations of the alignment for CO+(B 2Σ+) photoions over an extended energy range (0≤Ek≤210 eV). The polarization of CO+(B 2Σ+→X 2Σ+) fluorescence indicates that the photoions retain significant alignment even at high energies. Agreement between the measured and calculated polarization of the fluorescence is excellent.

  16. Orthodontics Align Crooked Teeth and Boost Self-Esteem

    MedlinePlus

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

  17. Uniaxially aligned nanofibrous cylinders by electrospinning.

    PubMed

    Jana, Soumen; Cooper, Ashleigh; Ohuchi, Fumio; Zhang, Miqin

    2012-09-26

    Aligned nanofibers have drawn increasing interest for applications in biomedical engineering, electronics, and energy storage systems owing to the unique physicochemical properties provided by their anisotropy and high surface-to-volume ratio. Nevertheless, direct fabrication or assembly of aligned nanofibers into a 3-dimensional standalone construct with practically applicable dimensions presents an enormous challenge. We report a facile method to fabricate aligned nanofibrous cylinders, a widely used geometric form, by electrospinning aligned nanofibers across the gap between a pair of pin electrodes placed apart uniaxially. With this approach, cylindrical nanofibrous constructs of several millimeters in diameter and several centimeters in length can be readily produced. The versatility of the approach was demonstrated with several commonly used polymeric and ceramic materials, including polycaprolactone (PCL), chitosan/PCL, polyvinylidene fluoride, and titania. For a model application in tissue engineering, skeletal muscle cells were cultured on nanofibrous cylinders, which effectively produced highly aligned and densely populated myotubes along the nanofiber orientation, favorable for muscle tissue regeneration. With high structural integrity and stability, these can be directly integrated into devices or implanted in vivo as a standalone construct without the support of a substrate, thus increasing the portability, efficiency, and applicability of aligned nanofibers.

  18. DALIX: optimal DALI protein structure alignment.

    PubMed

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

    2013-01-01

    We present a mathematical model and exact algorithm for optimally aligning protein structures using the DALI scoring model. This scoring model is based on comparing the interresidue distance matrices of proteins and is used in the popular DALI software tool, a heuristic method for protein structure alignment. Our model and algorithm extend an integer linear programming approach that has been previously applied for the related, but simpler, contact map overlap problem. To this end, we introduce a novel type of constraint that handles negative score values and relax it in a Lagrangian fashion. The new algorithm, which we call DALIX, is applicable to any distance matrix-based scoring scheme. We also review options that allow to consider fewer pairs of interresidue distances explicitly because their large number hinders the optimization process. Using four known data sets of varying structural similarity, we compute many provably score-optimal DALI alignments. This allowed, for the first time, to evaluate the DALI heuristic in sound mathematical terms. The results indicate that DALI usually computes optimal or close to optimal alignments. However, we detect a subset of small proteins for which DALI fails to generate any significant alignment, although such alignments do exist.

  19. Orthodontic Tooth Movement with Clear Aligners

    PubMed Central

    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. PMID:22928114

  20. Observational Evidence for Radiative Interstellar Grain Alignment

    NASA Astrophysics Data System (ADS)

    Andersson, B.; Potter, S. B.; Andersson, B.; Potter, S.

    2011-11-01

    The alignment mechanisms of interstellar dust grains is a long standing astrophysical problem. Interstellar polarization was first discovered in 1949 and soon thereafter attributed to dichroic extinction caused by asymmetric dust grains aligned with the magnetic field. For a long time the alignment mechanism was thought to involve paramagnetic relaxation in rapidly spinning dust grains. Modern theory indicates that the classical alignment mechanisms are likely not efficient, but rather favor alignment through direct radiative torques. We have used multi-band polarimetry towards stars probing six nearby clouds to show that the wavelength of maximum polarization is linearly correlated with the visual extinction (Andersson & Potter 2007; AP07; where further details can be found). We find a universal relation with a common positive slope between the clouds and a DC offset correlated with the average of the total-to-selective extinction < RV > . These results provide strong observational support for radiatively driven grain alignment. Recent observations of an additional set of ≍60 sightlines in the Taurus cloud confirm and strengthen these results.

  1. Aligning Biomolecular Networks Using Modular Graph Kernels

    NASA Astrophysics Data System (ADS)

    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.

  2. Elevation angle alignment of quasi optical receiver mirrors of collective Thomson scattering diagnostic by sawtooth measurementsa)

    NASA Astrophysics Data System (ADS)

    Moseev, D.; Meo, F.; Korsholm, S. B.; Bindslev, H.; Furtula, V.; Kantor, M.; Leipold, F.; Michelsen, P. K.; Nielsen, S. K.; Salewski, M.; Stejner, M.

    2012-10-01

    Localized measurements of the fast ion velocity distribution function and the plasma composition measurements are of significant interest for the fusion community. Collective Thomson scattering (CTS) diagnostics allow such measurements with spatial and temporal resolution. Localized measurements require a good alignment of the optical path in the transmission line. Monitoring the alignment during the experiment greatly benefits the confidence in the CTS measurements. An in situ technique for the assessment of the elevation angle alignment of the receiver is developed. Using the CTS diagnostic on TEXTOR without a source of probing radiation in discharges with sawtooth oscillations, an elevation angle misalignment of 0.9° was found with an accuracy of 0.25°.

  3. Laser alignment of rotating equipment at PNL

    SciTech Connect

    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.

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

    PubMed

    Banihashemi, Mohamadreza

    2016-10-01

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

  5. Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees

    PubMed Central

    Yamada, Kazunori D.; Tomii, Kentaro; Katoh, Kazutaka

    2016-01-01

    Motivation: Large multiple sequence alignments (MSAs), consisting of thousands of sequences, are becoming more and more common, due to advances in sequencing technologies. The MAFFT MSA program has several options for building large MSAs, but their performances have not been sufficiently assessed yet, because realistic benchmarking of large MSAs has been difficult. Recently, such assessments have been made possible through the HomFam and ContTest benchmark protein datasets. Along with the development of these datasets, an interesting theory was proposed: chained guide trees increase the accuracy of MSAs of structurally conserved regions. This theory challenges the basis of progressive alignment methods and needs to be examined by being compared with other known methods including computationally intensive ones. Results: We used HomFam, ContTest and OXFam (an extended version of OXBench) to evaluate several methods enabled in MAFFT: (1) a progressive method with approximate guide trees, (2) a progressive method with chained guide trees, (3) a combination of an iterative refinement method and a progressive method and (4) a less approximate progressive method that uses a rigorous guide tree and consistency score. Other programs, Clustal Omega and UPP, available for large MSAs, were also included into the comparison. The effect of method 2 (chained guide trees) was positive in ContTest but negative in HomFam and OXFam. Methods 3 and 4 increased the benchmark scores more consistently than method 2 for the three datasets, suggesting that they are safer to use. Availability and Implementation: http://mafft.cbrc.jp/alignment/software/ Contact: katoh@ifrec.osaka-u.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27378296

  6. A method for quantitatively analyzing the angle of direction for arbitral c-axis alignment with retardation measurements

    NASA Astrophysics Data System (ADS)

    Shimoi, Norihiro; Tanaka, Yasumitsu

    2015-01-01

    c-axis alignment in a polymer or crystal structure has drawn attention in numerous scientific and technological applications, including crystals, thin film growth, electro-optic devices, and phase difference optics. We here demonstrate a new approach based on retardation measurement that can obtain the direction of the c-axis alignment. This is employed to visualize the three-dimensional direction of continuous crystals as a thin optical film utilizing a liquid crystal panel, using retardation analysis equipment with high resolution measurement capability. The direction of the c-axis alignment is shown so as to allow a detailed characterization of the direction perpendicular to the plane. In this analysis, the direction of the c-axis alignment is identified, and differences between molecules at inequivalent sites are quantified. The results suggest that the excellent lubrication properties of the c-axis alignment may be due to a significant localization in lateral directions.

  7. Metabarcoding of marine nematodes – evaluation of similarity scores used in alignment-based taxonomy assignment approach

    PubMed Central

    2016-01-01

    Abstract Background The diversity of organisms is being commonly accessed using metabarcoding of environmental samples. Reliable identification of barcodes is one of the critical steps in the process and several taxonomy assignment methods were proposed to accomplish this task, including alignment-based approach that uses Basic Local Alignment Search Tool (BLAST) algorithm. This publication evaluates the variability of 5' end of 18S rRNA barcoding region as expressed by similarity scores (alignment score and identity score) produced by BLAST, and its impact on barcode identification to family-level taxonomic categories. New information In alignment-based taxonomy assignment approach, reliable identification of anonymous OTUs to supraspecific taxa depends on the correct application of similarity thresholds. Since various taxa show different level of genetic variation, practical application of alignment-based approach requires the determination and use of taxon-specific similarity thresholds. PMID:27932928

  8. Unrooted unordered homeomorphic subtree alignment of RNA trees

    PubMed Central

    2013-01-01

    We generalize some current approaches for RNA tree alignment, which are traditionally confined to ordered rooted mappings, to also consider unordered unrooted mappings. We define the Homeomorphic Subtree Alignment problem (HSA), and present a new algorithm which applies to several modes, combining global or local, ordered or unordered, and rooted or unrooted tree alignments. Our algorithm generalizes previous algorithms that either solved the problem in an asymmetric manner, or were restricted to the rooted and/or ordered cases. Focusing here on the most general unrooted unordered case, we show that for input trees T and S, our algorithm has an O(nTnS + min(dT,dS)LTLS) time complexity, where nT,LT and dT are the number of nodes, the number of leaves, and the maximum node degree in T, respectively (satisfying dT ≤ LT ≤ nT), and similarly for nS,LS and dS with respect to the tree S. This improves the time complexity of previous algorithms for less general variants of the problem. In order to obtain this time bound for HSA, we developed new algorithms for a generalized variant of the Min-Cost Bipartite Matching problem (MCM), as well as to two derivatives of this problem, entitled All-Cavity-MCM and All-Pairs-Cavity-MCM. For two input sets of size n and m, where n ≤ m, MCM and both its cavity derivatives are solved in O(n3 + nm) time, without the usage of priority queues (e.g. Fibonacci heaps) or other complex data structures. This gives the first cubic time algorithm for All-Pairs-Cavity-MCM, and improves the running times of MCM and All-Cavity-MCM problems in the unbalanced case where n ≪ m. We implemented the algorithm (in all modes mentioned above) as a graphical software tool which computes and displays similarities between secondary structures of RNA given as input, and employed it to a preliminary experiment in which we ran all-against-all inter-family pairwise alignments of RNAse P and Hammerhead RNA

  9. Alignment of voids in the cosmic web

    NASA Astrophysics Data System (ADS)

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

    2008-06-01

    We investigate the shapes and mutual alignment of voids in the large-scale matter distribution of a Λ cold dark matter (ΛCDM) cosmology simulation. The voids are identified using the novel watershed void finder (WVF) technique. The identified voids are quite non-spherical and slightly prolate, with axis ratios in the order of c:b:a ~ 0.5:0.7:1. Their orientations are strongly correlated with significant alignments spanning scales >30h-1Mpc. We also find an intimate link between the cosmic tidal field and the void orientations. Over a very wide range of scales we find a coherent and strong alignment of the voids with the tidal field computed from the smoothed density distribution. This orientation-tide alignment remains significant on scales exceeding twice the typical void size, which shows that the long-range external field is responsible for the alignment of the voids. This confirms the view that the large-scale tidal force field is the main agent for the large-scale spatial organization of the cosmic web.

  10. Multiple network alignment on quantum computers

    NASA Astrophysics Data System (ADS)

    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.

  11. LCLS Undulator Commissioning, Alignment, and Performance

    SciTech Connect

    Nuhn, Heinz-Dieter

    2009-10-30

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

  12. FRESCO: flexible alignment with rectangle scoring schemes.

    PubMed

    Dalca, A V; Brudno, M

    2008-01-01

    While the popular DNA sequence alignment tools incorporate powerful heuristics to allow for fast and accurate alignment of DNA, most of them still optimize the classical Needleman Wunsch scoring scheme. The development of novel scoring schemes is often hampered by the difficulty of finding an optimizing algorithm for each non-trivial scheme. In this paper we define the broad class of rectangle scoring schemes, and describe an algorithm and tool that can align two sequences with an arbitrary rectangle scoring scheme in polynomial time. Rectangle scoring schemes encompass some of the popular alignment scoring metrics currently in use, as well as many other functions. We investigate a novel scoring function based on minimizing the expected number of random diagonals observed with the given scores and show that it rivals the LAGAN and Clustal-W aligners, without using any biological or evolutionary parameters. The FRESCO program, freely available at http://compbio.cs.toronto.edu/fresco, gives bioinformatics researchers the ability to quickly compare the performance of other complex scoring formulas without having to implement new algorithms to optimize them.

  13. Leveraging FPGAs for Accelerating Short Read Alignment.

    PubMed

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

    2016-02-29

    One of the key challenges facing genomics today is how to efficiently analyse the massive amounts of data produced by next-generation sequencing platforms. With general-purpose computing systems struggling to address this challenge, specialised 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 2 mismatches. Our design is based on the FM-index, with optimisations to improve the alignment performance. In particular, the n-step FM-index, index oversampling, a seedand- compare stage, and bi-directional backtracking are included. Our design is implemented and evaluated on a 1U Maxeler MPC-X2000 dataflow node with 8 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 9 times faster than Soap3-dp running on an NVIDIA Tesla C2070 GPU.

  14. Multiple alignment tensors from a denatured protein.

    PubMed

    Gebel, Erika B; Ruan, Ke; Tolman, Joel R; Shortle, David

    2006-07-26

    The structural content of the denatured state has yet to be fully characterized. In recent years, large residual dipolar couplings (RDCs) from denatured proteins have been observed under alignment conditions produced by bicelles and strained polyacrylamide gels. In this report, we describe efforts to extend our picture of the residual structure in denatured nuclease by measuring RDCs with multiple alignment tensors. Backbone amide 15N-1H RDCs were collected from 4 M urea for a total of eight RDC data sets. The RDCs were analyzed by singular value decomposition (SVD) to determine the number of independent alignment tensors present in the data. On the basis of the resultant singular values and propagated error estimates, it is clear that there are at least three independent alignment tensors. These three independent RDC datasets can be reconstituted as orthogonal linear combinations, (OLC)-RDC datasets, of the eight actually recorded. The first, second, and third OLC-RDC datasets are highly robust to the removal of any single experimental RDC dataset, establishing the presence of three independent alignment tensors, sampled well above the level of experimental uncertainty. The observation that the RDC data span three or more dimensions of the five-dimensional parameter space demonstrates that the ensemble average structure of denatured nuclease must be asymmetric with respect to these three orthogonal principal axes, which is not inconsistent with earlier work demonstrating that it has a nativelike topology.

  15. Knee alignment in professional tennis players.

    PubMed

    Maquirriain, Javier

    2002-01-01

    This study determined lower-limb alignment and knee geometry in professional tennis players and compared the data with those from nonathletic individuals. Twenty-four radiographs from 12 asymptomatic players (mean age: 23.4+/-3.8 years) were prospectively studied. The three angles most useful for describing limb alignment and knee geometry in the coronal plane were measured: hip-knee-ankle, condylar-hip, and plateau-ankle. The condylar-plateau angle, frontal foot rotation angle, and the relationship between the mechanical axis and tibial plateau also were calculated. Varus limb alignment was predominant and the mechanical axis passed medially through the knee center; there was increased valgus inclination of the distal femur, varus angulation of the tibial plateau, near parallel alignment of the joint, and exaggerated external foot rotation. Hip-knee-ankle, condylar-hip, plateau-ankle, and frontal foot rotation angles were significantly different (P<.05, two-tailed t test) from previously reported angles of nonathletic individuals. Variations, probably due to repetitive dynamic demands imposed on lower limbs from an early age, seem to involve both femoral condyles and proximal tibial metaphyses, maintaining normal parallel joint alignment.

  16. Alignment and Integration of Lightweight Mirror Segments

    NASA Technical Reports Server (NTRS)

    Evans, Tyler; Biskach, Michael; Mazzarella, Jim; McClelland, Ryan; Saha, Timo; Zhang, Will; Chan, Kai-Wing

    2011-01-01

    The optics for the International X-Ray Observatory (IXO) require alignment and integration of about fourteen thousand thin mirror segments to achieve the mission goal of 3.0 square meters of effective area at 1.25 keV with an angular resolution of five arc-seconds. These mirror segments are 0.4 mm thick, and 200 to 400 mm in size, which makes it difficult not to impart distortion at the sub-arc-second level. This paper outlines the precise alignment, permanent bonding, and verification testing techniques developed at NASA's Goddard Space Flight Center (GSFC). Improvements in alignment include new hardware and automation software. Improvements in bonding include two module new simulators to bond mirrors into, a glass housing for proving single pair bonding, and a Kovar module for bonding multiple pairs of mirrors. Three separate bonding trials were x-ray tested producing results meeting the requirement of sub ten arc-second alignment. This paper will highlight these recent advances in alignment, testing, and bonding techniques and the exciting developments in thin x-ray optic technology development.

  17. Web-Beagle: a web server for the alignment of RNA secondary structures.

    PubMed

    Mattei, Eugenio; Pietrosanto, Marco; Ferrè, Fabrizio; Helmer-Citterich, Manuela

    2015-07-01

    Web-Beagle (http://beagle.bio.uniroma2.it) is a web server for the pairwise global or local alignment of RNA secondary structures. The server exploits a new encoding for RNA secondary structure and a substitution matrix of RNA structural elements to perform RNA structural alignments. The web server allows the user to compute up to 10 000 alignments in a single run, taking as input sets of RNA sequences and structures or primary sequences alone. In the latter case, the server computes the secondary structure prediction for the RNAs on-the-fly using RNAfold (free energy minimization). The user can also compare a set of input RNAs to one of five pre-compiled RNA datasets including lncRNAs and 3' UTRs. All types of comparison produce in output the pairwise alignments along with structural similarity and statistical significance measures for each resulting alignment. A graphical color-coded representation of the alignments allows the user to easily identify structural similarities between RNAs. Web-Beagle can be used for finding structurally related regions in two or more RNAs, for the identification of homologous regions or for functional annotation. Benchmark tests show that Web-Beagle has lower computational complexity, running time and better performances than other available methods.

  18. Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns

    DOE PAGES

    Tian, Wenhong; Samatova, Nagiza F.

    2013-01-01

    A number of tools for the alignment of protein-protein interaction (PPI) networks have laid the foundation for PPI network analysis. Most of alignment tools focus on finding conserved interaction regions across the PPI networks through either local or global mapping of similar sequences. Researchers are still trying to improve the speed, scalability, and accuracy of network alignment. In view of this, we introduce a connected-components based fast algorithm, HopeMap, for network alignment. Observing that the size of true orthologs across species is small comparing to the total number of proteins in all species, we take a different approach basedmore » on a precompiled list of homologs identified by KO terms. Applying this approach to S. cerevisiae (yeast) and D. melanogaster (fly), E. coli K12 and S. typhimurium , E. coli K12 and C. crescenttus , we analyze all clusters identified in the alignment. The results are evaluated through up-to-date known gene annotations, gene ontology (GO), and KEGG ortholog groups (KO). Comparing to existing tools, our approach is fast with linear computational cost, highly accurate in terms of KO and GO terms specificity and sensitivity, and can be extended to multiple alignments easily.« less

  19. Business-IT Alignment: A Current-State Evaluation of Strategic Alignment within the Hospital Organization

    ERIC Educational Resources Information Center

    Evers, Kevin W.

    2010-01-01

    More than thirty years of research has shown that the practical value of business-IT alignment is significant and that its importance derives from strategic impact on business outcomes. The purpose of this exploratory study is to identify the current-state of business-IT alignment maturity within the hospital organization. Data for this study was…

  20. TM-align: a protein structure alignment algorithm based on the TM-score

    PubMed Central

    Zhang, Yang; Skolnick, Jeffrey

    2005-01-01

    We have developed TM-align, a new algorithm to identify the best structural alignment between protein pairs that combines the TM-score rotation matrix and Dynamic Programming (DP). The algorithm is ∼4 times faster than CE and 20 times faster than DALI and SAL. On average, the resulting structure alignments have higher accuracy and coverage than those provided by these most often-used methods. TM-align is applied to an all-against-all structure comparison of 10 515 representative protein chains from the Protein Data Bank (PDB) with a sequence identity cutoff <95%: 1996 distinct folds are found when a TM-score threshold of 0.5 is used. We also use TM-align to match the models predicted by TASSER for solved non-homologous proteins in PDB. For both folded and misfolded models, TM-align can almost always find close structural analogs, with an average root mean square deviation, RMSD, of 3 Å and 87% alignment coverage. Nevertheless, there exists a significant correlation between the correctness of the predicted structure and the structural similarity of the model to the other proteins in the PDB. This correlation could be used to assist in model selection in blind protein structure predictions. The TM-align program is freely downloadable at . PMID:15849316

  1. Alignment of Standards and Assessment: A Theoretical and Empirical Study of Methods for Alignment

    ERIC Educational Resources Information Center

    Nasstrom, Gunilla; Henriksson, Widar

    2008-01-01

    Introduction: In a standards-based school-system alignment of policy documents with standards and assessment is important. To be able to evaluate whether schools and students have reached the standards, the assessment should focus on the standards. Different models and methods can be used for measuring alignment, i.e. the correspondence between…

  2. Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints

    PubMed Central

    Dowell, Robin D; Eddy, Sean R

    2006-01-01

    Background We are interested in the problem of predicting secondary structure for small sets of homologous RNAs, by incorporating limited comparative sequence information into an RNA folding model. The Sankoff algorithm for simultaneous RNA folding and alignment is a basis for approaches to this problem. There are two open problems in applying a Sankoff algorithm: development of a good unified scoring system for alignment and folding and development of practical heuristics for dealing with the computational complexity of the algorithm. Results We use probabilistic models (pair stochastic context-free grammars, pairSCFGs) as a unifying framework for scoring pairwise alignment and folding. A constrained version of the pairSCFG structural alignment algorithm was developed which assumes knowledge of a few confidently aligned positions (pins). These pins are selected based on the posterior probabilities of a probabilistic pairwise sequence alignment. Conclusion Pairwise RNA structural alignment improves on structure prediction accuracy relative to single sequence folding. Constraining on alignment is a straightforward method of reducing the runtime and memory requirements of the algorithm. Five practical implementations of the pairwise Sankoff algorithm – this work (Consan), David Mathews' Dynalign, Ian Holmes' Stemloc, Ivo Hofacker's PMcomp, and Jan Gorodkin's FOLDALIGN – have comparable overall performance with different strengths and weaknesses. PMID:16952317

  3. What Are We Aligning Tests to When We Report Test Alignment to the CEFR?

    ERIC Educational Resources Information Center

    Harsch, Claudia; Hartig, Johannes

    2015-01-01

    The study reported here investigates the validity of judgments made when aligning tests to the "Common European Framework of Reference" (CEFR). Listening tests operationalizing pre-defined difficulty-determining characteristics were to be aligned to CEFR levels. We employed a modified version of the item-descriptor-matching-method. Ten…

  4. Alignment of Standards and Assessments as an Accountability Criterion.

    ERIC Educational Resources Information Center

    La Marca, Paul M.

    2001-01-01

    Provides an overview of the concept of alignment and the role it plays in assessment and accountability systems. Discusses some methodological issues affecting the study of alignment and explores the relationship between alignment and test score interpretation. Alignment is not only a methodological requirement but also an ethical requirement.…

  5. Manifold alignment for classification of multitemporal hyperspectral image data

    NASA Astrophysics Data System (ADS)

    Yang, Hsiu-Han

    Analyzing remotely sensed images to obtain land cover classification maps is an effective approach for acquiring information over landscapes that can be accomplished over extended areas with limited ground surveys. Further, with advances in remote sensing technology, spaceborne hyperspectral sensors provide the capability to acquire a set of images that have both high spectral and temporal resolution. These images are suitable for monitoring and analyzing environmental changes with subtle spectral characteristics. However, inherent characteristics of multitemporal hyperspectral images, including high dimensionality, nonlinearity, and nonstationarity phenomena over time and across large areas, pose several challenges for classification. This research addresses the issues of classification tasks in the presence of spectral shifts within multitemporal hyperspectral images by leveraging the concept of the data manifold. Although manifold learning has been applied successfully in single image hyperspectral data classification to address high dimensionality and nonlinear spectral responses, research related to manifold learning for multitemporal classification studies is limited. The proposed approaches utilize spectral signatures and spatial proximity to construct similar "local" geometries of temporal images. By aligning these underlying manifolds optimally, the impacts of nonstationary effects are mitigated and classification is accomplished in a representative temporal data manifold. "Global" manifolds learned from temporal hyperspectral images have a major advantage in faithful representation of the data in an image, such as retaining relationships between different classes. Local manifolds are favored in discriminating difficult classes and for computation efficiency. A new hybrid global-local manifold alignment method that combines the advantages of global and local manifolds for effective multitemporal image classification is also proposed. Results illustrate the

  6. MAPPER alignment sensor evaluation on process wafers

    NASA Astrophysics Data System (ADS)

    Vergeer, N.; Lattard, L.; de Boer, G.; Couweleers, F.; Dave, D.; Pradelles, J.; Bustos, J.

    2013-03-01

    MAPPER Lithography is developing a maskless lithography technology based on massively-parallel electron-beam writing. In order to reduce costs and to minimize the footprint of this tool a new alignment sensor has been developed; based on technologies used for DVD optical heads. A wafer with an alignment mark is scanned with the sensor, resulting in an intensity pattern versus position. From this pattern the mark position can be calculated. Evaluations have been made over the performance of this type of sensor using different mark designs at several lithography process steps for FEOL and BEOL manufacturing. It has been shown that sub-nanometer reproducibility (3σ std) of alignment mark readings can be achieved while being robust against various process steps.

  7. Spent fuel container alignment device and method

    DOEpatents

    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.

  8. Mechanical alignment of substrates to a mask

    SciTech Connect

    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.

  9. Alignment method for spectrograms of DNA sequences.

    PubMed

    Bucur, Anca; van Leeuwen, Jasper; Dimitrova, Nevenka; Mittal, Chetan

    2010-01-01

    DNA spectrograms express the periodicities of each of the four nucleotides A, T, C, and G in one or several genomic sequences to be analyzed. DNA spectral analysis can be applied to systematically investigate DNA patterns, which may correspond to relevant biological features. As opposed to looking at nucleotide sequences, spectrogram analysis may detect structural characteristics in very long sequences that are not identifiable by sequence alignment. Alignment of DNA spectrograms can be used to facilitate analysis of very long sequences or entire genomes at different resolutions. Standard clustering algorithms have been used in spectral analysis to find strong patterns in spectra. However, as they use a global distance metric, these algorithms can only detect strong patterns coexisting in several frequencies. In this paper, we propose a new method and several algorithms for aligning spectra suitable for efficient spectral analysis and allowing for the easy detection of strong patterns in both single frequencies and multiple frequencies.

  10. Making Macroscopic Assemblies of Aligned Carbon Nanotubes

    NASA Technical Reports Server (NTRS)

    Smalley, Richard E.; Colbert, Daniel T.; Smith, Ken A.; Walters, Deron A.; Casavant, Michael J.; Qin, Xiaochuan; Yakobson, Boris; Hauge, Robert H.; Saini, Rajesh Kumar; Chiung, Wan-Ting; Huffman, Charles B.

    2005-01-01

    A method of aligning and assembling single-wall carbon nanotubes (SWNTs) to fabricate macroscopic structures has been invented. The method entails suspending SWNTs in a fluid, orienting the SWNTs by use of a magnetic and/or electric field, and then removing the aligned SWNTs from suspension in such a way as to assemble them while maintaining the alignment. SWNTs are essentially tubular extensions of fullerene molecules. It is desirable to assemble aligned SWNTs into macroscopic structures because the common alignment of the SWNTs in such a structure makes it possible to exploit, on a macroscopic scale, the unique mechanical, chemical, and electrical properties that individual oriented SWNTs exhibit at the molecular level. Because of their small size and high electrical conductivity, carbon nanotubes, and especially SWNTs, are useful for making electrical connectors in integrated circuits. Carbon nanotubes can be used as antennas at optical frequencies, and as probes in scanning tunneling microscopes, atomic-force microscopes, and the like. Carbon nanotubes can be used with or instead of carbon black in tires. Carbon nanotubes are useful as supports for catalysts. Ropes of SWNTs are metallic and, as such, are potentially useful in some applications in which electrical conductors are needed - for example, they could be used as additives in formulating electrically conductive paints. Finally, macroscopic assemblies of aligned SWNTs can serve as templates for the growth of more and larger structures of the same type. The great variety of tubular fullerene molecules and of the structures that could be formed by assembling them in various ways precludes a complete description of the present method within the limits of this article. It must suffice to present a typical example of the use of one of many possible variants of the method to form a membrane comprising SWNTs aligned substantially parallel to each other in the membrane plane. The apparatus used in this variant

  11. High-harmonic spectroscopy of aligned molecules

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

  12. Active alignment/contact verification system

    DOEpatents

    Greenbaum, William M.

    2000-01-01

    A system involving an active (i.e. electrical) technique for the verification of: 1) close tolerance mechanical alignment between two component, and 2) electrical contact between mating through an elastomeric interface. For example, the two components may be an alumina carrier and a printed circuit board, two mating parts that are extremely small, high density parts and require alignment within a fraction of a mil, as well as a specified interface point of engagement between the parts. The system comprises pairs of conductive structures defined in the surfaces layers of the alumina carrier and the printed circuit board, for example. The first pair of conductive structures relate to item (1) above and permit alignment verification between mating parts. The second pair of conductive structures relate to item (2) above and permit verification of electrical contact between mating parts.

  13. Purification process for vertically aligned carbon nanofibers

    NASA Technical Reports Server (NTRS)

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

    2003-01-01

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

  14. On the alignment for precession electron diffraction

    PubMed Central

    Liao, Yifeng; Marks, Laurence D.

    2013-01-01

    Precession electron diffraction has seen a fast increase in its adoption as a technique for solving crystallographic structures as well as an alternative to conventional selected-area and converged-beam diffraction methods. One of the key issues of precession is the pivot point alignment, as a stationary apparent beam does not guarantee a fixed pivot point. A large precession tilt angle, along with pre-field and post-field misalignment, induces shift in the image plane. We point out here that the beam should be aligned to the pre-field optic axis to keep the electron illumination stationary during the rocking process. A practical alignment procedure is suggested with the focus placed on minimizing the beam wandering on the specimen, and is demonstrated for a (110)-oriented silicon single crystal and for a carbide phase (~20 nm in size) within a cast cobalt–chromium–molybdenum alloy. PMID:22634134

  15. Prosody and alignment: a sequential perspective

    NASA Astrophysics Data System (ADS)

    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.

  16. System and method for 2D workpiece alignment

    DOEpatents

    Weaver, William T.; Carlson, Charles T.; Smith, Scott A.; Beck, Michael A.; Webb, Aaron P.; Strassner, James D.; Gravell, Lawrence R.; Simmons, Michael C.

    2015-07-14

    A carrier capable of holding one or more workpieces is disclosed. The carrier includes movable projections located along the sides of each cell in the carrier. This carrier, in conjunction with a separate alignment apparatus, aligns each workpiece within its respective cell against several alignment pins, using a multiple step alignment process to guarantee proper positioning of the workpiece in the cell. First, the workpieces are moved toward one side of the cell. Once the workpieces have been aligned against this side, the workpieces are then moved toward an adjacent orthogonal side such that the workpieces are aligned to two sides of the cell. Once aligned, the workpiece is held in place by the projections located along each side of each cell. In addition, the alignment pins are also used to align the associated mask, thereby guaranteeing that the mask is properly aligned to the workpiece.

  17. A Unified Model of Grain Alignment: Radiative Alignment of Interstellar Grains with Magnetic Inclusions

    NASA Astrophysics Data System (ADS)

    Hoang, Thiem; Lazarian, A.

    2016-11-01

    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 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 m to produce high-J attractor points as functions of q 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 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 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.

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

    NASA Technical Reports Server (NTRS)

    Chavez, Melissa A.

    2011-01-01

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

  19. Survey and Alignment of SLAC's B Factory

    SciTech Connect

    Pietryka, Matthew J.; Gaydosh, Michael L.; /SLAC

    2011-09-08

    The survey and alignment of SLAC's B-factory injector and high energy ring will be complete in March 1997. Modern digital electronic surveying tools are contributing to new, efficient alignment procedures. A laser tracker was used to fiducialize almost 300 quadrupole magnets. Digital levels were used to pre-set base plate elevations. Theodolites with very accurate co-axial distance meters were used for everything from layout to 3D magnet positioning to network surveys, all in free stationing mode. A number of procedures and measurement results are outlined.

  20. Fine alignment of a large segmented mirror

    NASA Technical Reports Server (NTRS)

    Dey, Thomas William (Inventor)

    2010-01-01

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

  1. Drift Chamber Alignment using Cosmic Rays

    SciTech Connect

    Kotwal, Ashutosh V.; Hays, Christopher P.

    2014-05-07

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

  2. Alignment Pins for Assembling and Disassembling Structures

    NASA Technical Reports Server (NTRS)

    Campbell, Oliver C.

    2008-01-01

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

  3. Electrospinning of continuous aligned polymer fibers

    NASA Astrophysics Data System (ADS)

    Sundaray, Bibekananda; Subramanian, V.; Natarajan, T. S.; Xiang, Rong-Zheng; Chang, Chia-Cheng; Fann, Wun-Shain

    2004-02-01

    Electrospinning is a technique employed for preparing polymer fibers having diameters in the range of 10 μm-10 nm using high electrostatic field. In this letter, we report the formation of aligned polymer fibers, several centimeters in length, with separation between the fibers in the range of 5-100 μm. Achieving alignment is an important step toward the exploitation of these fibers in applications. We have employed about 4500 V and a separation distance of about 1-3 cm between the electrodes. Smaller distance between electrodes, we believe, provides better control on the formation of the fibers.

  4. Field-aligned ICRF antenna design for EAST

    NASA Astrophysics Data System (ADS)

    Wukitch, S. J.; Lin, Y.; Qin, C.; Zhang, X.; Beck, W.; Koert, P.; Zhou, L.

    2015-12-01

    For ion cyclotron range of frequency (ICRF), a number of physics and technological challenges remain for steady state, toroidal devices. Among the most critical is maintaining good coupling and maximizing the coupled power through plasma variations including edge localized modes (ELMs) and confinement transitions. As pulse length increases, enhanced localized heat loads associated with antenna operation can challenge antenna integrity. In addition, ICRF impurity sources and contamination need to be minimized to enable effective plasma heating. Here, we report on a four strap field aligned (FA) antenna design for the EAST tokamak. A FA antenna is an antenna where the current straps and antenna side enclosure are perpendicular to the total magnetic field while the Faraday screen rods are parallel to the total magnetic field. In C-Mod, a FA antenna has been shown to be inherently load tolerant which allows for robust power delivery to the plasma. Furthermore, the RF enhanced heat flux and antenna impurity source were nearly eliminated. For both L and H-mode discharges, the core impurity contamination is 20-30% lower but not eliminated. The emerging physics understanding is that the local RF impurity sources and RF enhanced heat flux is reduced due to the geometric alignment of the FA antenna while impurity contamination is a result of far field sheaths. An important aspect of antenna design is to identify a core absorption scenario that is characterized by strong single pass absorption for a broad range of target discharges. To maximize power coupling, the antenna spectrum needs to balance the k|| needed for strong single pass absorption and high coupling efficiency through evanescent layer. The latest design for a FA four strap adapted to EAST device is balance between geometrical constraints and physics requirements.

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

    PubMed Central

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

    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

  7. Hummock alignment in Japanese volcanic debris avalanches controlled by pre-avalanche slope of depositional area

    NASA Astrophysics Data System (ADS)

    Yoshida, Hidetsugu

    2014-10-01

    This paper investigates the relationship of hummock orientation to the flow dynamics of volcanic debris avalanches. There are opposing views on whether hummocks are systematically aligned along debris avalanche paths, or not. To investigate this geomorphologically fundamental question, I investigated hummock orientation for six Japanese debris avalanches of two simple styles: four "freely spreading" debris avalanches, and two "valley-filling" debris avalanches. Quantitative GIS-based data analysis revealed that hummock orientation along the avalanche flow path alternated between dominantly parallel to and dominantly perpendicular to the flow direction. These changes of alignment reflect dynamic changes of the local stress field within the avalanche, alternating between extensional and compressional in response to changes of the slope of the pre-avalanche ground surface. Changes of hummock alignment from perpendicular to parallel indicate that the local stress regime has changed from compressional to extensional. Conversely, changes of hummock alignment from parallel to perpendicular indicate that the local stress regime has changed from extensional to compressional. Thus, this research demonstrated a clear relationship between hummock orientation and dynamic changes of stress regime within avalanches that are related to changes of the slope of the pre-avalanche ground surface.

  8. Aligning Technology Education Teaching with Brain Development

    ERIC Educational Resources Information Center

    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…

  9. Survey and alignment at the ALS

    SciTech Connect

    Krebs, G.F.; Lauritzen, T.; Thur, W.

    1995-11-01

    This paper describes survey and alignment at the Lawrence Berkeley National Laboratory`s Advanced Light Source (ALS) accelerators from 1993 to 1995. The ALS is a 1.0 - 1.9 GeV electron accelerator producing extremely bright synchrotron light in the UV and soft-X-ray wavelengths. At the ALS, electrons are accelerated in a LINAC to 50 MeV, injected into a booster ring for further acceleration and finally injected into the storage ring. This is shown schematically in Figure 1. The storage ring, some 200 m in circumference, has been run with electron currents above 400 mA with lifetimes as high as 24 hours. The ALS is a third generation light source and requires for efficient storage ring operation, magnets aligned to within 150 mm of their ideal position. To accomplish this a network of monuments was established and their positions measured with respect to one another. The data was reduced using GEONET`` and STAR*NET`` software. Using the monuments as reference points, magnet positions were measured and alignment confirmed using the Kem Electronic Coordinate Determination System (ECDS``). A number of other papers dealing with survey and alignment (S&A) at the ALS have been written that may further elucidate some details of the methods and systems described in this paper.

  10. General Education Reform: Opportunities for Institutional Alignment

    ERIC Educational Resources Information Center

    Fuess, Scott M., Jr.; Mitchell, Nancy D.

    2011-01-01

    General education reform provides strategic opportunities for departments. This article analyzes reform at the University of Nebraska-Lincoln, illustrating how departments could use the reform process to clarify their strategic planning, align with institutional goals, and steer the university closer to departmental objectives. (Contains 1 table.)

  11. Prosody and Alignment: A Sequential Perspective

    ERIC Educational Resources Information Center

    Reed, Beatrice Szczepek

    2010-01-01

    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…

  12. Aligning English Language Testing with Curriculum

    ERIC Educational Resources Information Center

    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…

  13. EST Reading Curriculum & Instruction: An Alignment Analysis

    ERIC Educational Resources Information Center

    Mohammed, Lubna Ali; Sidek, H. M.

    2015-01-01

    In order for a curriculum to achieve its goals, it is imperative that the curriculum is coherent at all levels. In order to determine the coherency of a curriculum, the alignment of its theoretical underpinning and the label of a curriculum is one of the aspects that can be examined. The purpose of the current study was to examine if the…

  14. Constructing Aligned Assessments Using Automated Test Construction

    ERIC Educational Resources Information Center

    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…

  15. Aligned genomic data compression via improved modeling.

    PubMed

    Ochoa, Idoia; Hernaez, Mikel; Weissman, Tsachy

    2014-12-01

    With the release of the latest Next-Generation Sequencing (NGS) machine, the HiSeq X by Illumina, the cost of sequencing the whole genome of a human is expected to drop to a mere $1000. This milestone in sequencing history marks the era of affordable sequencing of individuals and opens the doors to personalized medicine. In accord, unprecedented volumes of genomic data will require storage for processing. There will be dire need not only of compressing aligned data, but also of generating compressed files that can be fed directly to downstream applications to facilitate the analysis of and inference on the data. Several approaches to this challenge have been proposed in the literature; however, focus thus far has been on the low coverage regime and most of the suggested compressors are not based on effective modeling of the data. We demonstrate the benefit of data modeling for compressing aligned reads. Specifically, we show that, by working with data models designed for the aligned data, we can improve considerably over the best compression ratio achieved by previously proposed algorithms. Our results indicate that the pareto-optimal barrier for compression rate and speed claimed by Bonfield and Mahoney (2013) [Bonfield JK and Mahoneys MV, Compression of FASTQ and SAM format sequencing data, PLOS ONE, 8(3):e59190, 2013.] does not apply for high coverage aligned data. Furthermore, our improved compression ratio is achieved by splitting the data in a manner conducive to operations in the compressed domain by downstream applications.

  16. Photoionization of aligned molecular excited states

    NASA Astrophysics Data System (ADS)

    Appling, J. R.; White, M. G.; Kessler, W. J.; Fernandez, R.; Poliakoff, E. D.

    1988-02-01

    Photoelectron angular distributions of several excited states of NO have been measured in an effort to better elucidate the role of alignment in resonant multiphoton excitation processes of molecules. In contrast to previous molecular REMPI measurements on NO, (2+1) angular distributions taken for low rotational levels of the E 2Σ+ (4sσ) Rydberg state of NO exhibit complex angular behavior which is characteristic of strong spatial alignment of the optically prepared levels. Photoelectron angular distributions were also found to be strongly branch and J dependent with the lowest rotational levels of the R21+S11 branch exhibiting the full anisotropy expected for an overall three-photon process. Fluorescence anisotropies extracted from complementary two-photon fluorescence angular distribution measurements reveal small, but nonzero alignment in all rotational levels with J>1/2, in contrast to the photoelectron results. Additional photoelectron angular distributions taken for (1+1) REMPI via the A 2Σ+ (3sσ), v=0 state exhibit near ``cos2θ'' distributions characteristic of photoionization of unaligned target states. The observed photoelectron data are qualitatively interpreted on the basis of the angular momentum constraints of the excitation-induced alignment and photoionization dynamics which determine the observable moments in the angular distribution.

  17. P-16 Alignment of Educational Success

    ERIC Educational Resources Information Center

    Sanchez, Jafeth; Thornton, Bill; Usinger, Janet

    2009-01-01

    This paper focuses on the concept of P-16 alignment of educational systems. At a basic level, evidence of school efforts, improved student achievement, and stakeholder support are necessary for effective accountability. The needs and benefits for stakeholders' understanding of P-16 education are addressed, particularly for educational leaders at…

  18. ON ALIGNMENT OF SUN, EARTH, AND SATELLITE

    DTIC Science & Technology

    The results are reported of an investigation of the relations among the launch parameters of an earth satellite and the time and position of alignment of the sun , the earth, and the satellite. The effects of variations of the launch conditions upon the satellite’s time of transit across the solar disc are determined. (Author)

  19. Alignment for Learning: Reorganizing Classrooms and Campuses

    ERIC Educational Resources Information Center

    Tagg, John

    2004-01-01

    Students nowadays are getting mixed messages about the meaning of education. Evidence has emerged that what colleges have been saying to students were not aligned with what colleges have been doing for students. Students found that the values that seemed to drive policy shifted from department to department, course to course, term to term. As a…

  20. Dielectric Properties of Aligned Conducting Polymers

    DTIC Science & Technology

    1991-10-01

    It has been demonstrated that aligned polyacetylene and polyaniline possess remarkably enhanced conductivities. The increase in crystallinity and...and thermal stability compared to other CPs such as polyacetylenes, polythiophenes, and polyaniline . These favorable properties and the commercial...stretch-orientation of BF4- doped PPy films electrochemically deposited at -30,C, 7 pyrrole electropolymerization at a xylene/water interface, 8 and

  1. Scalable cell alignment on optical media substrates.

    PubMed

    Anene-Nzelu, Chukwuemeka G; Choudhury, Deepak; Li, Huipeng; Fraiszudeen, Azmall; Peh, Kah-Yim; Toh, Yi-Chin; Ng, Sum Huan; Leo, Hwa Liang; Yu, Hanry

    2013-07-01

    Cell alignment by underlying topographical cues has been shown to affect important biological processes such as differentiation and functional maturation in vitro. However, the routine use of cell culture substrates with micro- or nano-topographies, such as grooves, is currently hampered by the high cost and specialized facilities required to produce these substrates. Here we present cost-effective commercially available optical media as substrates for aligning cells in culture. These optical media, including CD-R, DVD-R and optical grating, allow different cell types to attach and grow well on them. The physical dimension of the grooves in these optical media allowed cells to be aligned in confluent cell culture with maximal cell-cell interaction and these cell alignment affect the morphology and differentiation of cardiac (H9C2), skeletal muscle (C2C12) and neuronal (PC12) cell lines. The optical media is amenable to various chemical modifications with fibronectin, laminin and gelatin for culturing different cell types. These low-cost commercially available optical media can serve as scalable substrates for research or drug safety screening applications in industry scales.

  2. Thematic Roles, Markedness Alignment and Processing Complexity

    ERIC Educational Resources Information Center

    Lee, Yoonhyoung; Kwon, Youan; Gordon, Peter C.

    2015-01-01

    Two experiments used eye-tracking during reading to investigate the role of the consistency of the relative markedness alignment of noun phrases (NPs) in the processing of complex sentences in Korean. To do so, the animacy of the first NP was varied in both experiments to manipulate the relative markedness of NPs. In addition, case markings of the…

  3. Kernel Manifold Alignment for Domain Adaptation.

    PubMed

    Tuia, Devis; Camps-Valls, Gustau

    2016-01-01

    The wealth of sensory data coming from different modalities has opened numerous opportunities for data analysis. The data are of increasing volume, complexity and dimensionality, thus calling for new methodological innovations towards multimodal data processing. However, multimodal architectures must rely on models able to adapt to changes in the data distribution. Differences in the density functions can be due to changes in acquisition conditions (pose, illumination), sensors characteristics (number of channels, resolution) or different views (e.g. street level vs. aerial views of a same building). We call these different acquisition modes domains, and refer to the adaptation problem as domain adaptation. In this paper, instead of adapting the trained models themselves, we alternatively focus on finding mappings of the data sources into a common, semantically meaningful, representation domain. This field of manifold alignment extends traditional techniques in statistics such as canonical correlation analysis (CCA) to deal with nonlinear adaptation and possibly non-corresponding data pairs between the domains. We introduce a kernel method for manifold alignment (KEMA) that can match an arbitrary number of data sources without needing corresponding pairs, just few labeled examples in all domains. KEMA has interesting properties: 1) it generalizes other manifold alignment methods, 2) it can align manifolds of very different complexities, performing a discriminative alignment preserving each manifold inner structure, 3) it can define a domain-specific metric to cope with multimodal specificities, 4) it can align data spaces of different dimensionality, 5) it is robust to strong nonlinear feature deformations, and 6) it is closed-form invertible, which allows transfer across-domains and data synthesis. To authors' knowledge this is the first method addressing all these important issues at once. We also present a reduced-rank version of KEMA for computational

  4. Kernel Manifold Alignment for Domain Adaptation

    PubMed Central

    Tuia, Devis; Camps-Valls, Gustau

    2016-01-01

    The wealth of sensory data coming from different modalities has opened numerous opportunities for data analysis. The data are of increasing volume, complexity and dimensionality, thus calling for new methodological innovations towards multimodal data processing. However, multimodal architectures must rely on models able to adapt to changes in the data distribution. Differences in the density functions can be due to changes in acquisition conditions (pose, illumination), sensors characteristics (number of channels, resolution) or different views (e.g. street level vs. aerial views of a same building). We call these different acquisition modes domains, and refer to the adaptation problem as domain adaptation. In this paper, instead of adapting the trained models themselves, we alternatively focus on finding mappings of the data sources into a common, semantically meaningful, representation domain. This field of manifold alignment extends traditional techniques in statistics such as canonical correlation analysis (CCA) to deal with nonlinear adaptation and possibly non-corresponding data pairs between the domains. We introduce a kernel method for manifold alignment (KEMA) that can match an arbitrary number of data sources without needing corresponding pairs, just few labeled examples in all domains. KEMA has interesting properties: 1) it generalizes other manifold alignment methods, 2) it can align manifolds of very different complexities, performing a discriminative alignment preserving each manifold inner structure, 3) it can define a domain-specific metric to cope with multimodal specificities, 4) it can align data spaces of different dimensionality, 5) it is robust to strong nonlinear feature deformations, and 6) it is closed-form invertible, which allows transfer across-domains and data synthesis. To authors’ knowledge this is the first method addressing all these important issues at once. We also present a reduced-rank version of KEMA for computational

  5. Primary mirror alignment and assembly for a multispectral space telescope

    NASA Astrophysics Data System (ADS)

    Lin, Wei-Cheng; Chang, Shenq-Tsong; Chang, Sheng-Hsiung; Chang, Chen-Peng; Lin, Yu-Chuan; Huang, Po-Hsuan; Tsay, Ho-Lin; Chin, Chi-Chieh; Pan, Hsu-Pin; Huang, Ting-Ming

    2013-10-01

    For a currently developing multispectral space Cassegrain telescope, the primary mirror with 450 mm clear aperture is made of Zerodur and lightweighted at a ratio about 50 % to meet both thermal and mass requirement. For this mirror, it is critical to reduce the astigmatism caused from the gravity effect, bonding process and the deformation from the mounting to the main structure of the telescope (main plate). In this article, the primary mirror alignment, MGSE, assembly process and the optical performance test for the primary mirror assembly are presented. The mechanical shim is the interface between the iso-static mount and main plate. It is used to compensate the manufacture errors of components and differences of local co-planarity errors to prevent the stress while iso-static mount (ISM) is screwed to main plate. After primary mirror assembly, an optical performance test method called bench test with novel algorithm is used to analyze the astigmatism caused from the gravity effect and the deformation from the mounting or supporter. In an effort to achieve the requirement for the tolerance in primary mirror assembly, the astigmatism caused from the gravity and deformation by the mounting force could be less than P-V 0.02λ at 633 nm. The consequence of these demonstrations indicates that the designed mechanical ground supported equipment (MGSE) for the alignment and assembly processes meet the critical requirements for primary mirror assembly of the telescope.

  6. On the Role of Phase Alignments on Planetary Ring Edges

    NASA Astrophysics Data System (ADS)

    Weiss, J. W.; Stewart, G. R.

    2004-05-01

    We present our work on the role of epicyclic phase alignments on the edges of self-gravitating planetary rings. We will show the results of our work with the narrow ring instability, first reported on at last year's meeting. In particular, we will demonstrate that the instability on the edges of the narrow rings are not a global fluid instability and are probably a local phenomenon. The driver for the instability appears to be the particles' need to advance in their epicyclic paths combined with the tight packing, which prevents them from being able to move along their orbits. We will demonstrate that the early stages of the instability do not involve communication across the narrow ring. Thus, the instability should be applicable to broad rings and not just to our unphysically narrow rings. We will also show the results of our models of the edges of broad rings. In this case, we see that the entire ring edge quickly comes into approximate phase alignment. Unlike previous studies, we only rely on the self-gravity of the ring and particle-particle collisions to get this state. Possible implications of these results will be discussed. This work is supported by a NASA GSRP and the Cassini mission.

  7. Explaining compact groups as change alignments

    NASA Technical Reports Server (NTRS)

    Mamon, Gary A.

    1990-01-01

    The physical nature of the apparently densest groups of galaxies, known as compact groups is a topic of some recent controversy, despite the detailed observations of a well-defined catalog of 100 isolated compact groups compiled by Hickson (1982). Whereas many authors have espoused the view that compact groups are bound systems, typically as dense as they appear in projection on the sky (e.g., Williams & Rood 1987; Sulentic 1987; Hickson & Rood 1988), others see them as the result of chance configurations within larger systems, either in 1D (chance alignments: Mamon 1986; Walke & Mamon 1989), or in 3D (transient cores: Rose 1979). As outlined in the companion review to this contribution (Mamon, in these proceedings), the implication of Hickson's compact groups (HCGs) being dense bound systems is that they would then constitute the densest isolated systems of galaxies in the Universe and the privileged site for galaxy interactions. In a previous paper (Mamon 1986), the author reviewed the arguments given for the different theories of compact groups. Since then, a dozen papers have been published on the subject, including a thorough and perceptive review by White (1990), thus more than doubling the amount written on the subject. Here, the author first enumerates the arguments that he brought up in 1986 substantiating the chance alignment hypothesis, then he reviews the current status of the numerous recent arguments arguing against chance alignments and/or for the bound dense group hypothesis (both for the majority of HCGs but not all of them), and finally he reconsiders each one of these anti-chance alignment arguments and shows that, rather than being discredited, the chance alignment hypothesis remains a fully consistent explanation for the nature of compact groups.

  8. Robust temporal alignment of multimodal cardiac sequences

    NASA Astrophysics Data System (ADS)

    Perissinotto, Andrea; Queirós, Sandro; Morais, Pedro; Baptista, Maria J.; Monaghan, Mark; Rodrigues, Nuno F.; D'hooge, Jan; Vilaça, João. L.; Barbosa, Daniel

    2015-03-01

    Given the dynamic nature of cardiac function, correct temporal alignment of pre-operative models and intraoperative images is crucial for augmented reality in cardiac image-guided interventions. As such, the current study focuses on the development of an image-based strategy for temporal alignment of multimodal cardiac imaging sequences, such as cine Magnetic Resonance Imaging (MRI) or 3D Ultrasound (US). First, we derive a robust, modality-independent signal from the image sequences, estimated by computing the normalized cross-correlation between each frame in the temporal sequence and the end-diastolic frame. This signal is a resembler for the left-ventricle (LV) volume curve over time, whose variation indicates different temporal landmarks of the cardiac cycle. We then perform the temporal alignment of these surrogate signals derived from MRI and US sequences of the same patient through Dynamic Time Warping (DTW), allowing to synchronize both sequences. The proposed framework was evaluated in 98 patients, which have undergone both 3D+t MRI and US scans. The end-systolic frame could be accurately estimated as the minimum of the image-derived surrogate signal, presenting a relative error of 1.6 +/- 1.9% and 4.0 +/- 4.2% for the MRI and US sequences, respectively, thus supporting its association with key temporal instants of the cardiac cycle. The use of DTW reduces the desynchronization of the cardiac events in MRI and US sequences, allowing to temporally align multimodal cardiac imaging sequences. Overall, a generic, fast and accurate method for temporal synchronization of MRI and US sequences of the same patient was introduced. This approach could be straightforwardly used for the correct temporal alignment of pre-operative MRI information and intra-operative US images.

  9. Image Correlation Method for DNA Sequence Alignment

    PubMed Central

    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. PMID:22761742

  10. Image correlation method for DNA sequence alignment.

    PubMed

    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.

  11. Isolated digit recognition without time alignment

    NASA Astrophysics Data System (ADS)

    Gay, Jeffrey Mark

    1994-12-01

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

  12. Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment

    PubMed Central

    Sundfeld, Daniel; Havgaard, Jakob H.; de Melo, Alba C. M. A.; Gorodkin, Jan

    2016-01-01

    Motivation: Structured RNAs can be hard to search for as they often are not well conserved in their primary structure and are local in their genomic or transcriptomic context. Thus, the need for tools which in particular can make local structural alignments of RNAs is only increasing. Results: To meet the demand for both large-scale screens and hands on analysis through web servers, we present a new multithreaded version of Foldalign. We substantially improve execution time while maintaining all previous functionalities, including carrying out local structural alignments of sequences with low similarity. Furthermore, the improvements allow for comparing longer RNAs and increasing the sequence length. For example, lengths in the range 2000–6000 nucleotides improve execution up to a factor of five. Availability and implementation: The Foldalign software and the web server are available at http://rth.dk/resources/foldalign Contact: gorodkin@rth.dk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26704597

  13. Improved calibration of IMU biases in analytic coarse alignment for AHRS

    NASA Astrophysics Data System (ADS)

    Lu, Jiazhen; Lei, Chaohua; Li, Baoguo; Wen, Ting

    2016-07-01

    An improved method for the inertial measurement unit (IMU) calibration of coarse alignment for the low-accuracy attitude heading reference system (AHRS) is proposed in this paper. The sensitivities of the Euler angles with respect to the inertial sensor biases are studied based on the analytic coarse alignment principle, and the errors of earth rotation rate and local gravity in the body frame caused by initial attitude error are analyzed. Then, an improved analytic coarse alignment algorithm with accelerometer and gyro bias calibration in an arbitrary three-position is proposed. Simulation and experiment results show that the novel method can calibrate accelerometer and gyro biases, reduce Euler angle attitude error, and improve navigation precision in practical applications. Moreover, this method can be applied to other low-accuracy inertial navigation systems.

  14. Zipping, entanglement, and the elastic modulus of aligned single-walled carbon nanotube films

    PubMed Central

    Won, Yoonjin; Gao, Yuan; Panzer, Matthew A.; Xiang, Rong; Maruyama, Shigeo; Kenny, Thomas W.; Cai, Wei; Goodson, Kenneth E.

    2013-01-01

    Reliably routing heat to and from conversion materials is a daunting challenge for a variety of innovative energy technologies––from thermal solar to automotive waste heat recovery systems––whose efficiencies degrade due to massive thermomechanical stresses at interfaces. This problem may soon be addressed by adhesives based on vertically aligned carbon nanotubes, which promise the revolutionary combination of high through-plane thermal conductivity and vanishing in-plane mechanical stiffness. Here, we report the data for the in-plane modulus of aligned single-walled carbon nanotube films using a microfabricated resonator method. Molecular simulations and electron microscopy identify the nanoscale mechanisms responsible for this property. The zipping and unzipping of adjacent nanotubes and the degree of alignment and entanglement are shown to govern the spatially varying local modulus, thereby providing the route to engineered materials with outstanding combinations of mechanical and thermal properties. PMID:24309375

  15. A numerical model of ionospheric convection derived from field-alignment currents and the corresponding conductivity

    NASA Astrophysics Data System (ADS)

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

    1991-08-01

    A numerical model for the calculation of ionospheric convection patterns from given distributions of field aligned current and ionospheric conductivity is described. The model includes a coupling between the conductivity and the field aligned current. The input contributions, the field aligned current and the conductivity, are parametrized. From the primary model output a number of other quantities can be computed: the potential in the inertial frame, the potential in the magnetospheric equatorial plane, the distribution of ionosheric current, and the Joule heating in the ionosphere. This model was used together with a technique to caculate the high latitude potential distribution prevailing during a particular event by combining information from global auroral images and local measurements of fields and particles. The model potential variation along the satellite orbit was found to be in agreement with that calculated from the measured electric field. The model was also used to study some fundamental properties of the electrodynamics of the high latitude ionosphere.

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

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

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

  17. Alignment of cell division axes in directed epithelial cell migration

    NASA Astrophysics Data System (ADS)

    Marel, Anna-Kristina; Podewitz, Nils; Zorn, Matthias; Oskar Rädler, Joachim; Elgeti, Jens

    2014-11-01

    Cell division is an essential dynamic event in tissue remodeling during wound healing, cancer and embryogenesis. In collective migration, tensile stresses affect cell shape and polarity, hence, the orientation of the cell division axis is expected to depend on cellular flow patterns. Here, we study the degree of orientation of cell division axes in migrating and resting epithelial cell sheets. We use microstructured channels to create a defined scenario of directed cell invasion and compare this situation to resting but proliferating cell monolayers. In experiments, we find a strong alignment of the axis due to directed flow while resting sheets show very weak global order, but local flow gradients still correlate strongly with the cell division axis. We compare experimental results with a previously published mesoscopic particle based simulation model. Most of the observed effects are reproduced by the simulations.

  18. Two Influential Primate Classifications Logically Aligned

    PubMed Central

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

    2016-01-01

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

  19. Tool for Inspecting Alignment of Twinaxial Connectors

    NASA Technical Reports Server (NTRS)

    Smith, Christopher R.

    2008-01-01

    A proposed tool would be used to inspect alignments of mating twinaxial-connector assemblies on interconnecting wiring harnesses. More specifically, the tool would be used to inspect the alignment of each contact pin of each connector on one assembly with the corresponding socket in the corresponding connector on the other assembly. It is necessary to inspect the alignment because if mating of the assemblies is attempted when any pin/socket pair is misaligned beyond tolerance, the connection will not be completed and the dielectric material in the socket will be damaged (see Figure 1). Although the basic principle of the tool is applicable to almost any type of mating connector assemblies, the specific geometry of the tool must match the pin-and-socket geometry of the specific mating assemblies to be inspected. In the original application for which the tool was conceived, each of the mating assemblies contains eight twinaxial connectors; the pin diameter is 0.014 in. (.0.35 mm), and the maximum allowable pin/socket misalignment is 0.007 in. (.0.18 mm). Incomplete connections can result in loss of flight data within the functional path to the space shuttle crew cockpit displays. The tool (see Figure 2) would consist mainly of a transparent disk with alignment clocking tabs that can be fitted onto either connector assembly. Sets of circles or equivalent reference markings are affixed to the face of the tool, located at the desired positions of the mating contact pairs. An inspector would simply fit the tool onto a connector assembly, engaging the clocking tabs until the tool fits tightly. The inspector would then align one set of circles positioning a line of sight perpendicular to one contact within the connector assembly. Mis alignments would be evidenced by the tip of a pin contact straying past the inner edge of the circle. Socket contact misalignments would be evidenced by a crescent-shaped portion of the white dielectric appearing within the circle. The tool

  20. ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches.

    PubMed

    Rognes, T

    2001-04-01

    There is a need for faster and more sensitive algorithms for sequence similarity searching in view of the rapidly increasing amounts of genomic sequence data available. Parallel processing capabilities in the form of the single instruction, multiple data (SIMD) technology are now available in common microprocessors and enable a single microprocessor to perform many operations in parallel. The ParAlign algorithm has been specifically designed to take advantage of this technology. The new algorithm initially exploits parallelism to perform a very rapid computation of the exact optimal ungapped alignment score for all diagonals in the alignment matrix. Then, a novel heuristic is employed to compute an approximate score of a gapped alignment by combining the scores of several diagonals. This approximate score is used to select the most interesting database sequences for a subsequent Smith-Waterman alignment, which is also parallelised. The resulting method represents a substantial improvement compared to existing heuristics. The sensitivity and specificity of ParAlign was found to be as good as Smith-Waterman implementations when the same method for computing the statistical significance of the matches was used. In terms of speed, only the significantly less sensitive NCBI BLAST 2 program was found to outperform the new approach. Online searches are available at http://dna.uio.no/search/

  1. Using automatic alignment to analyze endangered language data: testing the viability of untrained alignment.

    PubMed

    DiCanio, Christian; Nam, Hosung; Whalen, Douglas H; Bunnell, H Timothy; Amith, Jonathan D; García, Rey Castillo

    2013-09-01

    While efforts to document endangered languages have steadily increased, the phonetic analysis of endangered language data remains a challenge. The transcription of large documentation corpora is, by itself, a tremendous feat. Yet, the process of segmentation remains a bottleneck for research with data of this kind. This paper examines whether a speech processing tool, forced alignment, can facilitate the segmentation task for small data sets, even when the target language differs from the training language. The authors also examined whether a phone set with contextualization outperforms a more general one. The accuracy of two forced aligners trained on English (hmalign and p2fa) was assessed using corpus data from Yoloxóchitl Mixtec. Overall, agreement performance was relatively good, with accuracy at 70.9% within 30 ms for hmalign and 65.7% within 30 ms for p2fa. Segmental and tonal categories influenced accuracy as well. For instance, additional stop allophones in hmalign's phone set aided alignment accuracy. Agreement differences between aligners also corresponded closely with the types of data on which the aligners were trained. Overall, using existing alignment systems was found to have potential for making phonetic analysis of small corpora more efficient, with more allophonic phone sets providing better agreement than general ones.

  2. NoFold: RNA structure clustering without folding or alignment.

    PubMed

    Middleton, Sarah A; Kim, Junhyong

    2014-11-01

    Structures that recur across multiple different transcripts, called structure motifs, often perform a similar function-for example, recruiting a specific RNA-binding protein that then regulates translation, splicing, or subcellular localization. Identifying common motifs between coregulated transcripts may therefore yield significant insight into their binding partners and mechanism of regulation. However, as most methods for clustering structures are based on folding individual sequences or doing many pairwise alignments, this results in a tradeoff between speed and accuracy that can be problematic for large-scale data sets. Here we describe a novel method for comparing and characterizing RNA secondary structures that does not require folding or pairwise alignment of the input sequences. Our method uses the idea of constructing a distance function between two objects by their respective distances to a collection of empirical examples or models, which in our case consists of 1973 Rfam family covariance models. Using this as a basis for measuring structural similarity, we developed a clustering pipeline called NoFold to automatically identify and annotate structure motifs within large sequence data sets. We demonstrate that NoFold can simultaneously identify multiple structure motifs with an average sensitivity of 0.80 and precision of 0.98 and generally exceeds the performance of existing methods. We also perform a cross-validation analysis of the entire set of Rfam families, achieving an average sensitivity of 0.57. We apply NoFold to identify motifs enriched in dendritically localized transcripts and report 213 enriched motifs, including both known and novel structures.

  3. NoFold: RNA structure clustering without folding or alignment

    PubMed Central

    Middleton, Sarah A.

    2014-01-01

    Structures that recur across multiple different transcripts, called structure motifs, often perform a similar function—for example, recruiting a specific RNA-binding protein that then regulates translation, splicing, or subcellular localization. Identifying common motifs between coregulated transcripts may therefore yield significant insight into their binding partners and mechanism of regulation. However, as most methods for clustering structures are based on folding individual sequences or doing many pairwise alignments, this results in a tradeoff between speed and accuracy that can be problematic for large-scale data sets. Here we describe a novel method for comparing and characterizing RNA secondary structures that does not require folding or pairwise alignment of the input sequences. Our method uses the idea of constructing a distance function between two objects by their respective distances to a collection of empirical examples or models, which in our case consists of 1973 Rfam family covariance models. Using this as a basis for measuring structural similarity, we developed a clustering pipeline called NoFold to automatically identify and annotate structure motifs within large sequence data sets. We demonstrate that NoFold can simultaneously identify multiple structure motifs with an average sensitivity of 0.80 and precision of 0.98 and generally exceeds the performance of existing methods. We also perform a cross-validation analysis of the entire set of Rfam families, achieving an average sensitivity of 0.57. We apply NoFold to identify motifs enriched in dendritically localized transcripts and report 213 enriched motifs, including both known and novel structures. PMID:25234928

  4. DKIST visible broadband imager alignment in laboratory: first results

    NASA Astrophysics Data System (ADS)

    Sekulic, Predrag; Gregory, Scott B.; Hegwer, Steve L.; Ferayorni, Andrew; Woeger, Friedrich

    2016-08-01

    The Visible Broadband Imager (VBI) Blue and Red channels are the first Daniel K. Inouye Solar Telescope (DKIST) instruments that have been aligned and tested in a laboratory. This paper describes the optical alignment method of the VBI as performed in the laboratory. The objective of this preliminary alignment is to test and validate the optical alignment method that will be used during final alignment on the telescope, to measure the VBI performances and to verify that it meets specification. The optical alignment method is defined by three major steps. The first step is realized by combining the optical and mechanical models into the Spatial Analyzer (SA) software, and extracting the data serving as target values during alignment. The second step is the mechanical alignment and allows to accurately position the optics in the instrument coordinate system by using a Coordinate Measurement Machine (CMM) arm and a theodolite. This step has led to a great initial positioning and has allowed reaching an initial wavefront error before optical alignment close to the specification. The last step, performed by interferometry, allows fine alignment to compensate the residual aberrations created by misalignment and manufacturing tolerances. This paper presents also an alignment method to compute the shifts and tilts of compensating lenses to correct the residual aberrations. This paper describes first results of the VBI instruments performances measured in the laboratory and confirm the validity of the alignment process that will be reproduced during final alignment on the telescope.

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

    PubMed

    Louey, Melissa Gar Yee; Sangeux, Morgan

    2016-09-01

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

  6. Ecology of dark matter haloes -II. Effects of interactions on the alignment of halo pairs

    NASA Astrophysics Data System (ADS)

    L'Huillier, Benjamin; Park, Changbom; Kim, Juhan

    2017-01-01

    We use the Horizon Run 4 cosmological N-body simulation to study the effects of distant and close interactions on the alignments of the shapes, spins, and orbits of targets haloes with their neighbours, and their dependence on the local density environment and neighbour separation. Interacting targets have a significantly lower spin and higher sphericity and oblateness than all targets. Interacting pairs initially have anti-parallel spins, but the spins develop parallel alignment as time goes on. Neighbours tend to evolve in the plane of rotation of the target, and in the direction of the major axis of prolate haloes. Moreover, interactions are preferentially radial, while pairs with non-radial orbits are preferentially prograde. The alignment signals are stronger at high-mass and for close separations, and independent on the large-scale density. Positive alignment signals are found at redshifts up to 4, and increase with decreasing redshifts. Moreover, the orbits tend to become prograde at low redshift, while no alignment is found at high redshift (z = 4).

  7. Effect of Alignment on Transport Properties of Carbon Nanotube/Metallic Junctions

    NASA Technical Reports Server (NTRS)

    Wincheski, Buzz; Namkung, Min; Smits, Jan; Williams, Phillip; Harvey, Robert

    2003-01-01

    Ballistic and spin coherent transport in single walled carbon nanotubes (SWCNT) are predicted to enable high sensitivity single-nanotube devices for strain and magnetic field sensing. Based upon these phenomena, electron beam lithography procedures have been developed to study the transport properties of purified HiPCO single walled carbon nanotubes for development into sensory materials for nondestructive evaluation. Purified nanotubes are dispersed in solvent suspension and then deposited on the device substrate before metallic contacts are defined and deposited through electron beam lithography. This procedure produces randomly dispersed ropes, typically 2 - 20 nm in diameter, of single walled carbon nanotubes. Transport and scanning probe microscopy studies have shown a good correlation between the junction resistance and tube density, alignment, and contact quality. In order to improve transport properties of the junctions a technique has been developed to align and concentrate nanotubes at specific locations on the substrate surface. Lithographic techniques are used to define local areas where high frequency electric fields are to be concentrated. Application of the fields while the substrate is exposed to nanotube-containing solution results in nanotube arrays aligned with the electric field lines. A second electron beam lithography layer is then used to deposit metallic contacts across the aligned tubes. Experimental measurements are presented showing the increased tube alignment and improvement in the transport properties of the junctions.

  8. Alignment engineering in liquid crystalline elastomers: Free-form microstructures with multiple functionalities

    SciTech Connect

    Zeng, Hao; Cerretti, Giacomo; Wiersma, Diederik S. E-mail: wiersma@lens.unifi.it; Wasylczyk, Piotr; Martella, Daniele; Parmeggiani, Camilla E-mail: wiersma@lens.unifi.it

    2015-03-16

    We report a method to fabricate polymer microstructures with local control over the molecular orientation. Alignment control is achieved on molecular level in a structure of arbitrary form that can be from 1 to 100 μm in size, by fixing the local boundary conditions with micro-grating patterns. The method makes use of two-photon polymerization (Direct Laser Writing) and is demonstrated specifically in liquid-crystalline elastomers. This concept allows for the realization of free-form polymeric structures with multiple functionalities which are not possible to realize with existing techniques and which can be locally controlled by light in the micrometer scale.

  9. Assessment of a field-aligned ICRF antenna

    NASA Astrophysics Data System (ADS)

    Wukitch, S. J.; Brunner, D.; Ennever, P.; Garrett, M. L.; Hubbard, A.; Labombard, B.; Lau, C.; Lin, Y.; Lipschultz, B.; Miller, D.; Ochoukov, R.; Porkolab, M.; Reinke, M. L.; Terry, J. L.

    2014-02-01

    Impurity contamination and localized heat loads associated with ion cyclotron range of frequency (ICRF) antenna operation are among the most challenging issues for ICRF utilization.. Another challenge is maintaining maximum coupled power through plasma variations including edge localized modes (ELMs) and confinement transitions. Here, we report on an experimental assessment of a field aligned (FA) antenna with respect to impurity contamination, impurity sources, RF enhanced heat flux and load tolerance. In addition, we compare the modification of the scrape of layer (SOL) plasma potential of the FA antenna to a conventional, toroidally aligned (TA) antenna, in order to explore the underlying physics governing impurity contamination linked to ICRF heating. The FA antenna is a 4-strap ICRF antenna where the current straps and antenna enclosure sides are perpendicular to and the Faraday screen rods are parallel to the total magnetic field. In principle, alignment with respect to the total magnetic field minimizes integrated E∥ (electric field along a magnetic field line) via symmetry. Consistent with expectations, we observed that the impurity contamination and impurity source at the FA antenna are reduced compared to the TA antenna. In both L and H-mode discharges, the radiated power is 20-30% lower for a FA-antenna heated discharge than a discharge heated with the TA-antennas. Further we observe that the fraction of RF energy deposited upon the antenna is less than 0.4 % of the total injected RF energy in dipole phasing. The total deposited energy increases significantly when the FA antenna is operated in monopole phasing. The FA antenna also exhibits an unexpected load tolerance for ELMs and confinement transitions compared to the TA antennas. However, inconsistent with expectations, we observe RF induced plasma potentials to be nearly identical for FA and TA antennas when operated in dipole phasing. In monopole phasing, the FA antenna has the highest plasma

  10. Assessment of a field-aligned ICRF antenna

    SciTech Connect

    Wukitch, S. J.; Brunner, D.; Ennever, P.; Garrett, M. L.; Hubbard, A.; Labombard, B.; Lau, C.; Lin, Y.; Lipschultz, B.; Miller, D.; Ochoukov, R.; Porkolab, M.; Reinke, M. L.; Terry, J. L.

    2014-02-12

    Impurity contamination and localized heat loads associated with ion cyclotron range of frequency (ICRF) antenna operation are among the most challenging issues for ICRF utilization.. Another challenge is maintaining maximum coupled power through plasma variations including edge localized modes (ELMs) and confinement transitions. Here, we report on an experimental assessment of a field aligned (FA) antenna with respect to impurity contamination, impurity sources, RF enhanced heat flux and load tolerance. In addition, we compare the modification of the scrape of layer (SOL) plasma potential of the FA antenna to a conventional, toroidally aligned (TA) antenna, in order to explore the underlying physics governing impurity contamination linked to ICRF heating. The FA antenna is a 4-strap ICRF antenna where the current straps and antenna enclosure sides are perpendicular to and the Faraday screen rods are parallel to the total magnetic field. In principle, alignment with respect to the total magnetic field minimizes integrated E∥ (electric field along a magnetic field line) via symmetry. Consistent with expectations, we observed that the impurity contamination and impurity source at the FA antenna are reduced compared to the TA antenna. In both L and H-mode discharges, the radiated power is 20–30% lower for a FA-antenna heated discharge than a discharge heated with the TA-antennas. Further we observe that the fraction of RF energy deposited upon the antenna is less than 0.4 % of the total injected RF energy in dipole phasing. The total deposited energy increases significantly when the FA antenna is operated in monopole phasing. The FA antenna also exhibits an unexpected load tolerance for ELMs and confinement transitions compared to the TA antennas. However, inconsistent with expectations, we observe RF induced plasma potentials to be nearly identical for FA and TA antennas when operated in dipole phasing. In monopole phasing, the FA antenna has the highest plasma

  11. Molecular orbital imaging for partially aligned molecules

    NASA Astrophysics Data System (ADS)

    Qin, Meiyan; Zhu, Xiaosong

    2017-01-01

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

  12. Stakeholder Alignment and Changing Geospatial Information Capabilities

    NASA Astrophysics Data System (ADS)

    Winter, S.; Cutcher-Gershenfeld, J.; King, J. L.

    2015-12-01

    Changing geospatial information capabilities can have major economic and social effects on activities such as drought monitoring, weather forecasts, agricultural productivity projections, water and air quality assessments, the effects of forestry practices and so on. Whose interests are served by such changes? Two common mistakes are assuming stability in the community of stakeholders and consistency in stakeholder behavior. Stakeholder communities can reconfigure dramatically as some leave the discussion, others enter, and circumstances shift — all resulting in dynamic points of alignment and misalignment . New stakeholders can bring new interests, and existing stakeholders can change their positions. Stakeholders and their interests need to be be considered as geospatial information capabilities change, but this is easier said than done. New ways of thinking about stakeholder alignment in light of changes in capability are presented.

  13. Aligning Astronomical Telescopes via Identification of Stars

    NASA Technical Reports Server (NTRS)

    Whorton, Mark

    2010-01-01

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

  14. Strategies and tools for whole genome alignments

    SciTech Connect

    Couronne, Olivier; Poliakov, Alexander; Bray, Nicolas; Ishkhanov,Tigran; Ryaboy, Dmitriy; Rubin, Edward; Pachter, Lior; Dubchak, Inna

    2002-11-25

    The availability of the assembled mouse genome makespossible, for the first time, an alignment and comparison of two largevertebrate genomes. We have investigated different strategies ofalignment for the subsequent analysis of conservation of genomes that areeffective for different quality assemblies. These strategies were appliedto the comparison of the working draft of the human genome with the MouseGenome Sequencing Consortium assembly, as well as other intermediatemouse assemblies. Our methods are fast and the resulting alignmentsexhibit a high degree of sensitivity, covering more than 90 percent ofknown coding exons in the human genome. We have obtained such coveragewhile preserving specificity. With a view towards the end user, we havedeveloped a suite of tools and websites for automatically aligning, andsubsequently browsing and working with whole genome comparisons. Wedescribe the use of these tools to identify conserved non-coding regionsbetween the human and mouse genomes, some of which have not beenidentified by other methods.

  15. Uniformly spaced field-aligned ionization ducts

    NASA Technical Reports Server (NTRS)

    Gross, S. H.; Muldrew, D. B.

    1984-01-01

    A number of interesting cases of combination mode ducted echoes for mid- and low-latitude regions are presented that show nearly uniformly spaced multiple combination mode traces on the ionograms in the frequency range above 1 MHz. These traces suggest that a parallel system of field-aligned ducts is present. Ray tracing studies are made to determine the structure that would explain the observations using the electron density profile derivable from the vertical trace and assuming field-aligned ducts. Spacing perpendicular to the ducts is found to be as much as 70 km. Some of these parallel duct structures are found to extend to the conjugate hemisphere, possibly to the F peak.

  16. Alignment of the Fermilab D0 Detector

    SciTech Connect

    Babatunde O'Sheg Oshinowo

    2001-07-20

    The Fermilab D0 detector was used for the discovery of the top quark during Run I in 1996. It is currently being upgraded to exploit the physics potential to be presented by the Main Injector and the Tevatron Collider during Run II in the Fall of 2000. Some of the essential elements of this upgrade is the upgrade of the Solenoid Magnet, the Central Fiber Tracker, the Preshower Detectors, the Calorimeter System, and the Muon System. This paper discusses the survey and alignment of the these detectors with emphasis on the Muon detector system. The alignment accuracy is specified as better than 0.5mm. A combination of the Laser Tracker, BETS, and V-STARS systems are used for the survey.

  17. Aligning the demonstration model of CHEOPS

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

    CHEOPS (CHaracterizing ExOPlanets Satellite) is an ESA Small Mission, planned to be launched in mid-2018 and whose main goal is the photometric precise characterization of radii of exoplanets orbiting bright stars (V<12) already known to host planets. Given the fast-track nature of this mission, we developed a non-flying Demonstration Model, whose optics are flight representative and whose mechanics provides the same interfaces of the flight model, but is not thermally representative. In this paper, we describe CHEOPS Demonstration Model handling, integration, tests, alignment and characterization, emphasizing the verification of the uncertainties in the optical quality measurements introduced by the starlight simulator and the way the alignment and optical surfaces are measured.

  18. Evryscope Robotilter automated camera / ccd alignment system

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  19. Regional Alignment: Phase Zero Logistics Implications

    DTIC Science & Technology

    2014-05-01

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

  20. Postgrowth Microwave Treatment to Align Carbon Nanotubes

    DTIC Science & Technology

    2013-03-01

    pp. 8671–8675. [47] Chen, C. M., Chen, M., Peng, Y. W., Yu, H. W., and Chen, C. F., 2006, “High Efficiency Microwave Digestion Purification of Multi...Y. W., Lin, C. H., Chang, L. W., and Chen, C. F., 2005, “ Microwave Digestion and Acidic Treatment Procedures for the Purification of Multi-Walled...Postgrowth Microwave Treatment to Align Carbon Nanotubes J. J. Nguyen T. L. Bougher P. Pour Shahid Saeed Abadi A. Sharma George W. Woodruff School of

  1. Superposition and alignment of labeled point clouds.

    PubMed

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

    2011-01-01

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

  2. Controlled Deposition and Alignment of Carbon Nanotubes

    NASA Technical Reports Server (NTRS)

    Smits, Jan M. (Inventor); Wincheski, Russell A. (Inventor); Ingram, JoAnne L. (Inventor); Watkins, Anthony Neal (Inventor); Jordan, Jeffrey D. (Inventor)

    2009-01-01

    A carbon nanotube (CNT) attraction material is deposited on a substrate in the gap region between two electrodes on the . substrate. An electric potential is applied to the two electrodes. The CNT attraction material is wetted with a solution defined by a carver liquid having carbon nanotubes (CNTs) suspended therein. A portion of the CNTs align with the electric field and adhere to The CNT attraction material. The carrier liquid and any CNTs not adhered to the CNT attraction material are then removed.

  3. Controlled Deposition and Alignment of Carbon Nanotubes

    NASA Technical Reports Server (NTRS)

    Smits, Jan M. (Inventor); Wincheski, Russell A. (Inventor); Patry, JoAnne L. (Inventor); Watkins, Anthony Neal (Inventor); Jordan, Jeffrey D. (Inventor)

    2012-01-01

    A carbon nanotube (CNT) attraction material is deposited on a substrate in the gap region between two electrodes on the substrate. An electric potential is applied to the two electrodes. The CNT attraction material is wetted with a solution defined by a carrier liquid having carbon nanotubes (CNTs) suspended therein. A portion of the CNTs align with the electric field and adhere to the CNT attraction material. The carrier liquid and any CNTs not adhered to the CNT attraction material are then removed.

  4. Alignment of Liquid Crystals by Surface Gratings

    DTIC Science & Technology

    1979-10-31

    UV / ozone cleaning 30 is effective in removing traces of most organic contaminants including evapo- rated carbon films. Substrates which were UV...the substrates to short wavelength UV. Even the UV / ozone cleaning may not guarantee that substrates will be free from organic contaminants, though it...homeotropic alignment of M1313A (and the heptyl/butyl mixture) is obtained. Exposure of the DMOAP-coated quartz to the UV / ozone cleaning process for

  5. Mounting and Alignment of IXO Mirror Segments

    NASA Technical Reports Server (NTRS)

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

    2010-01-01

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

  6. Self-Aligning, Spline-Locking Fastener

    NASA Technical Reports Server (NTRS)

    Vranish, John M.

    1992-01-01

    Self-aligning, spline-locking fastener is two-part mechanism operated by robot, using one tool and simple movements. Spline nut on springloaded screw passes through mating spline fitting. Operator turns screw until vertical driving surfaces on spline nut rest against corresponding surfaces of spline fitting. Nut rides upward, drawing pieces together. Used to join two parts of structure, to couple vehicles, or to mount payload in vehicle.

  7. Experience report with the Alignment Diagnostic System

    SciTech Connect

    Gassner, Georg; /SLAC

    2011-03-03

    Since 2009 an Alignment Diagnostic System (ADS) has been operating at the undulator of the new Linac Coherent Light Source at SLAC National Accelerator Laboratory. The undulator spans a distance of 132 meters and is structured into 33 segments. Each segment is equipped with four hydrostatic leveling sensors and four wire position monitors. This report describes the set up and reflects the experience gained with the ADS.

  8. Vertical bounce of two vertically aligned balls

    NASA Astrophysics Data System (ADS)

    Cross, Rod

    2007-11-01

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

  9. A novel partial sequence alignment tool for finding large deletions.

    PubMed

    Aruk, Taner; Ustek, Duran; Kursun, Olcay

    2012-01-01

    Finding large deletions in genome sequences has become increasingly more useful in bioinformatics, such as in clinical research and diagnosis. Although there are a number of publically available next generation sequencing mapping and sequence alignment programs, these software packages do not correctly align fragments containing deletions larger than one kb. We present a fast alignment software package, BinaryPartialAlign, that can be used by wet lab scientists to find long structural variations in their experiments. For BinaryPartialAlign, we make use of the Smith-Waterman (SW) algorithm with a binary-search-based approach for alignment with large gaps that we called partial alignment. BinaryPartialAlign implementation is compared with other straight-forward applications of SW. Simulation results on mtDNA fragments demonstrate the effectiveness (runtime and accuracy) of the proposed method.

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

    PubMed

    Hung, Che-Lun; Lin, Yaw-Ling

    2013-01-01

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

  11. Collective alignment of polar filaments by molecular motors.

    PubMed

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

    2009-04-01

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

  12. SQUARE--determining reliable regions in sequence alignments.

    PubMed

    Tress, Michael L; Graña, Osvaldo; Valencia, Alfonso

    2004-04-12

    The Server for Quick Alignment Reliability Evaluation (SQUARE) is a Web-based version of the method we developed to predict regions of reliably aligned residues in sequence alignments. Given an alignment between a query sequence and a sequence of known structure, SQUARE is able to predict which residues are reliably aligned. The server accesses a database of profiles of sequences of known three-dimensional structures in order to calculate the scores for each residue in the alignment. SQUARE produces a graphical output of the residue profile-derived alignment scores along with an indication of the reliability of the alignment. In addition, the scores can be compared against template secondary structure, conserved residues and important sites.

  13. Blasting and Zipping: Sequence Alignment and Mutual Information

    NASA Astrophysics Data System (ADS)

    Penner, Orion; Grassberger, Peter; Paczuski, Maya

    2009-03-01

    Alignment of biological sequences such as DNA, RNA or proteins is one of the most widely used tools in computational bioscience. While the accomplishments of sequence alignment algorithms are undeniable the fact remains that these algorithms are based upon heuristic scoring schemes. Therefore, these algorithms do not provide model independent and objective measures for how similar two (or more) sequences actually are. Although information theory provides such a similarity measure - the mutual information (MI) - numerous previous attempts to connect sequence alignment and information have not produced realistic estimates for the MI from a given alignment. We report on a simple and flexible approach to get robust estimates of MI from global alignments. The presented results may help establish MI as a reliable tool for evaluating the quality of global alignments, judging the relative merits of different alignment algorithms, and estimating the significance of specific alignments.

  14. Camber Angle Inspection for Vehicle Wheel Alignments

    PubMed Central

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

    2017-01-01

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

  15. Regular Language Constrained Sequence Alignment Revisited

    NASA Astrophysics Data System (ADS)

    Kucherov, Gregory; Pinhas, Tamar; Ziv-Ukelson, Michal

    Imposing constraints in the form of a finite automaton or a regular expression is an effective way to incorporate additional a priori knowledge into sequence alignment procedures. With this motivation, Arslan [1] introduced the Regular Language Constrained Sequence Alignment Problem and proposed an O(n 2 t 4) time and O(n 2 t 2) space algorithm for solving it, where n is the length of the input strings and t is the number of states in the non-deterministic automaton, which is given as input. Chung et al. [2] proposed a faster O(n 2 t 3) time algorithm for the same problem. In this paper, we further speed up the algorithms for Regular Language Constrained Sequence Alignment by reducing their worst case time complexity bound to O(n 2 t 3/logt). This is done by establishing an optimal bound on the size of Straight-Line Programs solving the maxima computation subproblem of the basic dynamic programming algorithm. We also study another solution based on a Steiner Tree computation. While it does not improve the run time complexity in the worst case, our simulations show that both approaches are efficient in practice, especially when the input automata are dense.

  16. Functionalization of vertically aligned carbon nanotubes

    PubMed Central

    Snyders, Rony; Colomer, Jean-François

    2013-01-01

    Summary 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. PMID:23504581

  17. Alignment limit of the NMSSM Higgs sector

    DOE PAGES

    Carena, Marcela; Haber, Howard E.; Low, Ian; ...

    2016-02-17

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

  18. Mask-to-wafer alignment system

    DOEpatents

    Sweatt, William C.; Tichenor, Daniel A.; Haney, Steven J.

    2003-11-04

    A modified beam splitter that has a hole pattern that is symmetric in one axis and anti-symmetric in the other can be employed in a mask-to-wafer alignment device. The device is particularly suited for rough alignment using visible light. The modified beam splitter transmits and reflects light from a source of electromagnetic radiation and it includes a substrate that has a first surface facing the source of electromagnetic radiation and second surface that is reflective of said electromagnetic radiation. The substrate defines a hole pattern about a central line of the substrate. In operation, an input beam from a camera is directed toward the modified beam splitter and the light from the camera that passes through the holes illuminates the reticle on the wafer. The light beam from the camera also projects an image of a corresponding reticle pattern that is formed on the mask surface of the that is positioned downstream from the camera. Alignment can be accomplished by detecting the radiation that is reflected from the second surface of the modified beam splitter since the reflected radiation contains both the image of the pattern from the mask and a corresponding pattern on the wafer.

  19. Alignement automatise de fibres optiques amorces monomodes

    NASA Astrophysics Data System (ADS)

    St-Amant, Yves

    Cette these jette les bases necessaires au developpement d'algorithmes a base de modele pour l'automatisation de l'alignement de fibres amorces monomodes. A partir de la methode de l'integrale de recouvrement et de deux solutions approximatives existantes, un modele analytique d'efficacite de couplage optique permettant d'estimer la puissance transmise entre un composant et une fibre amorce monomode est d'abord formule. Avec celui-ci, sept proprietes pouvant etre utiles au developpement d'algorithmes a base de modele sont ensuite identifiees et validees. Enfin, a l'aide de ces proprietes, une strategie d'alignement a base de modele est developpee et validee experimentalement. Les resultats obtenus demontrent clairement la repetitivite, la robustesse, la precision et la rapidite de la strategie proposee. Ils demontrent aussi qu'il est possible de realiser un alignement complet sans l'utilisation de systemes auxiliaires tels des systemes de vision, des cameras infrarouges, des capteurs de contact ou des systemes de fixation hautement precis.

  20. Aligning genomes with inversions and swaps

    SciTech Connect

    Holloway, J.L.; Cull, P.

    1994-12-31

    The decision about what operators to allow and how to charge for these operations when aligning strings that arise in a biological context is the decision about what model of evolution to assume. Frequently the operators used to construct an alignment between biological sequences axe limited to deletion, insertion, or replacement of a character or block of characters, but there is biological evidence for the evolutionary operations of exchanging the positions of two segments in a sequence and the replacement of a segment by its reversed complement. In this paper we describe a family of heuristics designed to compute alignments of biological sequences assuming a model of evolution with swaps and inversions. The heuristics will necessarily be approximate since the appropriate way to charge for the evolutionary events (delete, insert, substitute, swap, and invert) is not known. The paper concludes with a pair-wise comparison of 20 Picornavirus genomes, and a detailed comparison of the hepatitis delta virus with the citrus exocortis viroid.