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Sample records for alignment algorithm determined

  1. New Attitude Sensor Alignment Calibration Algorithms

    Science.gov (United States)

    Hashmall, Joseph A.; Sedlak, Joseph E.; Harman, Richard (Technical Monitor)

    2002-01-01

    Accurate spacecraft attitudes may only be obtained if the primary attitude sensors are well calibrated. Launch shock, relaxation of gravitational stresses and similar effects often produce large enough alignment shifts so that on-orbit alignment calibration is necessary if attitude accuracy requirements are to be met. A variety of attitude sensor alignment algorithms have been developed to meet the need for on-orbit calibration. Two new algorithms are presented here: ALICAL and ALIQUEST. Each of these has advantages in particular circumstances. ALICAL is an attitude independent algorithm that uses near simultaneous measurements from two or more sensors to produce accurate sensor alignments. For each set of simultaneous observations the attitude is overdetermined. The information content of the extra degrees of freedom can be combined over numerous sets to provide the sensor alignments. ALIQUEST is an attitude dependent algorithm that combines sensor and attitude data into a loss function that has the same mathematical form as the Wahba problem. Alignments can then be determined using any of the algorithms (such as the QUEST quaternion estimator) that have been developed to solve the Wahba problem for attitude. Results from the use of these methods on active missions are presented.

  2. Algorithms for Automatic Alignment of Arrays

    Science.gov (United States)

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

    1996-01-01

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

  3. Cactus: Algorithms for genome multiple sequence alignment

    OpenAIRE

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

    2011-01-01

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

  4. FOGSAA: Fast Optimal Global Sequence Alignment Algorithm

    Science.gov (United States)

    Chakraborty, Angana; Bandyopadhyay, Sanghamitra

    2013-04-01

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

  5. A Clustal Alignment Improver Using Evolutionary Algorithms

    DEFF Research Database (Denmark)

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

    2002-01-01

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

  6. Convergent algorithms for protein structural alignment

    Directory of Open Access Journals (Sweden)

    Martínez José

    2007-08-01

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

  7. Enhanced Dynamic Algorithm of Genome Sequence Alignments

    Directory of Open Access Journals (Sweden)

    Arabi E. keshk

    2014-05-01

    Full Text Available The merging of biology and computer science has created a new field called computational biology that explore the capacities of computers to gain knowledge from biological data, bioinformatics. Computational biology is rooted in life sciences as well as computers, information sciences, and technologies. The main problem in computational biology is sequence alignment that is a way of arranging the sequences of DNA, RNA or protein to identify the region of similarity and relationship between sequences. This paper introduces an enhancement of dynamic algorithm of genome sequence alignment, which called EDAGSA. It is filling the three main diagonals without filling the entire matrix by the unused data. It gets the optimal solution with decreasing the execution time and therefore the performance is increased. To illustrate the effectiveness of optimizing the performance of the proposed algorithm, it is compared with the traditional methods such as Needleman-Wunsch, Smith-Waterman and longest common subsequence algorithms. Also, database is implemented for using the algorithm in multi-sequence alignments for searching the optimal sequence that matches the given sequence.

  8. MEANS FOR DETERMINING CENTRIFUGE ALIGNMENT

    Science.gov (United States)

    Smith, W.Q.

    1958-08-26

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

  9. SPA: a probabilistic algorithm for spliced alignment.

    Directory of Open Access Journals (Sweden)

    Erik van Nimwegen

    2006-04-01

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

  10. Cover song identification by sequence alignment algorithms

    Science.gov (United States)

    Wang, Chih-Li; Zhong, Qian; Wang, Szu-Ying; Roychowdhury, Vwani

    2011-10-01

    Content-based music analysis has drawn much attention due to the rapidly growing digital music market. This paper describes a method that can be used to effectively identify cover songs. A cover song is a song that preserves only the crucial melody of its reference song but different in some other acoustic properties. Hence, the beat/chroma-synchronous chromagram, which is insensitive to the variation of the timber or rhythm of songs but sensitive to the melody, is chosen. The key transposition is achieved by cyclically shifting the chromatic domain of the chromagram. By using the Hidden Markov Model (HMM) to obtain the time sequences of songs, the system is made even more robust. Similar structure or length between the cover songs and its reference are not necessary by the Smith-Waterman Alignment Algorithm.

  11. An adaptive phase alignment algorithm for cartesian feedback loops

    Science.gov (United States)

    Gimeno-Martin, A.; Pardo-Martin, J.; Ortega-Gonzalez, F.

    2010-01-01

    An adaptive algorithm to correct phase misalignments in Cartesian feedback linearization loops for power amplifiers has been presented. It yields an error smaller than 0.035 rad between forward and feedback loop signals once convergence is reached. Because this algorithm enables a feedback system to process forward and feedback samples belonging to almost the same algorithm iteration, it is suitable to improve the performance not only of power amplifiers but also any other digital feedback system for communications systems and circuits such as all digital phase locked loops. Synchronizing forward and feedback paths of Cartesian feedback loops takes a small period of time after the system starts up. The phase alignment algorithm needs to converge before the feedback Cartesian loop can start its ideal behavior. However, once the steady state is reached, both paths can be considered synchronized, and the Cartesian feedback loop will only depend on the loop parameters (open-loop gain, loop bandwidth, etc.). It means that the linearization process will also depend only on these parameters since the misalignment effect disappears. Therefore, this algorithm relieves the power amplifier linearizer circuit design of any task required for solving phase misalignment effects inherent to Cartesian feedback systems. Furthermore, when a feedback Cartesian loop has to be designed, the designer can consider that forward and feedback paths are synchronized, since the phase alignment algorithm will do this task. This will reduce the simulation complexity. Then, all efforts are applied to determining the suitable loop parameters that will make the linearization process more efficient.

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

    Science.gov (United States)

    Afridi, Muhammad Ishaq

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Pereira Luísa

    2009-07-01

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

  14. Genomic multiple sequence alignments: refinement using a genetic algorithm

    Directory of Open Access Journals (Sweden)

    Lefkowitz Elliot J

    2005-08-01

    Full Text Available Abstract Background Genomic sequence data cannot be fully appreciated in isolation. Comparative genomics – the practice of comparing genomic sequences from different species – plays an increasingly important role in understanding the genotypic differences between species that result in phenotypic differences as well as in revealing patterns of evolutionary relationships. One of the major challenges in comparative genomics is producing a high-quality alignment between two or more related genomic sequences. In recent years, a number of tools have been developed for aligning large genomic sequences. Most utilize heuristic strategies to identify a series of strong sequence similarities, which are then used as anchors to align the regions between the anchor points. The resulting alignment is globally correct, but in many cases is suboptimal locally. We describe a new program, GenAlignRefine, which improves the overall quality of global multiple alignments by using a genetic algorithm to improve local regions of alignment. Regions of low quality are identified, realigned using the program T-Coffee, and then refined using a genetic algorithm. Because a better COFFEE (Consistency based Objective Function For alignmEnt Evaluation score generally reflects greater alignment quality, the algorithm searches for an alignment that yields a better COFFEE score. To improve the intrinsic slowness of the genetic algorithm, GenAlignRefine was implemented as a parallel, cluster-based program. Results We tested the GenAlignRefine algorithm by running it on a Linux cluster to refine sequences from a simulation, as well as refine a multiple alignment of 15 Orthopoxvirus genomic sequences approximately 260,000 nucleotides in length that initially had been aligned by Multi-LAGAN. It took approximately 150 minutes for a 40-processor Linux cluster to optimize some 200 fuzzy (poorly aligned regions of the orthopoxvirus alignment. Overall sequence identity increased only

  15. General space-efficient sampling algorithm for suboptimal alignment

    Institute of Scientific and Technical Information of China (English)

    CHEN; Yi; BAI; Yan-qin

    2009-01-01

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

  16. Quality measures for HRR alignment based ISAR imaging algorithms

    CSIR Research Space (South Africa)

    Janse van Rensburg, V

    2013-05-01

    Full Text Available Some Inverse Synthetic Aperture Radar (ISAR) algorithms form the image in a two-step process of range alignment and phase conjugation. This paper discusses a comprehensive set of measures used to quantify the quality of range alignment, with the aim...

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

    Directory of Open Access Journals (Sweden)

    Tatusova Tatiana

    2008-05-01

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

  18. SkyAlign: a portable, work-efficient skyline algorithm for multicore and GPU architectures

    DEFF Research Database (Denmark)

    Bøgh, Kenneth Sejdenfaden; Chester, Sean; Assent, Ira

    2016-01-01

    The skyline operator determines points in a multidimensional dataset that offer some optimal trade-off. State-of-the-art CPU skyline algorithms exploit quad-tree partitioning with complex branching to minimise the number of point-to-point comparisons. Branch-phobic GPU skyline algorithms rely...... on compute throughput rather than partitioning, but fail to match the performance of sequential algorithms. In this paper, we introduce a new skyline algorithm, SkyAlign, that is designed for the GPU, and a GPU-friendly, grid-based tree structure upon which the algorithm relies. The search tree allows us...... to dramatically reduce the amount of work done by the GPU algorithm by avoiding most point-to-point comparisons at the cost of some compute throughput. This trade-off allows SkyAlign to achieve orders of magnitude faster performance than its predecessors. Moreover, a NUMA-oblivious port of SkyAlign outperforms...

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

    Science.gov (United States)

    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.

  20. Alignment of Custom Standards by Machine Learning Algorithms

    Directory of Open Access Journals (Sweden)

    Adela Sirbu

    2010-09-01

    Full Text Available Building an efficient model for automatic alignment of terminologies would bring a significant improvement to the information retrieval process. We have developed and compared two machine learning based algorithms whose aim is to align 2 custom standards built on a 3 level taxonomy, using kNN and SVM classifiers that work on a vector representation consisting of several similarity measures. The weights utilized by the kNN were optimized with an evolutionary algorithm, while the SVM classifier's hyper-parameters were optimized with a grid search algorithm. The database used for train was semi automatically obtained by using the Coma++ tool. The performance of our aligners is shown by the results obtained on the test set.

  1. Trigger Algorithms for Alignment and Calibration at the CMS Experiment

    CERN Document Server

    Fernandez Perez Tomei, Thiago Rafael

    2017-01-01

    The data needs of the Alignment and Calibration group at the CMS experiment are reasonably different from those of the physics studies groups. Data are taken at CMS through the online event selection system, which is implemented in two steps. The Level-1 Trigger is implemented on custom-made electronics and dedicated to analyse the detector information at a coarse-grained scale, while the High Level Trigger (HLT) is implemented as a series of software algorithms, running in a computing farm, that have access to the full detector information. In this paper we describe the set of trigger algorithms that is deployed to address the needs of the Alignment and Calibration group, how it fits in the general infrastructure of the HLT, and how it feeds the Prompt Calibration Loop (PCL), allowing for a fast turnaround for the alignment and calibration constants.

  2. LASAGNA: A novel algorithm for transcription factor binding site alignment

    Science.gov (United States)

    2013-01-01

    Background Scientists routinely scan DNA sequences for transcription factor (TF) binding sites (TFBSs). Most of the available tools rely on position-specific scoring matrices (PSSMs) constructed from aligned binding sites. Because of the resolutions of assays used to obtain TFBSs, databases such as TRANSFAC, ORegAnno and PAZAR store unaligned variable-length DNA segments containing binding sites of a TF. These DNA segments need to be aligned to build a PSSM. While the TRANSFAC database provides scoring matrices for TFs, nearly 78% of the TFs in the public release do not have matrices available. As work on TFBS alignment algorithms has been limited, it is highly desirable to have an alignment algorithm tailored to TFBSs. Results We designed a novel algorithm named LASAGNA, which is aware of the lengths of input TFBSs and utilizes position dependence. Results on 189 TFs of 5 species in the TRANSFAC database showed that our method significantly outperformed ClustalW2 and MEME. We further compared a PSSM method dependent on LASAGNA to an alignment-free TFBS search method. Results on 89 TFs whose binding sites can be located in genomes showed that our method is significantly more precise at fixed recall rates. Finally, we described LASAGNA-ChIP, a more sophisticated version for ChIP (Chromatin immunoprecipitation) experiments. Under the one-per-sequence model, it showed comparable performance with MEME in discovering motifs in ChIP-seq peak sequences. Conclusions We conclude that the LASAGNA algorithm is simple and effective in aligning variable-length binding sites. It has been integrated into a user-friendly webtool for TFBS search and visualization called LASAGNA-Search. The tool currently stores precomputed PSSM models for 189 TFs and 133 TFs built from TFBSs in the TRANSFAC Public database (release 7.0) and the ORegAnno database (08Nov10 dump), respectively. The webtool is available at http://biogrid.engr.uconn.edu/lasagna_search/. PMID:23522376

  3. SMETANA: Accurate and Scalable Algorithm for Probabilistic Alignment of Large-Scale Biological Networks: e67995

    National Research Council Canada - National Science Library

    Sayed Mohammad Ebrahim Sahraeian; Byung-Jun Yoon

    2013-01-01

    .... We demonstrate that the proposed algorithm, called SMETANA, outperforms many state-of-the-art network alignment techniques, in terms of computational efficiency, alignment accuracy, and scalability...

  4. SMETANA: accurate and scalable algorithm for probabilistic alignment of large-scale biological networks

    National Research Council Canada - National Science Library

    Sahraeian, Sayed Mohammad Ebrahim; Yoon, Byung-Jun

    2013-01-01

    .... We demonstrate that the proposed algorithm, called SMETANA, outperforms many state-of-the-art network alignment techniques, in terms of computational efficiency, alignment accuracy, and scalability...

  5. Aligning multiple protein sequences by parallel hybrid genetic algorithm.

    Science.gov (United States)

    Nguyen, Hung Dinh; Yoshihara, Ikuo; Yamamori, Kunihito; Yasunaga, Moritoshi

    2002-01-01

    This paper presents a parallel hybrid genetic algorithm (GA) for solving the sum-of-pairs multiple protein sequence alignment. A new chromosome representation and its corresponding genetic operators are proposed. A multi-population GENITOR-type GA is combined with local search heuristics. It is then extended to run in parallel on a multiprocessor system for speeding up. Experimental results of benchmarks from the BAliBASE show that the proposed method is superior to MSA, OMA, and SAGA methods with regard to quality of solution and running time. It can be used for finding multiple sequence alignment as well as testing cost functions.

  6. A Genetic Algorithm on Multiple Sequences Alignment Problems in Biology

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The study and comparison of sequences of characters from a finite alphabet is relevant to various areas of science, notably molecular biology. The measurement of sequence similarity involves the consideration of the possible sequence alignments in order to find an optimal one for which the "distance" between sequences is minimum. In biology informatics area, it is a more important and difficult problem due to the long length (100 at least) of sequence, this cause the compute complexity and large memory require. By associating a path in a lattice to each alignment, a geometric insight can be brought into the problem of finding an optimal alignment, this give an obvious encoding of each path. This problem can be solved by applying genetic algorithm, which is more efficient than dynamic programming and hidden Markov model using commomly now.

  7. Interference Alignment and Fairness Algorithms for MIMO Cognitive Radio Systems

    Directory of Open Access Journals (Sweden)

    Feng Zhao

    2015-01-01

    Full Text Available Interference alignment (IA is an effective technique to eliminate the interference among wireless nodes. In a multiinput multi-output (MIMO cognitive radio system, multiple secondary users can coexist with the primary user without generating any interference by using the IA technology. However, few works have considered the fairness of secondary users. In this paper, not only is the interference eliminated by IA, but also the fairness of secondary users is considered by two kinds of algorithms. Without losing generality, one primary user and K secondary users are considered in the network. Assuming perfect channel knowledge at the primary user, the interference from secondary users to the primary user is aligned into the unused spatial dimension which is obtained by water-filling among primary user. Also, the interference between secondary users can be eliminated by a modified maximum signal-to-interference-plus-noise algorithm using channel reciprocity. In addition, two kinds of fairness algorithms, max-min fairness and proportional fairness, among secondary users are proposed. Simulation results show the effectiveness of the proposed algorithms in terms of suppressed interference and fairness of secondary nodes. What is more, the performances of the two fairness algorithms are compared.

  8. MICAN: a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, C(α) only models, Alternative alignments, and Non-sequential alignments.

    Science.gov (United States)

    Minami, Shintaro; Sawada, Kengo; Chikenji, George

    2013-01-18

    Protein pairs that have the same secondary structure packing arrangement but have different topologies have attracted much attention in terms of both evolution and physical chemistry of protein structures. Further investigation of such protein relationships would give us a hint as to how proteins can change their fold in the course of evolution, as well as a insight into physico-chemical properties of secondary structure packing. For this purpose, highly accurate sequence order independent structure comparison methods are needed. We have developed a novel protein structure alignment algorithm, MICAN (a structure alignment algorithm that can handle Multiple-chain complexes, Inverse direction of secondary structures, Cα only models, Alternative alignments, and Non-sequential alignments). The algorithm was designed so as to identify the best structural alignment between protein pairs by disregarding the connectivity between secondary structure elements (SSE). One of the key feature of the algorithm is utilizing the multiple vector representation for each SSE, which enables us to correctly treat bent or twisted nature of long SSE. We compared MICAN with other 9 publicly available structure alignment programs, using both reference-dependent and reference-independent evaluation methods on a variety of benchmark test sets which include both sequential and non-sequential alignments. We show that MICAN outperforms the other existing methods for reproducing reference alignments of non-sequential test sets. Further, although MICAN does not specialize in sequential structure alignment, it showed the top level performance on the sequential test sets. We also show that MICAN program is the fastest non-sequential structure alignment program among all the programs we examined here. MICAN is the fastest and the most accurate program among non-sequential alignment programs we examined here. These results suggest that MICAN is a highly effective tool for automatically detecting non

  9. MICAN : a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, Cα only models, Alternative alignments, and Non-sequential alignments

    Science.gov (United States)

    2013-01-01

    Background Protein pairs that have the same secondary structure packing arrangement but have different topologies have attracted much attention in terms of both evolution and physical chemistry of protein structures. Further investigation of such protein relationships would give us a hint as to how proteins can change their fold in the course of evolution, as well as a insight into physico-chemical properties of secondary structure packing. For this purpose, highly accurate sequence order independent structure comparison methods are needed. Results We have developed a novel protein structure alignment algorithm, MICAN (a structure alignment algorithm that can handle Multiple-chain complexes, Inverse direction of secondary structures, Cα only models, Alternative alignments, and Non-sequential alignments). The algorithm was designed so as to identify the best structural alignment between protein pairs by disregarding the connectivity between secondary structure elements (SSE). One of the key feature of the algorithm is utilizing the multiple vector representation for each SSE, which enables us to correctly treat bent or twisted nature of long SSE. We compared MICAN with other 9 publicly available structure alignment programs, using both reference-dependent and reference-independent evaluation methods on a variety of benchmark test sets which include both sequential and non-sequential alignments. We show that MICAN outperforms the other existing methods for reproducing reference alignments of non-sequential test sets. Further, although MICAN does not specialize in sequential structure alignment, it showed the top level performance on the sequential test sets. We also show that MICAN program is the fastest non-sequential structure alignment program among all the programs we examined here. Conclusions MICAN is the fastest and the most accurate program among non-sequential alignment programs we examined here. These results suggest that MICAN is a highly effective tool

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

    Science.gov (United States)

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

    2006-12-15

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

  11. Introduction of a distance cut-off into structural alignment by the double dynamic programming algorithm.

    Science.gov (United States)

    Toh, H

    1997-08-01

    Two approximations were introduced into the double dynamic programming algorithm, in order to reduce the computational time for structural alignment. One of them was the so-called distance cut-off, which approximately describes the structural environment of each residue by its local environment. In the approximation, a sphere with a given radius is placed at the center of the side chain of each residue. The local environment of a residue is constituted only by the residues with side chain centers that are present within the sphere, which is expressed by a set of center-to-center distances from the side chain of the residue to those of all the other constituent residues. The residues outside the sphere are neglected from the local environment. Another approximation is associated with the distance cut-off, which is referred to here as the delta N cut-off. If two local environments are similar to each other, the numbers of residues constituting the environments are expected to be similar. The delta N cut-off was introduced based on the idea. If the difference between the numbers of the constituent residues of two local environments is greater than a given threshold value, delta N, the evaluation of the similarity between the local environments is skipped. The introduction of the two approximations dramatically reduced the computational time for structural alignment by the double dynamic programming algorithm. However, the approximations also decreased the accuracy of the alignment. To improve the accuracy with the approximations, a program with a two-step alignment algorithm was constructed. At first, an alignment was roughly constructed with the approximations. Then, the epsilon-suboptimal region for the alignment was determined. Finally, the double dynamic programming algorithm with full structural environments was applied to the residue pairs within the epsilon-suboptimal region to produce an improved alignment.

  12. Evaluation of Laser Based Alignment Algorithms Under Additive Random and Diffraction Noise

    Energy Technology Data Exchange (ETDEWEB)

    McClay, W A; Awwal, A; Wilhelmsen, K; Ferguson, W; McGee, M; Miller, M

    2004-09-30

    The purpose of the automatic alignment algorithm at the National Ignition Facility (NIF) is to determine the position of a laser beam based on the position of beam features from video images. The position information obtained is used to command motors and attenuators to adjust the beam lines to the desired position, which facilitates the alignment of all 192 beams. One of the goals of the algorithm development effort is to ascertain the performance, reliability, and uncertainty of the position measurement. This paper describes a method of evaluating the performance of algorithms using Monte Carlo simulation. In particular we show the application of this technique to the LM1{_}LM3 algorithm, which determines the position of a series of two beam light sources. The performance of the algorithm was evaluated for an ensemble of over 900 simulated images with varying image intensities and noise counts, as well as varying diffraction noise amplitude and frequency. The performance of the algorithm on the image data set had a tolerance well beneath the 0.5-pixel system requirement.

  13. An Improved Search Algorithm for Optimal Multiple-Sequence Alignment

    CERN Document Server

    Schroedl, S

    2011-01-01

    Multiple sequence alignment (MSA) is a ubiquitous problem in computational biology. Although it is NP-hard to find an optimal solution for an arbitrary number of sequences, due to the importance of this problem researchers are trying to push the limits of exact algorithms further. Since MSA can be cast as a classical path finding problem, it is attracting a growing number of AI researchers interested in heuristic search algorithms as a challenge with actual practical relevance. In this paper, we first review two previous, complementary lines of research. Based on Hirschbergs algorithm, Dynamic Programming needs O(kN^(k-1)) space to store both the search frontier and the nodes needed to reconstruct the solution path, for k sequences of length N. Best first search, on the other hand, has the advantage of bounding the search space that has to be explored using a heuristic. However, it is necessary to maintain all explored nodes up to the final solution in order to prevent the search from re-expanding them at hig...

  14. Analysis of computational complexity for HT-based fingerprint alignment algorithms on java card environment

    CSIR Research Space (South Africa)

    Mlambo, CS

    2015-01-01

    Full Text Available In this paper, implementations of three Hough Transform based fingerprint alignment algorithms are analyzed with respect to time complexity on Java Card environment. Three algorithms are: Local Match Based Approach (LMBA), Discretized Rotation Based...

  15. A new automatic alignment technology for single mode fiber-waveguide based on improved genetic algorithm

    Institute of Scientific and Technical Information of China (English)

    ZHENG Yu; CHEN Zhuang-zhuang; LI Ya-juan; DUAN Jian

    2009-01-01

    A novel automatic alignment algorithm of single mode fiber-waveguide based on improved genetic algorithm is proposed. The genetic searching is based on the dynamic crossover operator and the adaptive mutation operator to solve the premature convergence of simple genetic algorithm The improved genetic algorithm combines with hill-climbing method and pattern searching algorithm, to solve low precision of simple genetic algorithm in later searching. The simulation results indicate that the improved genetic algorithm can rise the alignment precision and reach the coupling loss of 0.01 dB when platform moves near 207 space points averagely.

  16. A survey of sequence alignment algorithms for next-generation sequencing.

    Science.gov (United States)

    Li, Heng; Homer, Nils

    2010-09-01

    Rapidly evolving sequencing technologies produce data on an unparalleled scale. A central challenge to the analysis of this data is sequence alignment, whereby sequence reads must be compared to a reference. A wide variety of alignment algorithms and software have been subsequently developed over the past two years. In this article, we will systematically review the current development of these algorithms and introduce their practical applications on different types of experimental data. We come to the conclusion that short-read alignment is no longer the bottleneck of data analyses. We also consider future development of alignment algorithms with respect to emerging long sequence reads and the prospect of cloud computing.

  17. Robust precision alignment algorithm for micro tube laser forming

    NARCIS (Netherlands)

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

    2016-01-01

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

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

    NARCIS (Netherlands)

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

    2011-01-01

    Protein structural alignment is an important problem in computational biology. In this paper, we present first successes on provably optimal pairwise alignment of protein inter-residue distance matrices, using the popular DALI scoring function. We introduce the structural alignment problem formally,

  19. Robust precision alignment algorithm for micro tube laser forming

    NARCIS (Netherlands)

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

    2016-01-01

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

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

    DEFF Research Database (Denmark)

    Nielsen, Morten; Lund, Ole

    2009-01-01

    through presentation of extracellularly derived peptides to helper T cells. Identification of which peptides will bind a given MHC molecule is thus of great importance for the understanding of host-pathogen interactions, and large efforts have been placed in developing algorithms capable of predicting...... this binding event. RESULTS: Here, we present a novel artificial neural network-based method, NN-align that allows for simultaneous identification of the MHC class II binding core and binding affinity. NN-align is trained using a novel training algorithm that allows for correction of bias in the training data...... class II alleles, and is demonstrated to outperform other state-of-the-art MHC class II prediction methods. CONCLUSION: The NN-align method is competitive with the state-of-the-art MHC class II peptide binding prediction algorithms. The method is publicly available at http...

  1. A comprehensive evaluation of alignment algorithms in the context of RNA-seq.

    Science.gov (United States)

    Lindner, Robert; Friedel, Caroline C

    2012-01-01

    Transcriptome sequencing (RNA-Seq) overcomes limitations of previously used RNA quantification methods and provides one experimental framework for both high-throughput characterization and quantification of transcripts at the nucleotide level. The first step and a major challenge in the analysis of such experiments is the mapping of sequencing reads to a transcriptomic origin including the identification of splicing events. In recent years, a large number of such mapping algorithms have been developed, all of which have in common that they require algorithms for aligning a vast number of reads to genomic or transcriptomic sequences. Although the FM-index based aligner Bowtie has become a de facto standard within mapping pipelines, a much larger number of possible alignment algorithms have been developed also including other variants of FM-index based aligners. Accordingly, developers and users of RNA-seq mapping pipelines have the choice among a large number of available alignment algorithms. To provide guidance in the choice of alignment algorithms for these purposes, we evaluated the performance of 14 widely used alignment programs from three different algorithmic classes: algorithms using either hashing of the reference transcriptome, hashing of reads, or a compressed FM-index representation of the genome. Here, special emphasis was placed on both precision and recall and the performance for different read lengths and numbers of mismatches and indels in a read. Our results clearly showed the significant reduction in memory footprint and runtime provided by FM-index based aligners at a precision and recall comparable to the best hash table based aligners. Furthermore, the recently developed Bowtie 2 alignment algorithm shows a remarkable tolerance to both sequencing errors and indels, thus, essentially making hash-based aligners obsolete.

  2. A comprehensive evaluation of alignment algorithms in the context of RNA-seq.

    Directory of Open Access Journals (Sweden)

    Robert Lindner

    Full Text Available Transcriptome sequencing (RNA-Seq overcomes limitations of previously used RNA quantification methods and provides one experimental framework for both high-throughput characterization and quantification of transcripts at the nucleotide level. The first step and a major challenge in the analysis of such experiments is the mapping of sequencing reads to a transcriptomic origin including the identification of splicing events. In recent years, a large number of such mapping algorithms have been developed, all of which have in common that they require algorithms for aligning a vast number of reads to genomic or transcriptomic sequences. Although the FM-index based aligner Bowtie has become a de facto standard within mapping pipelines, a much larger number of possible alignment algorithms have been developed also including other variants of FM-index based aligners. Accordingly, developers and users of RNA-seq mapping pipelines have the choice among a large number of available alignment algorithms. To provide guidance in the choice of alignment algorithms for these purposes, we evaluated the performance of 14 widely used alignment programs from three different algorithmic classes: algorithms using either hashing of the reference transcriptome, hashing of reads, or a compressed FM-index representation of the genome. Here, special emphasis was placed on both precision and recall and the performance for different read lengths and numbers of mismatches and indels in a read. Our results clearly showed the significant reduction in memory footprint and runtime provided by FM-index based aligners at a precision and recall comparable to the best hash table based aligners. Furthermore, the recently developed Bowtie 2 alignment algorithm shows a remarkable tolerance to both sequencing errors and indels, thus, essentially making hash-based aligners obsolete.

  3. Research on SINS Alignment Algorithm Based on FIR Filters

    Institute of Scientific and Technical Information of China (English)

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

    2007-01-01

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

  4. A DNA sequence alignment algorithm using quality information and a fuzzy inference method

    Institute of Scientific and Technical Information of China (English)

    Kwangbaek Kim; Minhwan Kim; Youngwoon Woo

    2008-01-01

    DNA sequence alignment algorithms in computational molecular biology have been improved by diverse methods.In this paper.We propose a DNA sequence alignment that Uses quality information and a fuzzy inference method developed based on the characteristics of DNA fragments and a fuzzy logic system in order to improve conventional DNA sequence alignment methods that uses DNA sequence quality information.In conventional algorithms.DNA sequence alignment scores are calculated by the global sequence alignment algorithm proposed by Needleman-Wunsch,which is established by using quality information of each DNA fragment.However,there may be errors in the process of calculating DNA sequence alignment scores when the quality of DNA fragment tips is low.because only the overall DNA sequence quality information are used.In our proposed method.an exact DNA sequence alignment can be achieved in spite of the low quality of DNA fragment tips by improvement of conventional algorithms using quality information.Mapping score parameters used to calculate DNA sequence alignment scores are dynamically adjusted by the fuzzy logic system utilizing lengths of DNA fragments and frequencies of low quality DNA bases in the fragments.From the experiments by applying real genome data of National Center for Bioteclmology Information,we could see that the proposed method is more efficient than conventional algorithms.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1997-12-01

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

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Lund Ole

    2009-09-01

    Full Text Available Abstract Background The major histocompatibility complex (MHC molecule plays a central role in controlling the adaptive immune response to infections. MHC class I molecules present peptides derived from intracellular proteins to cytotoxic T cells, whereas MHC class II molecules stimulate cellular and humoral immunity through presentation of extracellularly derived peptides to helper T cells. Identification of which peptides will bind a given MHC molecule is thus of great importance for the understanding of host-pathogen interactions, and large efforts have been placed in developing algorithms capable of predicting this binding event. Results Here, we present a novel artificial neural network-based method, NN-align that allows for simultaneous identification of the MHC class II binding core and binding affinity. NN-align is trained using a novel training algorithm that allows for correction of bias in the training data due to redundant binding core representation. Incorporation of information about the residues flanking the peptide-binding core is shown to significantly improve the prediction accuracy. The method is evaluated on a large-scale benchmark consisting of six independent data sets covering 14 human MHC class II alleles, and is demonstrated to outperform other state-of-the-art MHC class II prediction methods. Conclusion The NN-align method is competitive with the state-of-the-art MHC class II peptide binding prediction algorithms. The method is publicly available at http://www.cbs.dtu.dk/services/NetMHCII-2.0.

  8. Protein alignment algorithms with an efficient backtracking routine on multiple GPUs

    Directory of Open Access Journals (Sweden)

    Kierzynka Michal

    2011-05-01

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

  9. An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast

    Directory of Open Access Journals (Sweden)

    Taneda Akito

    2008-12-01

    Full Text Available Abstract Background Aligning RNA sequences with low sequence identity has been a challenging problem since such a computation essentially needs an algorithm with high complexities for taking structural conservation into account. Although many sophisticated algorithms for the purpose have been proposed to date, further improvement in efficiency is necessary to accelerate its large-scale applications including non-coding RNA (ncRNA discovery. Results We developed a new genetic algorithm, Cofolga2, for simultaneously computing pairwise RNA sequence alignment and consensus folding, and benchmarked it using BRAliBase 2.1. The benchmark results showed that our new algorithm is accurate and efficient in both time and memory usage. Then, combining with the originally trained SVM, we applied the new algorithm to novel ncRNA discovery where we compared S. cerevisiae genome with six related genomes in a pairwise manner. By focusing our search to the relatively short regions (50 bp to 2,000 bp sandwiched by conserved sequences, we successfully predict 714 intergenic and 1,311 sense or antisense ncRNA candidates, which were found in the pairwise alignments with stable consensus secondary structure and low sequence identity (≤ 50%. By comparing with the previous predictions, we found that > 92% of the candidates is novel candidates. The estimated rate of false positives in the predicted candidates is 51%. Twenty-five percent of the intergenic candidates has supports for expression in cell, i.e. their genomic positions overlap those of the experimentally determined transcripts in literature. By manual inspection of the results, moreover, we obtained four multiple alignments with low sequence identity which reveal consensus structures shared by three species/sequences. Conclusion The present method gives an efficient tool complementary to sequence-alignment-based ncRNA finders.

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

    Science.gov (United States)

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

    2011-01-01

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

  11. Registration algorithm for sensor alignment based on stochastic fuzzy neural network

    Institute of Scientific and Technical Information of China (English)

    Li Jiao; Jing Zhongliang; He Jiaona; Wang An

    2005-01-01

    Multiple sensor registration is an important link in multi-sensors data fusion. The existed algorithm is all based on the assumption that system errors come from a fixed deviation set. But there are many other factors, which can result system errors. So traditional registration algorithms have limitation. This paper presents a registration algorithm for sensor alignment based on stochastic fuzzy neural network (SNFF), and utilized fuzzy clustering algorithm obtaining the number of fuzzy rules. Finally, the simulative result illuminate that this way could gain a satisfing result.

  12. A global optimization algorithm for protein surface alignment

    Directory of Open Access Journals (Sweden)

    Guerra Concettina

    2010-09-01

    Full Text Available Abstract Background A relevant problem in drug design is the comparison and recognition of protein binding sites. Binding sites recognition is generally based on geometry often combined with physico-chemical properties of the site since the conformation, size and chemical composition of the protein surface are all relevant for the interaction with a specific ligand. Several matching strategies have been designed for the recognition of protein-ligand binding sites and of protein-protein interfaces but the problem cannot be considered solved. Results In this paper we propose a new method for local structural alignment of protein surfaces based on continuous global optimization techniques. Given the three-dimensional structures of two proteins, the method finds the isometric transformation (rotation plus translation that best superimposes active regions of two structures. We draw our inspiration from the well-known Iterative Closest Point (ICP method for three-dimensional (3D shapes registration. Our main contribution is in the adoption of a controlled random search as a more efficient global optimization approach along with a new dissimilarity measure. The reported computational experience and comparison show viability of the proposed approach. Conclusions Our method performs well to detect similarity in binding sites when this in fact exists. In the future we plan to do a more comprehensive evaluation of the method by considering large datasets of non-redundant proteins and applying a clustering technique to the results of all comparisons to classify binding sites.

  13. Review of alignment and SNP calling algorithms for next-generation sequencing data.

    Science.gov (United States)

    Mielczarek, M; Szyda, J

    2016-02-01

    Application of the massive parallel sequencing technology has become one of the most important issues in life sciences. Therefore, it was crucial to develop bioinformatics tools for next-generation sequencing (NGS) data processing. Currently, two of the most significant tasks include alignment to a reference genome and detection of single nucleotide polymorphisms (SNPs). In many types of genomic analyses, great numbers of reads need to be mapped to the reference genome; therefore, selection of the aligner is an essential step in NGS pipelines. Two main algorithms-suffix tries and hash tables-have been introduced for this purpose. Suffix array-based aligners are memory-efficient and work faster than hash-based aligners, but they are less accurate. In contrast, hash table algorithms tend to be slower, but more sensitive. SNP and genotype callers may also be divided into two main different approaches: heuristic and probabilistic methods. A variety of software has been subsequently developed over the past several years. In this paper, we briefly review the current development of NGS data processing algorithms and present the available software.

  14. DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment

    Directory of Open Access Journals (Sweden)

    Kaufmann Michael

    2005-03-01

    Full Text Available Abstract Background We present a complete re-implementation of the segment-based approach to multiple protein alignment that contains a number of improvements compared to the previous version 2.2 of DIALIGN. This previous version is superior to Needleman-Wunsch-based multi-alignment programs on locally related sequence sets. However, it is often outperformed by these methods on data sets with global but weak similarity at the primary-sequence level. Results In the present paper, we discuss strengths and weaknesses of DIALIGN in view of the underlying objective function. Based on these results, we propose several heuristics to improve the segment-based alignment approach. For pairwise alignment, we implemented a fragment-chaining algorithm that favours chains of low-scoring local alignments over isolated high-scoring fragments. For multiple alignment, we use an improved greedy procedure that is less sensitive to spurious local sequence similarities. To evaluate our method on globally related protein families, we used the well-known database BAliBASE. For benchmarking tests on locally related sequences, we created a new reference database called IRMBASE which consists of simulated conserved motifs implanted into non-related random sequences. Conclusion On BAliBASE, our new program performs significantly better than the previous version of DIALIGN and is comparable to the standard global aligner CLUSTAL W, though it is outperformed by some newly developed programs that focus on global alignment. On the locally related test sets in IRMBASE, our method outperforms all other programs that we evaluated.

  15. Multiple sequence alignment based on combining genetic algorithm with chaotic sequences.

    Science.gov (United States)

    Gao, C; Wang, B; Zhou, C J; Zhang, Q

    2016-06-24

    In bioinformatics, sequence alignment is one of the most common problems. Multiple sequence alignment is an NP (nondeterministic polynomial time) problem, which requires further study and exploration. The chaos optimization algorithm is a type of chaos theory, and a procedure for combining the genetic algorithm (GA), which uses ergodicity, and inherent randomness of chaotic iteration. It is an efficient method to solve the basic premature phenomenon of the GA. Applying the Logistic map to the GA and using chaotic sequences to carry out the chaotic perturbation can improve the convergence of the basic GA. In addition, the random tournament selection and optimal preservation strategy are used in the GA. Experimental evidence indicates good results for this process.

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

    Science.gov (United States)

    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.

  17. A Point Cloud Alignment Algorithm Based on Stereo Vision Using Random Pattern Projection

    Directory of Open Access Journals (Sweden)

    Chen-Sheng Chen

    2016-03-01

    Full Text Available This paper proposes a point cloud alignment algorithm based on stereo vision using Random Pattern Projection (RPP. In the application of stereo vision, it is rather difficult to find correspondences between stereo images of texture-less objects. To overcome this issue, RPP is used to enhance the object’s features, thus increasing the accuracy of the identified correspondences of the stereo images. In the 3D alignment algorithm, the down sample technique is used to filter out the outliers of the point cloud data to improve system efficiency. Furthermore, the extracted features of the down sample point cloud data were applied in the matching process. Finally, the object’s pose was estimated by the alignment algorithm based on object features. In experiments, the maximum error and standard deviation of rotation are respectively about 0.031°and 0.199°, while the maximum error and standard deviation of translation are respectively about 0.565 mm and 0.902 mm . The execution time for pose estimation is about 230ms.

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

    Science.gov (United States)

    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.

  19. Evaluation of GMI and PMI diffeomorphic-based demons algorithms for aligning PET and CT Images.

    Science.gov (United States)

    Yang, Juan; Wang, Hongjun; Zhang, You; Yin, Yong

    2015-07-08

    Fusion of anatomic information in computed tomography (CT) and functional information in 18F-FDG positron emission tomography (PET) is crucial for accurate differentiation of tumor from benign masses, designing radiotherapy treatment plan and staging of cancer. Although current PET and CT images can be acquired from combined 18F-FDG PET/CT scanner, the two acquisitions are scanned separately and take a long time, which may induce potential positional errors in global and local caused by respiratory motion or organ peristalsis. So registration (alignment) of whole-body PET and CT images is a prerequisite for their meaningful fusion. The purpose of this study was to assess the performance of two multimodal registration algorithms for aligning PET and CT images. The proposed gradient of mutual information (GMI)-based demons algorithm, which incorporated the GMI between two images as an external force to facilitate the alignment, was compared with the point-wise mutual information (PMI) diffeomorphic-based demons algorithm whose external force was modified by replacing the image intensity difference in diffeomorphic demons algorithm with the PMI to make it appropriate for multimodal image registration. Eight patients with esophageal cancer(s) were enrolled in this IRB-approved study. Whole-body PET and CT images were acquired from a combined 18F-FDG PET/CT scanner for each patient. The modified Hausdorff distance (d(MH)) was used to evaluate the registration accuracy of the two algorithms. Of all patients, the mean values and standard deviations (SDs) of d(MH) were 6.65 (± 1.90) voxels and 6.01 (± 1.90) after the GMI-based demons and the PMI diffeomorphic-based demons registration algorithms respectively. Preliminary results on oncological patients showed that the respiratory motion and organ peristalsis in PET/CT esophageal images could not be neglected, although a combined 18F-FDG PET/CT scanner was used for image acquisition. The PMI diffeomorphic-based demons

  20. SkyAlign: a portable, work-efficient skyline algorithm for multicore and GPU architectures

    DEFF Research Database (Denmark)

    Bøgh, Kenneth Sejdenfaden; Chester, Sean; Assent, Ira

    2016-01-01

    The skyline operator determines points in a multidimensional dataset that offer some optimal trade-off. State-of-the-art CPU skyline algorithms exploit quad-tree partitioning with complex branching to minimise the number of point-to-point comparisons. Branch-phobic GPU skyline algorithms rely on ...

  1. Development and Beam Tests of an Automatic Algorithm for Alignment of LHC Collimators with Embedded BPMs

    CERN Document Server

    Valentino, G; Gasior, M; Mirarchi, D; Nosych, A A; Redaelli, S; Salvachua, B; Assmann, R W; Sammut, N

    2013-01-01

    Collimators with embedded Beam Position Monitor (BPM) buttons will be installed in the LHC during the upcoming long shutdown period. During the subsequent operation, the BPMs will allow the collimator jaws to be kept centered around the beam trajectory. In this manner, the best possible beam cleaning efficiency and machine protection can be provided at unprecedented higher beam energies and intensities. A collimator alignment algorithm is proposed to center the jaws automatically around the beam. The algorithm is based on successive approximation, as the BPM measurements are affected by non-linearities, which vary with the distance between opposite buttons, as well as the difference between the beam and the jaw centers. The successful test results, as well as some considerations for eventual operation in the LHC are also presented.

  2. Successive approximation algorithm for beam-position-monitor-based LHC collimator alignment

    Science.gov (United States)

    Valentino, Gianluca; Nosych, Andriy A.; Bruce, Roderik; Gasior, Marek; Mirarchi, Daniele; Redaelli, Stefano; Salvachua, Belen; Wollmann, Daniel

    2014-02-01

    Collimators with embedded beam position monitor (BPM) button electrodes will be installed in the Large Hadron Collider (LHC) during the current long shutdown period. For the subsequent operation, BPMs will allow the collimator jaws to be kept centered around the beam orbit. In this manner, a better beam cleaning efficiency and machine protection can be provided at unprecedented higher beam energies and intensities. A collimator alignment algorithm is proposed to center the jaws automatically around the beam. The algorithm is based on successive approximation and takes into account a correction of the nonlinear BPM sensitivity to beam displacement and an asymmetry of the electronic channels processing the BPM electrode signals. A software implementation was tested with a prototype collimator in the Super Proton Synchrotron. This paper presents results of the tests along with some considerations for eventual operation in the LHC.

  3. Improvement of Performance of MegaBlast Algorithm for DNA Sequence Alignment

    Institute of Scientific and Technical Information of China (English)

    Guang-Ming Tan; Lin Xu; Dong-Bo Bu; Sheng-Zhong Feng; Ning-Hui Sun

    2006-01-01

    MegaBlast is one of the most important programs in NCBI BLAST (Basic Local Alignment Search Tool)toolkits. However, MegaBlast is computation and I/O intensive. It consumes a great deal of memory which is proportional to the size of the query sequences set and subject (database) sequences set of product. This paper proposes a new strategy for optimizing MegaBlast. The new strategy exchanges the query and subject sequences sets, and builds a hash table based on new subject sequences. It overlaps I/O with computation, shortens the overall time and reduces the cost of memory,since the memory here is only proportional to the size of subject sequences set. The optimized algorithm is suitable to be parallelized in cluster systems. The parallel algorithm uses query segmentation method. As our experiments shown, the parallel program which is implemented with MPI has fine scalability.

  4. Optical derotator alignment using image-processing algorithm for tracking laser vibrometer measurements of rotating objects

    Science.gov (United States)

    Khalil, Hossam; Kim, Dongkyu; Jo, Youngjoon; Park, Kyihwan

    2017-06-01

    An optical component called a Dove prism is used to rotate the laser beam of a laser-scanning vibrometer (LSV). This is called a derotator and is used for measuring the vibration of rotating objects. The main advantage of a derotator is that it works independently from an LSV. However, this device requires very specific alignment, in which the axis of the Dove prism must coincide with the rotational axis of the object. If the derotator is misaligned with the rotating object, the results of the vibration measurement are imprecise, owing to the alteration of the laser beam on the surface of the rotating object. In this study, a method is proposed for aligning a derotator with a rotating object through an image-processing algorithm that obtains the trajectory of a landmark attached to the object. After the trajectory of the landmark is mathematically modeled, the amount of derotator misalignment with respect to the object is calculated. The accuracy of the proposed method for aligning the derotator with the rotating object is experimentally tested.

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

    Science.gov (United States)

    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.

  6. QuickProbs—A Fast Multiple Sequence Alignment Algorithm Designed for Graphics Processors

    Science.gov (United States)

    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. PMID:24586435

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

    Directory of Open Access Journals (Sweden)

    Adam Gudyś

    Full Text Available 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.

  8. A New Continuous Rotation IMU Alignment Algorithm Based on Stochastic Modeling for Cost Effective North-Finding Applications

    Directory of Open Access Journals (Sweden)

    Yun Li

    2016-12-01

    Full Text Available Based on stochastic modeling of Coriolis vibration gyros by the Allan variance technique, this paper discusses Angle Random Walk (ARW, Rate Random Walk (RRW and Markov process gyroscope noises which have significant impacts on the North-finding accuracy. A new continuous rotation alignment algorithm for a Coriolis vibration gyroscope Inertial Measurement Unit (IMU is proposed in this paper, in which the extended observation equations are used for the Kalman filter to enhance the estimation of gyro drift errors, thus improving the north-finding accuracy. Theoretical and numerical comparisons between the proposed algorithm and the traditional ones are presented. The experimental results show that the new continuous rotation alignment algorithm using the extended observation equations in the Kalman filter is more efficient than the traditional two-position alignment method. Using Coriolis vibration gyros with bias instability of 0.1°/h, a north-finding accuracy of 0.1° (1σ is achieved by the new continuous rotation alignment algorithm, compared with 0.6° (1σ north-finding accuracy for the two-position alignment and 1° (1σ for the fixed-position alignment.

  9. A New Continuous Rotation IMU Alignment Algorithm Based on Stochastic Modeling for Cost Effective North-Finding Applications

    Science.gov (United States)

    Li, Yun; Wu, Wenqi; Jiang, Qingan; Wang, Jinling

    2016-01-01

    Based on stochastic modeling of Coriolis vibration gyros by the Allan variance technique, this paper discusses Angle Random Walk (ARW), Rate Random Walk (RRW) and Markov process gyroscope noises which have significant impacts on the North-finding accuracy. A new continuous rotation alignment algorithm for a Coriolis vibration gyroscope Inertial Measurement Unit (IMU) is proposed in this paper, in which the extended observation equations are used for the Kalman filter to enhance the estimation of gyro drift errors, thus improving the north-finding accuracy. Theoretical and numerical comparisons between the proposed algorithm and the traditional ones are presented. The experimental results show that the new continuous rotation alignment algorithm using the extended observation equations in the Kalman filter is more efficient than the traditional two-position alignment method. Using Coriolis vibration gyros with bias instability of 0.1°/h, a north-finding accuracy of 0.1° (1σ) is achieved by the new continuous rotation alignment algorithm, compared with 0.6° (1σ) north-finding accuracy for the two-position alignment and 1° (1σ) for the fixed-position alignment. PMID:27983585

  10. Mutual Understanding Determinants for Effective Communication in Business and IT Strategic Alignment Planning

    Directory of Open Access Journals (Sweden)

    Nurul `Izzati Mohmad Adnan

    2016-12-01

    Full Text Available Business and IT strategic alignment is continuously explored from different facets motivated by the demands for organisation to be well aligned in its business and IT strategies for business continuity. The management aspect rather than technological issues often causes misalignment in business and IT strategies more significantly. One of the issues is the communication ineffectiveness between business and IT people involved in planning the business and IT strategic alignment. Difficulty to achieve mutual understanding between these two teams is a critical problem in communication and hinders the successful alignment. Therefore, a set of determinants for mutual understanding is proposed. Extensive analysis on literature has been carried out to identify and define the determining factors. The review can serve as a reference for business and IT executives to improve in their communication effectiveness towards achieving well aligned business and IT strategic alignment.

  11. TMO: time and memory optimized algorithm applicable for more accurate alignment of trinucleotide repeat disorders associated genes

    Directory of Open Access Journals (Sweden)

    Done Stojanov

    2016-03-01

    Full Text Available In this study, time and memory optimized (TMO algorithm is presented. Compared with Smith–Waterman's algorithm, TMO is applicable for a more accurate detection of continuous insertion/deletions (indels in genes’ fragments, associated with disorders caused by over-repetition of a certain codon. The improvement comes from the tendency to pinpoint indels in the least preserved nucleotide pairs. All nucleotide pairs that occur less frequently are classified as less preserved and they are considered as mutated codons whose mid-nucleotides were deleted. Other benefit of the proposed algorithm is its general tendency to maximize the number of matching nucleotides included per alignment, regardless of any specific alignment metrics. Since the structure of the solution, when applying Smith–Waterman, depends on the adjustment of the alignment parameters and, therefore, an incomplete (shortened solution may be derived, our algorithm does not reject any of the consistent matching nucleotides that can be included in the final solution. In terms of computational aspects, our algorithm runs faster than Smith–Waterman for very similar DNA and requires less memory than the most memory efficient dynamic programming algorithms. The speed up comes from the reduced number of nucleotide comparisons that have to be performed, without having to imperil the completeness of the solution. Due to the fact that four integers (16 Bytes are required for tracking matching fragment, regardless its length, our algorithm requires less memory than Huang's algorithm.

  12. Genetic Algorithm Phase Retrieval for the Systematic Image-Based Optical Alignment Testbed

    Science.gov (United States)

    Taylor, Jaime; Rakoczy, John; Steincamp, James

    2003-01-01

    Phase retrieval requires calculation of the real-valued phase of the pupil fimction from the image intensity distribution and characteristics of an optical system. Genetic 'algorithms were used to solve two one-dimensional phase retrieval problem. A GA successfully estimated the coefficients of a polynomial expansion of the phase when the number of coefficients was correctly specified. A GA also successfully estimated the multiple p h e s of a segmented optical system analogous to the seven-mirror Systematic Image-Based Optical Alignment (SIBOA) testbed located at NASA s Marshall Space Flight Center. The SIBOA testbed was developed to investigate phase retrieval techniques. Tiphilt and piston motions of the mirrors accomplish phase corrections. A constant phase over each mirror can be achieved by an independent tip/tilt correction: the phase Conection term can then be factored out of the Discrete Fourier Tranform (DFT), greatly reducing computations.

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

    Science.gov (United States)

    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.

  14. Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets

    Directory of Open Access Journals (Sweden)

    Hoffmann Nils

    2012-08-01

    Full Text Available Abstract Background Modern analytical methods in biology and chemistry use separation techniques coupled to sensitive detectors, such as gas chromatography-mass spectrometry (GC-MS and liquid chromatography-mass spectrometry (LC-MS. These hyphenated methods provide high-dimensional data. Comparing such data manually to find corresponding signals is a laborious task, as each experiment usually consists of thousands of individual scans, each containing hundreds or even thousands of distinct signals. In order to allow for successful identification of metabolites or proteins within such data, especially in the context of metabolomics and proteomics, an accurate alignment and matching of corresponding features between two or more experiments is required. Such a matching algorithm should capture fluctuations in the chromatographic system which lead to non-linear distortions on the time axis, as well as systematic changes in recorded intensities. Many different algorithms for the retention time alignment of GC-MS and LC-MS data have been proposed and published, but all of them focus either on aligning previously extracted peak features or on aligning and comparing the complete raw data containing all available features. Results In this paper we introduce two algorithms for retention time alignment of multiple GC-MS datasets: multiple alignment by bidirectional best hits peak assignment and cluster extension (BIPACE and center-star multiple alignment by pairwise partitioned dynamic time warping (CeMAPP-DTW. We show how the similarity-based peak group matching method BIPACE may be used for multiple alignment calculation individually and how it can be used as a preprocessing step for the pairwise alignments performed by CeMAPP-DTW. We evaluate the algorithms individually and in combination on a previously published small GC-MS dataset studying the Leishmania parasite and on a larger GC-MS dataset studying grains of wheat (Triticum aestivum. Conclusions We

  15. Spacecraft Alignment Determination and Control for Dual Spacecraft Precision Formation Flying

    Science.gov (United States)

    Calhoun, Philip C.; Novo-Gradac, Anne-Marie; Shah, Neerav

    2017-01-01

    Many proposed formation flying missions seek to advance the state of the art in spacecraft science imaging by utilizing precision dual spacecraft formation flying to enable a virtual space telescope. Using precision dual spacecraft alignment, very long focal lengths can be achieved by locating the optics on one spacecraft and the detector on the other. Proposed science missions include astrophysics concepts with spacecraft separations from 1000 km to 25,000 km, such as the Milli-Arc-Second Structure Imager (MASSIM) and the New Worlds Observer, and Heliophysics concepts for solar coronagraphs and X-ray imaging with smaller separations (50m 500m). All of these proposed missions require advances in guidance, navigation, and control (GNC) for precision formation flying. In particular, very precise astrometric alignment control and estimation is required for precise inertial pointing of the virtual space telescope to enable science imaging orders of magnitude better than can be achieved with conventional single spacecraft instruments. This work develops design architectures, algorithms, and performance analysis of proposed GNC systems for precision dual spacecraft astrometric alignment. These systems employ a variety of GNC sensors and actuators, including laser-based alignment and ranging systems, optical imaging sensors (e.g. guide star telescope), inertial measurement units (IMU), as well as micro-thruster and precision stabilized platforms. A comprehensive GNC performance analysis is given for Heliophysics dual spacecraft PFF imaging mission concept.

  16. 一种新的局部空间排列算法%A New Local Space Alignment Algorithm

    Institute of Scientific and Technical Information of China (English)

    刘胜蓝; 冯林; 金博; 吴振宇

    2013-01-01

    Recently,manifold learning has been widely exploited in pattern recognition and data mining.Local tangent space alignment (LTSA) is a classical non-linear manifold learning method,which is efficient for non-linear dimensionality reduction.However,it fails to learn locally high curvature dataset.To address this problem,this paper describes the data set of the locally curvature by the given parameter and presents a new algorithm called locally minimal deviation space alignment (LMDSA).Considering the low-robust deficiencies in local tangent space,LMDSA can find the locally high curvature while computing locally minimal deviation spaces.The algorithm also reduces the probability of locally high curvature space with parameter control and the joint information between neighborhood information.Then the algorithm applies space alignment technique to reduce dimensionality.Besides the advantages above,LMDSA has the ability to learn sparse dataset.Extensive experiments on both synthetic manifold and real-world images indicate the efficiency of our algorithm.In synthetic manifold,LMDSA is compared with LTSA in two local high curvature datasets and one dataset with a hole.The experimental results show our algorithm learns correct manifold structure in low-dimension space.In sparse real-world datasets,LMDSA outperforms other algorithms in this paper.%局部切空间排列算法(local tangent space alignment,LTSA)是一种经典的非线性流形学习方法,能够有效地对非线性分布数据进行降维,但它无法学习局部高曲率数据集.针对此问题,给出了描述数据集局部曲率的参数,并提出一种局部最小偏差空间排列(locally minimal deviation spacealignment,LMDSA)算法.该算法考虑到局部切空间低鲁棒性的缺陷,在计算局部最小偏差空间的同时,能够发现数据的局部高曲率现象,通过参数控制及邻域间的连接信息,减少计算局部高曲率空间的可能,进而利用空间排列技术进行降

  17. Determining OBS Instrument Orientations: A Comparison of Algorithms

    Science.gov (United States)

    Doran, A. K.; Laske, G.

    2015-12-01

    The alignment of the orientation of the horizontal seismometer components with the geographical coordinate system is critical for a wide variety of seismic analyses, but the traditional deployment method of ocean bottom seismometers (OBS) precludes knowledge of this parameter. Current techniques for determining the orientation predominantly rely on body and surface wave data recorded from teleseismic events with sufficiently large magnitudes. Both wave types experience lateral refraction between the source and receiver as a result of heterogeneity and anisotropy, and therefore the arrival angle of any one phase can significantly deviate from the great circle minor arc. We systematically compare the results and uncertainties obtained through current determination methods, as well as describe a new algorithm that uses body wave, surface wave, and differential pressure gauge data (where available) to invert for horizontal orientation. To start with, our method is based on the easily transportable computer code of Stachnik et al. (2012) that is publicly available through IRIS. A major addition is that we utilize updated global dispersion maps to account for lateral refraction, as was done by Laske (1995). We also make measurements in a wide range of frequencies, and analyze surface wave trains of repeat orbits. Our method has the advantage of requiring fewer total events to achieve high precision estimates, which is beneficial for OBS deployments that can be as short as weeks. Although the program is designed for the purpose of use with OBS instruments, it also works with standard land installations. We intend to provide the community with a program that is easy to use, requires minimal user input, and is optimized to work with data cataloged at the IRIS DMC.

  18. Determination of atomic cluster structure with cluster fusion algorithm

    DEFF Research Database (Denmark)

    Obolensky, Oleg I.; Solov'yov, Ilia; Solov'yov, Andrey V.

    2005-01-01

    We report an efficient scheme of global optimization, called cluster fusion algorithm, which has proved its reliability and high efficiency in determination of the structure of various atomic clusters.......We report an efficient scheme of global optimization, called cluster fusion algorithm, which has proved its reliability and high efficiency in determination of the structure of various atomic clusters....

  19. Simulation of beamline alignment operations

    Energy Technology Data Exchange (ETDEWEB)

    Annese, C; Miller, M G

    1999-02-02

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

  20. A comparative assessment of alternatives to the full-leg radiograph for determining knee joint alignment

    Directory of Open Access Journals (Sweden)

    Navali Amir M

    2012-10-01

    Full Text Available Abstract Background The purpose of this study was to assess the concurrent validity of alternative measures of frontal plane knee alignment, namely the radiographic anatomic axis and two clinical measures in patients complaining of knee malalignment as compared with the mechanical axis on full-length radiograph of lower limbs. Methods The knee-alignment angle was measured in 100 knees of 50 subjects with the chief complaint of frontal knee malalignment according to the following methods: lower-limb mechanical axis on radiograph, lower-limb anatomic axis on radiograph, distance between medial femoral condyles or medial malleoli using a calliper and lower-limb alignment using a goniometer. Data were analyzed using Pearson’s correlation coefficient and simple linear regression. Results The anatomic axis best correlated with the mechanical axis (r = 0.93, P Conclusions The anatomic axis on radiograph, the calliper method and to a lesser extent the goniometer measurement appear to be valid alternatives to the mechanical axis on full-leg radiograph for determining frontal plane knee alignment. These alternative measures have the potential to provide useful information regarding knee alignment and may increase the assessment of this parameter by clinicians and researchers.

  1. A Novel Image Alignment Algorithm Based on Rotation-Discriminating Ring-Shifted Projection for Automatic Optical Inspection

    Directory of Open Access Journals (Sweden)

    Chin-Sheng Chen

    2016-05-01

    Full Text Available This paper proposes a novel image alignment algorithm based on rotation-discriminating ring-shifted projection for automatic optical inspection. This new algorithm not only identifies the location of the template image within an inspection image but also provides precise rotation information during the template-matching process by using a novel rotation estimation scheme, the so-called ring-shifted technique. We use a two stage framework with an image pyramid searching technique for realizing the proposed image alignment algorithm; in the first stage, the similarity based on hybrid projection transformation with the image pyramid searching technique is employed for quick selection and location of the candidates in the inspection image. In the second stage, the rotation angle of the object is estimated by a novel ring-shifted technique. The estimation is performed only for the most likely candidate which is the one having the highest similarity in the first stage. The experimental results show that the proposed method provides accurate estimation for template matching with arbitrary rotations and is applicable in various environmental conditions.

  2. 一种流形仿射对齐算法%An algorithm for affine alignment of manifolds

    Institute of Scientific and Technical Information of China (English)

    徐雪; 周荷琴

    2009-01-01

    For the problem of finding and aligning the shared hidden structure of high-dimensional data sets,a semi-supervised algorithm for affine alignment of manifolds was presented.Un-matching points were used to improve the learning effect when the proportion of matching points was small.The extended spectral regression technique was applied,which made it possible for linear aligning algorithm to preserve the local geometry information of high-dimensional data.The experiments showed that the embedded manifolds could be successfully found and aligned when the proportion of matching points was small,and less cost was needed to project a new point.%研究了高维数据集中共享隐空间的寻找和对齐问题,提出了半监督的流形仿射对齐算法.未匹配点的局部分布信息被有效地利用起来,以改善在匹配点比例较低情况下的学习效果;扩展的谱回归技术的应用,使得线性对齐也能较好地保持高维数据的局部几何信息.实验表明该算法能够找出高维数据的相关性方向,并将其内部隐空间较好地对齐在一起,映射新点的开销也很小.

  3. Finding conserved and non-conserved reactions using a metabolic pathway alignment algorithm.

    Science.gov (United States)

    Clemente, José C; Satou, Kenji; Valiente, Gabriel

    2006-01-01

    Using a metabolic pathway alignment method we developed, we studied highly conserved reactions in different groups of organisms and found out that biological functions vital for each of the groups are effectively expressed in the set of conserved reactions. We also studied the metabolic alignment of different strains of three bacteria and found out several non-conserved reactions. We suggest that these reactions could be either misannotations or reactions with a relevant but yet to be specified biological role, and should therefore be further investigated.

  4. 改进的自适应汉维句子对齐%Improved adaptive algorithm for Chinese-Uyghur sentence alignment

    Institute of Scientific and Technical Information of China (English)

    田生伟; 禹龙; 杨飞宇

    2011-01-01

    This paper proposes an improved adaptive algorithm for Chinese-Uyghur sentence alignment.Traditional alignment methods can not well adapt to change in types of corpus,the algorithm makes ues of current Chinese-Uyghur text length ratio of bytes and historical matching model, modifies the alignment model parameters dynamically to meet the changes in types of corpus and improves sentence alignment algorithm performance.Compared with alignment algorithm based on length, alignment improves alignment accuarcy 3.5 percentage and recall 2.7 percentage, compared with mixed-aligned model .alignment improves 1.9 percentage and 1.8 percentage.Experimental results show that the algorithm can adapt to change in types of corpus well.%提出了改进的自适应汉维句子对齐算法对齐汉维语句子.针对传统对齐方法不能较好地适应语料类型的变化,算法利用当前待对齐汉维文本的字节长度比和历史匹配模式数据,动态修正对齐模型的参数,使其适应语料类型的变化,提高了汉维句子对齐算法的性能,对齐的正确率和召回率较长度对齐模型分别提高了3.5个百分点和2.7个百分点,较混合对齐提高了1.9个百分点和1.8个百分点.实验结果验证了该算法能够有效地适应语料类型的变化.

  5. An algorithm to determine backscattering ratio and single scattering albedo

    Digital Repository Service at National Institute of Oceanography (India)

    Suresh, T.; Desa, E.; Matondkar, S.G.P.; Mascarenhas, A.A.M.Q.; Nayak, S.R.; Naik, P.

    Algorithms to determine the inherent optical properties of water, backscattering probability and single scattering albedo at 490 and 676 nm from the apparent optical property, remote sensing reflectance are presented here. The measured scattering...

  6. Computational Algorithm for Orbit and Mass Determination of Visual Binaries

    CERN Document Server

    Sharaf, Mohamed; Saad, Abdel Naby; Elkhateeb, Magdy; Saad, Somaya

    2014-01-01

    In this paper we introduce an algorithm for determining the orbital elements and individual masses of visual binaries. The algorithm uses an optimal point, which minimizes a specific function describing the average length between the least-squares solution and the exact solution. The objective function to be minimized is exact, without any approximation. The algorithm is applied to Kowalsky's method for orbital parameter computation, and to Reed's method for the determination of the dynamical parallax and individual masses. The procedure is applied to A 1145 and ADS 15182.

  7. Prediction of Antimicrobial Peptides Based on Sequence Alignment and Support Vector Machine-Pairwise Algorithm Utilizing LZ-Complexity

    Directory of Open Access Journals (Sweden)

    Xin Yi Ng

    2015-01-01

    Full Text Available This study concerns an attempt to establish a new method for predicting antimicrobial peptides (AMPs which are important to the immune system. Recently, researchers are interested in designing alternative drugs based on AMPs because they have found that a large number of bacterial strains have become resistant to available antibiotics. However, researchers have encountered obstacles in the AMPs designing process as experiments to extract AMPs from protein sequences are costly and require a long set-up time. Therefore, a computational tool for AMPs prediction is needed to resolve this problem. In this study, an integrated algorithm is newly introduced to predict AMPs by integrating sequence alignment and support vector machine- (SVM- LZ complexity pairwise algorithm. It was observed that, when all sequences in the training set are used, the sensitivity of the proposed algorithm is 95.28% in jackknife test and 87.59% in independent test, while the sensitivity obtained for jackknife test and independent test is 88.74% and 78.70%, respectively, when only the sequences that has less than 70% similarity are used. Applying the proposed algorithm may allow researchers to effectively predict AMPs from unknown protein peptide sequences with higher sensitivity.

  8. Problem of algorithm in precision orbit determination

    Institute of Scientific and Technical Information of China (English)

    刘林; 张强; 廖新浩

    1999-01-01

    In orbit determination, the precision ephemeris and state transition matrix are usually obtained by solving two groups of ordinary differential equations with numerical integration method due to the complexity of the force models. A kind of simplified analytical method to compute the state transition matrix is given. The method is not only very efficient for the case where the orbit arc is not too long, but also can avoid the integration of two groups of ordinary differential equations at the same time. Some practical test examples also show the efficiency of the method.

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

    Science.gov (United States)

    Sudha Sadasivam, G; Baktavatchalam, G

    2010-01-01

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

  10. Algorithm of orbit determination using one or two GPS satellites

    Institute of Scientific and Technical Information of China (English)

    刘艳芳; 洪炳荣; 郭建宁; 巨涛

    1999-01-01

    The problem of orbit determination using one or two GPS satellites is discussed. Methods of getting initial values based on linear translation is presented; the Secant method and the descend Newton iterative procedure and the continuation algorithm are used synthetically to solve the nonlinear equations. Computer simulation shows that this algorithm can give preliminary state of satellite orbit with a certain precision in short time.

  11. Band alignment at the interface of PbTe/SnTe heterojunction determined by X-ray photoelectron spectroscopy

    Science.gov (United States)

    Shu, Tianyu; Ye, Zhenyu; Lu, Pengqi; Chen, Lu; Xu, Gangyi; Zhou, Jie; Wu, Huizhen

    2016-11-01

    We report the determination of band alignment of PbTe/SnTe (111) heterojunction interfaces using X-ray photoelectron spectroscopy (XPS). Multiple core levels of Pb and Sn were utilized to determine the valence band offset (VBO) of the heterojunction. The XPS result shows a type-III band alignment with the VBO of 1.37+/- 0.18 \\text{eV} and the conduction band offset (CBO) of 1.23+/- 0.18 \\text{eV} . The experimental determination of the band alignment of the PbTe/SnTe heterojunction shall benefit the improvement of PbTe/SnTe-related optoelectronic and electronic devices.

  12. 复杂网络结构比对算法研究进展%Advances in algorithms for construction alignment of complex networks research

    Institute of Scientific and Technical Information of China (English)

    刘富; 姜奕含; 邹青宇

    2015-01-01

    The construction alignment of complex networks problems in biological science、computer science、social science and other fields have practical signification.In recent years, different types of construction alignment of complex networks have been sprung up.In this paper, we mainly analysed the construction alignment algorithms based on graph and construction alignment algorithms and mathematical framework.Illustrating the key problem in the study of the networks alignment algorithm is analyzed and compared the algorithms of construction alignment. We explained their advantages and disadvantages,at last we forecast the future progress of algorithms for construc-tion alignment of complex networks.%复杂网络的结构比对问题在生物科学、计算机科学和社会科学等多个领域都具有很重要的现实意义。近年来涌现出了很多针对不同类型复杂网络的结构对比算法,对现有的网络结构比对算法进行梳理,重点分析了基于图的网络结构比对方法和基于数学框架网络结构比对方法。对这2种方法的特点进行了总结与比较,重点阐述了网络结构比对研究中的关键问题,分析和总结了现有的网络结构比对算法,阐述了网络结构比对中优势和不足。以此为基础提出了复杂网络结构比对问题未来的研究方向。

  13. Determination of precise crystallographic directions for mask alignment in wet bulk micromachining for MEMS

    Science.gov (United States)

    Singh, Sajal Sagar; Pal, Prem; Pandey, Ashok Kumar; Xing, Yan; Sato, Kazuo

    2016-12-01

    In wet bulk micromachining, the etching characteristics are orientation dependent. As a result, prolonged etching of mask openings of any geometric shape on both Si{100} and Si{110} wafers results in a structure defined by the slowest etching planes. In order to fabricate microstructures with high dimensional accuracy, it is vital to align the mask edges along the crystal directions comprising of these slowest etching planes. Thus, precise alignment of mask edges is important in micro/nano fabrication. As a result, the determination of accurate crystal directions is of utmost importance and is in fact the first step to ensure dimensionally accurate microstructures for improved performance. In this review article, we have presented a comprehensive analysis of different techniques to precisely determine the crystallographic directions. We have covered various techniques proposed in the span of more than two decades to determine the crystallographic directions on both Si{100} and Si{110} wafers. Apart from a detailed discussion of each technique along with their design and implementation, we have provided a critical analysis of the associated constraints, benefits and shortcomings. We have also summed up the critical aspects of each technique and presented in a tabular format for easy reference for readers. This review article comprises of an exhaustive discussion and is a handy reference for researchers who are new in the field of wet anisotropic etching or who want to get abreast with the techniques of determination of crystal directions.

  14. Can a semi-automated surface matching and principal axis-based algorithm accurately quantify femoral shaft fracture alignment in six degrees of freedom?

    Science.gov (United States)

    Crookshank, Meghan C; Beek, Maarten; Singh, Devin; Schemitsch, Emil H; Whyne, Cari M

    2013-07-01

    Accurate alignment of femoral shaft fractures treated with intramedullary nailing remains a challenge for orthopaedic surgeons. The aim of this study is to develop and validate a cone-beam CT-based, semi-automated algorithm to quantify the malalignment in six degrees of freedom (6DOF) using a surface matching and principal axes-based approach. Complex comminuted diaphyseal fractures were created in nine cadaveric femora and cone-beam CT images were acquired (27 cases total). Scans were cropped and segmented using intensity-based thresholding, producing superior, inferior and comminution volumes. Cylinders were fit to estimate the long axes of the superior and inferior fragments. The angle and distance between the two cylindrical axes were calculated to determine flexion/extension and varus/valgus angulation and medial/lateral and anterior/posterior translations, respectively. Both surfaces were unwrapped about the cylindrical axes. Three methods of matching the unwrapped surface for determination of periaxial rotation were compared based on minimizing the distance between features. The calculated corrections were compared to the input malalignment conditions. All 6DOF were calculated to within current clinical tolerances for all but two cases. This algorithm yielded accurate quantification of malalignment of femoral shaft fractures for fracture gaps up to 60 mm, based on a single CBCT image of the fractured limb.

  15. Determination of band alignment in the single-layer MoS2/WSe2 heterojunction

    KAUST Repository

    Chiu, Ming-Hui

    2015-07-16

    The emergence of two-dimensional electronic materials has stimulated proposals of novel electronic and photonic devices based on the heterostructures of transition metal dichalcogenides. Here we report the determination of band offsets in the heterostructures of transition metal dichalcogenides by using microbeam X-ray photoelectron spectroscopy and scanning tunnelling microscopy/spectroscopy. We determine a type-II alignment between MoS2 and WSe2 with a valence band offset value of 0.83 eV and a conduction band offset of 0.76 eV. First-principles calculations show that in this heterostructure with dissimilar chalcogen atoms, the electronic structures of WSe2 and MoS2 are well retained in their respective layers due to a weak interlayer coupling. Moreover, a valence band offset of 0.94 eV is obtained from density functional theory, consistent with the experimental determination.

  16. Genetic Algorithm Optimization for Determining Fuzzy Measures from Fuzzy Data

    Directory of Open Access Journals (Sweden)

    Chen Li

    2013-01-01

    Full Text Available Fuzzy measures and fuzzy integrals have been successfully used in many real applications. How to determine fuzzy measures is a very difficult problem in these applications. Though there have existed some methodologies for solving this problem, such as genetic algorithms, gradient descent algorithms, neural networks, and particle swarm algorithm, it is hard to say which one is more appropriate and more feasible. Each method has its advantages. Most of the existed works can only deal with the data consisting of classic numbers which may arise limitations in practical applications. It is not reasonable to assume that all data are real data before we elicit them from practical data. Sometimes, fuzzy data may exist, such as in pharmacological, financial and sociological applications. Thus, we make an attempt to determine a more generalized type of general fuzzy measures from fuzzy data by means of genetic algorithms and Choquet integrals. In this paper, we make the first effort to define the σ-λ rules. Furthermore we define and characterize the Choquet integrals of interval-valued functions and fuzzy-number-valued functions based on σ-λ rules. In addition, we design a special genetic algorithm to determine a type of general fuzzy measures from fuzzy data.

  17. Comparison of algorithms for determination of solar wind regimes

    Science.gov (United States)

    Neugebauer, Marcia; Reisenfeld, Daniel; Richardson, Ian G.

    2016-09-01

    This study compares the designation of different solar wind flow regimes (transient, coronal hole, and streamer belt) according to two algorithms derived from observations by the Solar Wind Ion Composition Spectrometer, the Solar Wind Electron Proton Alpha Monitor, and the Magnetometer on the ACE spacecraft, with a similar regime determination performed on board the Genesis spacecraft. The comparison is made for the interval from late 2001 to early 2004 when Genesis was collecting solar wind ions for return to Earth. The agreement between hourly regime assignments from any pair of algorithms was less than two thirds, while the simultaneous agreement between all three algorithms was only 49%. When the results of the algorithms were compared to a catalog of interplanetary coronal mass ejection events, it was found that almost all the events in the catalog were confirmed by the spacecraft algorithms. On the other hand, many short transient events, lasting 1 to 13 h, that were unanimously selected as transient like by the algorithms, were not included in the catalog.

  18. Hierarchical Genetic Algorithm Approach to Determine Pulse Sequences in NMR

    CERN Document Server

    Ajoy, Ashok

    2009-01-01

    We develop a new class of genetic algorithm that computationally determines efficient pulse sequences to implement a quantum gate U in a three-qubit system. The method is shown to be quite general, and the same algorithm can be used to derive efficient sequences for a variety of target matrices. We demonstrate this by implementing the inversion-on-equality gate efficiently when the spin-spin coupling constants $J_{12}=J_{23}=J$ and $J_{13}=0$. We also propose new pulse sequences to implement the Parity gate and Fanout gate, which are about 50% more efficient than the previous best efforts. Moreover, these sequences are shown to require significantly less RF power for their implementation. The proposed algorithm introduces several new features in the conventional genetic algorithm framework. We use matrices instead of linear chains, and the columns of these matrices have a well defined hierarchy. The algorithm is a genetic algorithm coupled to a fast local optimizer, and is hence a hybrid GA. It shows fast con...

  19. DETERMINATION OF BALL COHESIVE AND FRICTIONAL FORCES WITH TOOL AT POLISHING BETWEEN ALIGNED RINGS AND DISK

    Directory of Open Access Journals (Sweden)

    K. G. Schetnikovich

    2010-01-01

    Full Text Available The paper provides a design description of a tool used for polishing balls made of brittle materials between bottom driving disk and two rings. An external stationary ring has a ring turning of rectangular profile that helps the ring to be based directly on the balls which are to be polished and take self-aligned position in relation to tool rotation axis.  Forces acting on the balls in the points of contact with the tool with due account of friction against a separator and conditions of ball sliding along ring working surfaces are determined in the paper. Dependence for determination of stationary and driving ring load ratio when balls are sliding along two contact surfaces of the tool is ascertained in the paper. The paper contains recommendations on selection of modes for ball polishing at its initial and finishing stages.

  20. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal

    2011-08-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-10-15

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

  2. 基于布尔逻辑的双序列搜索比对算法%Pairwise Sequences Search and Alignment Algorithm Based on Boolean Logic

    Institute of Scientific and Technical Information of China (English)

    郭宁; 冯萍; 康继昌

    2011-01-01

    Traditional pairwise sequences alignment algorithms are mostly based on dynamic programming, there are some problems when using dynamic programming to align for its slow speed and low accuracy. Pairwise sequences search and alignment algorithm based on Boolean logic is proposed in this paper. The algorithm searches homologous regions in the pairwise sequence using a fixed-length base fragment in one sequence, and performs the alignment between the homologous regions at once, including the alignment of the bases in the homologous regions and the alignment between the subsequence and the other sequence. It also makes use of concurrent execution mechanism to realize the parallel speed up. Simulation experimental results show that the algorithm has higer real-time and accuracy.%传统双序列比对算法使用动态规划进行序列比对的速度慢,且准确性不高.为解决该问题,提出一种基于布尔逻辑的双序列搜索比对算法.根据一条序列中定长的碱基片段搜索2条序列的相似区,对相似区进行比对,包括相似区中碱基的比对以及子序列与另一条序列的比对,并通过并行执行机制实现加速比对.仿真实验结果表明,该算法具有较高的准确性和较好的实时性.

  3. Vectorcardiographic loop alignment for fetal movement detection using the expectation-maximization algorithm and support vector machines.

    Science.gov (United States)

    Vullings, R; Mischi, M

    2013-01-01

    Reduced fetal movement is an important parameter to assess fetal distress. Currently, no suitable methods are available that can objectively assess fetal movement during pregnancy. Fetal vectorcardiographic (VCG) loop alignment could be such a method. In general, the goal of VCG loop alignment is to correct for motion-induced changes in the VCGs of (multiple) consecutive heartbeats. However, the parameters used for loop alignment also provide information to assess fetal movement. Unfortunately, current methods for VCG loop alignment are not robust against low-quality VCG signals. In this paper, a more robust method for VCG loop alignment is developed that includes a priori information on the loop alignment, yielding a maximum a posteriori loop alignment. Classification, based on movement parameters extracted from the alignment, is subsequently performed using support vector machines, resulting in correct classification of (absence of) fetal movement in about 75% of cases. After additional validation and optimization, this method can possibly be employed for continuous fetal movement monitoring.

  4. 基于SWGPSO算法的多序列比对%Multiple Sequence Alignment Based on SWGPSO Algorithm

    Institute of Scientific and Technical Information of China (English)

    徐小俊; 雷秀娟; 郭玲

    2011-01-01

    In this paper, a new method of getting inertia weight, Subsection Weight(SW) is proposed in order to solve the Particle Swarm Optimization(PSO) disadvantages which are likely to fall into local optimum and slow converge. The diversity of swarm increases at the prophase and the convergence is accelerated in the later period. Meanwhile, the combination of SW and GB can improve the evolutionary equation of PSO and makes it perform better. Experimental result shows that the algorithm can effectively avoid converging too early and increase the precision in solving multiple sequence alignment.%针对粒子群优化(PSO)易陷入局部最优、收敛速度慢的现象,提出一种新的惯性权重取值方法--分段取值惯性权重(SW)方法.该方法在算法前期增加粒子多样性,后期加速算法收敛.针对PSO仅使用2个最优值寻优的问题,引入第3个最优值GB,将SW与GB结合,改进PSO的进化方程.实验结果表明,该算法解决多序列比对问题时,可以有效地避免算法早熟,并提高解的精度.

  5. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal

    2011-11-01

    Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. We introduce fast alignment algorithm, called \\'Alignment By Scanning\\' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the \\'GAP\\' (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  6. Error analysis on heading determination via genetic algorithms

    Institute of Scientific and Technical Information of China (English)

    Zhong Bing; Xu Jiangning; Ma Heng

    2006-01-01

    A new error analysis method is presented via genetic algorithms for high precise heading determination model based on two total positioning stations (TPSs). The method has the ability to search all possible solution space by the genetic operators of elitist model and restriction. The result of analyzing the error of this model shows that the accuracy of this model is precise enough to meet the need of calibration for navigation systems on ship, and the search space is only 0.03% of the total search space, and the precision of heading determination is 4" in a general dock.

  7. Computer-Based Algorithmic Determination of Muscle Movement Onset Using M-Mode Ultrasonography

    Science.gov (United States)

    2017-04-01

    from baseline. Computerized algorithms Computed MO was determined by three separate classes of algorithms using RStudio: (i) a novel standard...ARL-RP-0596 ● APR 2017 US Army Research Laboratory Computer -Based Algorithmic Determination of Muscle Movement Onset Using M...the originator. ARL-RP-0596 ● APR 2017 US Army Research Laboratory Computer -Based Algorithmic Determination of Muscle Movement

  8. 粒子群优化算法在传递对准中的应用%Application of particle swarm optimization algorithm in transfer alignment

    Institute of Scientific and Technical Information of China (English)

    夏家和; 秦永元; 贾继超

    2009-01-01

    A PSO(particle swarm optimization) algorithm-based transfer alignment method is presented. The transfer alignment requirement and the relation between the master inertial sensors and slave inertial sensors are analyzed. The transfer alignment problem is treated as a parameter optimization problem, and the PSO algorithm-based alignment mathematics model is given. The transfer alignment optimization function is defined, and the PSO algorithm is introduced. The PSO algorithm is employed to search the global minima, then the misalignment can be estimated. The algorithm is validated by simulation. The heading error can be <0.1° under the simulation condition that the gyro's accuracy is 0.1 (°)/h. The algorithm is greatly affected by the maneuver as other alignment methods. Attitude maneuver is usually needed to increase the gyro's signal-to-noise rate.%给出了一种基于粒子群优化算法的捷联惯导传递对准算法.简单分析了传递对准任务要求和主子惯导惯性器件输出之间的关系,将传递对准问题作为参数优化问题进行求解,给出了基于粒子群优化算法进行传递对准的数学模型.定义了传递对准的优化目标函数,介绍了粒子群优化算法及其应用于传递对准的具体算法设置.用粒子群优化算法求解目标函数的最小值,可获得主子惯导之间的失准角,进行一次校正即可完成传递对准过程.通过计算机仿真对算法进行了验证分析,在仿真条件下(陀螺精度为0.1°/h),能达到方位0.1°的精度.与其他对准算法一样,算法受载体机动条件的影响较大,一般需要姿态机动来提高陀螺的信噪比.

  9. Algorithms for Determining Physical Responses of Structures Under Load

    Science.gov (United States)

    Richards, W. Lance; Ko, William L.

    2012-01-01

    Ultra-efficient real-time structural monitoring algorithms have been developed to provide extensive information about the physical response of structures under load. These algorithms are driven by actual strain data to measure accurately local strains at multiple locations on the surface of a structure. Through a single point load calibration test, these structural strains are then used to calculate key physical properties of the structure at each measurement location. Such properties include the structure s flexural rigidity (the product of the structure's modulus of elasticity, and its moment of inertia) and the section modulus (the moment of inertia divided by the structure s half-depth). The resulting structural properties at each location can be used to determine the structure s bending moment, shear, and structural loads in real time while the structure is in service. The amount of structural information can be maximized through the use of highly multiplexed fiber Bragg grating technology using optical time domain reflectometry and optical frequency domain reflectometry, which can provide a local strain measurement every 10 mm on a single hair-sized optical fiber. Since local strain is used as input to the algorithms, this system serves multiple purposes of measuring strains and displacements, as well as determining structural bending moment, shear, and loads for assessing real-time structural health. The first step is to install a series of strain sensors on the structure s surface in such a way as to measure bending strains at desired locations. The next step is to perform a simple ground test calibration. For a beam of length l (see example), discretized into n sections and subjected to a tip load of P that places the beam in bending, the flexural rigidity of the beam can be experimentally determined at each measurement location x. The bending moment at each station can then be determined for any general set of loads applied during operation.

  10. Theoretical study of determining orientation and alignment of symmetric top molecule using laser-induced fluorescence

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    General expressions used for extracting the orientation and alignment parameters of a symmetric top molecule from laser-induced fluorescence (LIF) intensity are derived by employing the density matrix approach. The molecular orientation and alignment are described by molecular state multipoles. Excitation and detection are circularly and linearly polarized lights, respectively. In general cases, the LIF intensity is a complex function of the initial molecular state multipoles, the dynamic factors and the excitation-detection geometrical factors. It contains a population, ten orientation and fourteen alignment multipoles. The problem of how to extract the initial molecular state multipoles from the resolved LIF intensity is discussed.

  11. Genetic Algorithm for Initial Orbit Determination with Too Short Arc

    Science.gov (United States)

    Xin-ran, Li; Xin, Wang

    2017-01-01

    A huge quantity of too-short-arc (TSA) observational data have been obtained in sky surveys of space objects. However, reasonable results for the TSAs can hardly be obtained with the classical methods of initial orbit determination (IOD). In this paper, the IOD is reduced to a two-stage hierarchical optimization problem containing three variables for each stage. Using the genetic algorithm, a new method of the IOD for TSAs is established, through the selections of the optimized variables and the corresponding genetic operators for specific problems. Numerical experiments based on the real measurements show that the method can provide valid initial values for the follow-up work.

  12. Molecular structure determination from x-ray scattering patterns of laser-aligned symmetric-top molecules.

    Science.gov (United States)

    Ho, P J; Starodub, D; Saldin, D K; Shneerson, V L; Ourmazd, A; Santra, R

    2009-10-07

    We investigate the molecular structure information contained in the x-ray diffraction patterns of an ensemble of rigid CF(3)Br molecules aligned by an intense laser pulse at finite rotational temperature. The diffraction patterns are calculated at an x-ray photon energy of 20 keV to probe molecular structure at angstrom-scale resolution. We find that a structural reconstruction algorithm based on iterative phase retrieval fails to extract a reliable structure. However, the high atomic number of Br compared with C or F allows each diffraction pattern to be treated as a hologram. Using this approach, the azimuthal projection of the molecular electron density about the alignment axis may be retrieved.

  13. FANUC CNC automatic alignment algorithm%FANUC 加工中心五点碰数自动找正算法的研究

    Institute of Scientific and Technical Information of China (English)

    钟如全

    2014-01-01

    针对传统定位加工技术存在的问题,提出了五点碰数自动找正的方法。研究五点碰数自动找正方法的算法,从而实现工件角度和位置的找正,省去了人工找正和设计精密夹具。此方法保证了产品对刀及找正的准确性、可靠性和高效性,具有良好的应用前景。%Processing technology for the traditional positioning problems ,put forward the “five-point touch a few”automatic align-ment method .Study the“five-point touch a few” automatic alignment method algorithm ,the angle and position of the workpiece in order to achieve the alignment ,eliminating the need for manual alignment and design of precision fixtures .This method ensures that the product is on the knife and look for the accuracy ,reliability,efficiency.Have a good prospect.

  14. Research of Dijkstra algorithm in protein sequence alignment%Dijkstra算法在蛋白质序列比对中的研究

    Institute of Scientific and Technical Information of China (English)

    祁长红; 郁芸; 韩新焕

    2012-01-01

    A sequence alignment algorithm based on Dijkstra algorithm is put forward, which is mainly used to seek the shortest path while the problem of sequence alignment can be transformed into a problem to look for the shortest path in directed acyclic graph. For a small amount of sequences, Dijkstra algorithm is easier to seek the optimal solution. For multiple sequences alignment, the shortest path seeked in the Af-dimensional space can be obtained in the two-dimensional space. It can be proved that the problem is greatly simplified and the sub-optimal solution can be obtained.%提出一种基于Dijkstra算法的序列比对方法,该算法主要用于求最短路径,而序列比对可以转化为在有向无环图中寻找最短路径问题.对于少量序列比对,使用该算法可以求出最优解.对于多序列比对,可将在N维空间求解最短路径问题转化为在二维空间求解最短路径.该算法可以简化问题复杂度,能求得相对最优解.

  15. Algorithm for Determination of Orion Ascent Abort Mode Achievability

    Science.gov (United States)

    Tedesco, Mark B.

    2011-01-01

    For human spaceflight missions, a launch vehicle failure poses the challenge of returning the crew safely to earth through environments that are often much more stressful than the nominal mission. Manned spaceflight vehicles require continuous abort capability throughout the ascent trajectory to protect the crew in the event of a failure of the launch vehicle. To provide continuous abort coverage during the ascent trajectory, different types of Orion abort modes have been developed. If a launch vehicle failure occurs, the crew must be able to quickly and accurately determine the appropriate abort mode to execute. Early in the ascent, while the Launch Abort System (LAS) is attached, abort mode selection is trivial, and any failures will result in a LAS abort. For failures after LAS jettison, the Service Module (SM) effectors are employed to perform abort maneuvers. Several different SM abort mode options are available depending on the current vehicle location and energy state. During this region of flight the selection of the abort mode that maximizes the survivability of the crew becomes non-trivial. To provide the most accurate and timely information to the crew and the onboard abort decision logic, on-board algorithms have been developed to propagate the abort trajectories based on the current launch vehicle performance and to predict the current abort capability of the Orion vehicle. This paper will provide an overview of the algorithm architecture for determining abort achievability as well as the scalar integration scheme that makes the onboard computation possible. Extension of the algorithm to assessing abort coverage impacts from Orion design modifications and launch vehicle trajectory modifications is also presented.

  16. 舰载捷联惯导动基座 F-QUEST 初始对准方法%Shipborne SINS in-movement F-QUEST initial alignment algorithm

    Institute of Scientific and Technical Information of China (English)

    李杨; 高敬东; 胡柏青; 李开龙

    2014-01-01

    Aiming at the problems of low information availability and the decline of alignment accuracy due to an uncertain selection of vector observations as far as the strapdown inertial navigation system (SINS)in-movement alignment method based on the inertial frames,this paper proposes a new ship-borne SINS in-movement filter quaternion estimation (F-QUEST)alignment algorithm and offeres an in-movement initial alignment model of SINS.The chain rule of the attitude matrix is used to lead the initial alignment of SINS to the attitude determination.Then the F-QUEST algorithm is used to cal-culate the attitude matrix so as to acquire the in-movement alignment of SINS.The vehicle test results show that the proposed method is of higher alignment accuracy and faster convergence than the tradi-tional method,especially with the horizontal posture angle error being able to converge to 0.01°in 3 s.%针对目前基于惯性系的捷联惯导动基座对准方法信息利用率不高及矢量观测选取不确定性导致对准精度下降的问题,提出了一种新的舰载捷联惯导动基座滤波四元数估计(filter quaternion estimation,F-QUEST)对准方法。构建了捷联惯导动基座初始对准模型,并利用姿态矩阵链式法则将惯导初始对准转化为姿态确定问题,进而采用 F-QUEST 算法求取姿态矩阵以实现捷联惯导动基座对准。车载试验结果表明:相比传统方法,新方法具有更高的对准精度和更快的收敛速度,水平姿态角误差只需3 s 即可收敛到0.01°。

  17. The alignment-distribution graph

    Science.gov (United States)

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

    1993-01-01

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

  18. Two Simple and Efficient Algorithms to Compute the SP-Score Objective Function of a Multiple Sequence Alignment

    Science.gov (United States)

    Ranwez, Vincent

    2016-01-01

    Background Multiple sequence alignment (MSA) is a crucial step in many molecular analyses and many MSA tools have been developed. Most of them use a greedy approach to construct a first alignment that is then refined by optimizing the sum of pair score (SP-score). The SP-score estimation is thus a bottleneck for most MSA tools since it is repeatedly required and is time consuming. Results Given an alignment of n sequences and L sites, I introduce here optimized solutions reaching O(nL) time complexity for affine gap cost, instead of O(n2L), which are easy to implement. PMID:27505054

  19. Use of a Closed-Loop Tracking Algorithm for Orientation Bias Determination of an S-Band Ground Station

    Science.gov (United States)

    Welch, Bryan W.; Schrage, Dean S.; Piasecki, Marie T.

    2015-01-01

    The Space Communications and Navigation (SCaN) Testbed project completed installation and checkout testing of a new S-Band ground station at the NASA Glenn Research Center in Cleveland, Ohio in 2015. As with all ground stations, a key alignment process must be conducted to obtain offset angles in azimuth (AZ) and elevation (EL). In telescopes with AZ-EL gimbals, this is normally done with a two-star alignment process, where telescope-based pointing vectors are derived from catalogued locations with the AZ-EL bias angles derived from the pointing vector difference. For an antenna, the process is complicated without an optical asset. For the present study, the solution was to utilize the gimbal control algorithms closed-loop tracking capability to acquire the peak received power signal automatically from two distinct NASA Tracking and Data Relay Satellite (TDRS) spacecraft, without a human making the pointing adjustments. Briefly, the TDRS satellite acts as a simulated optical source and the alignment process proceeds exactly the same way as a one-star alignment. The data reduction process, which will be discussed in the paper, results in two bias angles which are retained for future pointing determination. Finally, the paper compares the test results and provides lessons learned from the activity.

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

    Science.gov (United States)

    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. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. CUSP: an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations

    Directory of Open Access Journals (Sweden)

    Offmann Bernard

    2008-05-01

    Full Text Available Abstract Background Distantly related proteins adopt and retain similar structural scaffolds despite length variations that could be as much as two-fold in some protein superfamilies. In this paper, we describe an analysis of indel regions that accommodate length variations amongst related proteins. We have developed an algorithm CUSP, to examine multi-membered PASS2 superfamily alignments to identify indel regions in an automated manner. Further, we have used the method to characterize the length, structural type and biochemical features of indels in related protein domains. Results CUSP, examines protein domain structural alignments to distinguish regions of conserved structure common to related proteins from structurally unconserved regions that vary in length and type of structure. On a non-redundant dataset of 353 domain superfamily alignments from PASS2, we find that 'length- deviant' protein superfamilies show > 30% length variation from their average domain length. 60% of additional lengths that occur in indels are short-length structures ( 15 residues in length. Structural types in indels also show class-specific trends. Conclusion The extent of length variation varies across different superfamilies and indels show class-specific trends for preferred lengths and structural types. Such indels of different lengths even within a single protein domain superfamily could have structural and functional consequences that drive their selection, underlying their importance in similarity detection and computational modelling. The availability of systematic algorithms, like CUSP, should enable decision making in a domain superfamily-specific manner.

  2. Novel genetic algorithm search procedure for LEED surface structure determination.

    Science.gov (United States)

    Viana, M L; dos Reis, D D; Soares, E A; Van Hove, M A; Moritz, W; de Carvalho, V E

    2014-06-04

    Low Energy Electron Diffraction (LEED) is one of the most powerful experimental techniques for surface structure analysis but until now only a trial-and-error approach has been successful. So far, fitting procedures developed to optimize structural and nonstructural parameters-by minimization of the R-factor-have had a fairly small convergence radius, suitable only for local optimization. However, the identification of the global minimum among the several local minima is essential for complex surface structures. Global optimization methods have been applied to LEED structure determination, but they still require starting from structures that are relatively close to the correct one, in order to find the final structure. For complex systems, the number of trial structures and the resulting computation time increase so rapidly that the task of finding the correct model becomes impractical using the present methodologies. In this work we propose a new search method, based on Genetic Algorithms, which is able to determine the correct structural model starting from completely random structures. This method-called here NGA-LEED for Novel Genetic Algorithm for LEED-utilizes bond lengths and symmetry criteria to select reasonable trial structures before performing LEED calculations. This allows a reduction of the parameter space and, consequently of the calculation time, by several orders of magnitude. A refinement of the parameters by least squares fit of simulated annealing is performed only at some intermediate stages and in the final step. The method was successfully tested for two systems, Ag(1 1 1)(4 × 4)-O and Au(1 1 0)-(1 × 2), both in theory versus theory and in theory versus experiment comparisons. Details of the implementation as well as the results for these two systems are presented.

  3. ChimeRScope: a novel alignment-free algorithm for fusion transcript prediction using paired-end RNA-Seq data.

    Science.gov (United States)

    Li, You; Heavican, Tayla B; Vellichirammal, Neetha N; Iqbal, Javeed; Guda, Chittibabu

    2017-07-27

    The RNA-Seq technology has revolutionized transcriptome characterization not only by accurately quantifying gene expression, but also by the identification of novel transcripts like chimeric fusion transcripts. The 'fusion' or 'chimeric' transcripts have improved the diagnosis and prognosis of several tumors, and have led to the development of novel therapeutic regimen. The fusion transcript detection is currently accomplished by several software packages, primarily relying on sequence alignment algorithms. The alignment of sequencing reads from fusion transcript loci in cancer genomes can be highly challenging due to the incorrect mapping induced by genomic alterations, thereby limiting the performance of alignment-based fusion transcript detection methods. Here, we developed a novel alignment-free method, ChimeRScope that accurately predicts fusion transcripts based on the gene fingerprint (as k-mers) profiles of the RNA-Seq paired-end reads. Results on published datasets and in-house cancer cell line datasets followed by experimental validations demonstrate that ChimeRScope consistently outperforms other popular methods irrespective of the read lengths and sequencing depth. More importantly, results on our in-house datasets show that ChimeRScope is a better tool that is capable of identifying novel fusion transcripts with potential oncogenic functions. ChimeRScope is accessible as a standalone software at (https://github.com/ChimeRScope/ChimeRScope/wiki) or via the Galaxy web-interface at (https://galaxy.unmc.edu/). © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Business alignment in the procurement domain: a study of antecedents and determinants of supply chain performance

    Directory of Open Access Journals (Sweden)

    Patrick Mikalef

    2014-01-01

    Full Text Available With organizations now placing an increasing amount on attention on the management of their supply chain activities, the role of Information Technology (IT in supporting these operations has been put in the spotlight. In spite of extensive research examining how IT can be employed in various activities of supply chain management, the majority of studies are limited in identifying enablers and inhibitors of adoption. Empirical studies examining post-adoption conditions that facilitate performance improvement still remain scarce. In this study we focus on procurement as part of the supply chain management activities. We apply the business-IT alignment perspective to the domain of procurement, and examine how certain organizational factors impact the attainment of this state. Additionally, we research the effect that procurement alignment has on supply chain management performance. In order to do so, we apply Partial Least Squares (PLS analysis on a sample of 172 European companies. We find that firms that opt for a centralized governance structure, as well as larger firms, are more likely to attain a state of procurement alignment. Furthermore, our results empirically support the statement that procurement alignment is positively correlated with operational efficiency and competitive performance of the supply chain.

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

    Science.gov (United States)

    Yumura, Takashi; Yamamoto, Wataru

    2017-09-20

    We employed density functional theory (DFT) calculations with dispersion corrections to investigate energetically preferred alignments of certain p,p'-dimethylaminonitrostilbene (DANS) molecules inside an armchair (m,m) carbon nanotube (n × DANS@(m,m)), where the number of inner molecules (n) is no greater than 3. Here, three types of alignments of DANS are considered: a linear alignment in a parallel fashion and stacking alignments in parallel and antiparallel fashions. According to DFT calculations, a threshold tube diameter for containing DANS molecules in linear or stacking alignments was found to be approximately 1.0 nm. Nanotubes with diameters smaller than 1.0 nm result in the selective formation of linearly aligned DANS molecules due to strong confinement effects within the nanotubes. By contrast, larger diameter nanotubes allow DANS molecules to align in a stacking and linear fashion. The type of alignment adopted by the DANS molecules inside a nanotube is responsible for their second-order non-linear optical properties represented by their static hyperpolarizability (β0 values). In fact, we computed β0 values of DANS assemblies taken from optimized n × DANS@(m,m) structures, and their values were compared with those of a single DANS molecule. DFT calculations showed that β0 values of DANS molecules depend on their alignment, which decrease in the following order: linear alignment > parallel stacking alignment > antiparallel stacking alignment. In particular, a linear alignment has a β0 value more significant than that of the same number of isolated molecules. Therefore, the linear alignment of DANS molecules, which is only allowed inside smaller diameter nanotubes, can strongly enhance their second-order non-linear optical properties. Since the nanotube confinement determines the alignment of DANS molecules, a restricted nanospace can be utilized to control their second-order non-linear optical properties. These DFT findings can assist in the design

  6. Determination of the effective Young's modulus of vertically aligned carbon nanotube arrays: a simple nanotube-based varactor.

    Science.gov (United States)

    Olofsson, Niklas; Ek-Weis, Johan; Eriksson, Anders; Idda, Tonio; Campbell, Eleanor E B

    2009-09-23

    The electromechanical properties of arrays of vertically aligned multiwalled carbon nanotubes were studied in a parallel plate capacitor geometry. The electrostatic actuation was visualized using both optical microscopy and scanning electron microscopy, and highly reproducible behaviour was achieved for actuation voltages below the pull-in voltage. The walls of vertically aligned carbon nanotubes behave as solid cohesive units. The effective Young's modulus for the carbon nanotube arrays was determined by comparing the actuation results with the results of electrostatic simulations and was found to be exceptionally low, of the order of 1-10 MPa. The capacitance change and Q-factor were determined by measuring the frequency dependence of the radio-frequency transmission. Capacitance changes of over 20% and Q-factors in the range 100-10 were achieved for a frequency range of 0.2-1.5 GHz.

  7. Bayesian coestimation of phylogeny and sequence alignment

    Directory of Open Access Journals (Sweden)

    Jensen Jens

    2005-04-01

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

  8. Algorithms for a Precise Determination of the Betatron Tune

    CERN Document Server

    Bartolini, R; Giovannozzi, Massimo; Todesco, Ezio; Scandale, Walter

    1996-01-01

    In circular accelerators the precise knowledge of the betatron tune is of paramount importance both for routine operation and for theoretical investigations. The tune is measured by sampling the transverse position of the beam for N turns and by performing the FFT of the stored data. One can also evaluate it by computing the Average Phase Advance (APA) over N turns. These approaches have an intrinsic error proportional to 1/N. However, there are special cases where either a better precision or a faster measurement is desired. More efficient algorithms can be used, as those suggested by E.Asseo [1] and recently by J. Laskar [2]. They provide tune estimates by far more precise than those of a plain FFT, as discussed in Ref. [3]. Another important isssue is the effect of the finite resolution of the instrumentation used to measure the beam position. This introduces a noise and the frequency response of the beam is modified [4,5} thus reducing the precision by which the tune is determined. In Section 2 we recall ...

  9. Theoretical Determination of Band Edge Alignments at the Water-CuInS2(112) Semiconductor Interface.

    Science.gov (United States)

    Senftle, Thomas P; Carter, Emily A

    2017-06-06

    Knowledge of a semiconductor electrode's band edge alignment is essential for optimizing processes that occur at the semiconductor/electrolyte interface. Photocatalytic processes are particularly sensitive to such alignments, as they govern the transfer of photoexcited electrons or holes from the surface to reactants in the electrolyte solution. Reconstructions of a semiconductor surface during operation, as well as its interaction with the electrolyte solution, must be considered when determining band edge alignment. Here, we employ density functional theory + U theory to assess the stability of reconstructed CuInS2 surfaces, a system which has shown promise for the active and selective photoelectrocatalytic reduction of CO2 to CH3OH. Using many-body Green's function theory combined with calculations of surface work functions, we determine band edge positions of explicitly solvated, reconstructed CuInS2 surfaces. We find that there is a linear relationship between band edge position and net surface dipole, with the most stable solvent/surface structures tending to minimize this dipole because of generally weak interactions between the surface and solvating water molecules. We predict a conduction band minimum (CBM) of the solvated, reconstructed CuInS2 surface of -2.44 eV vs vacuum at the zero-dipole intercept of the dipole/CBM trendline, in reasonable agreement with the experimentally reported CBM position at -2.64 eV vs vacuum. This methodology offers a simplified approach for approximating the band edge positions at complex semiconductor/electrolyte interfaces.

  10. Determination of Pavement Rehabilitation Activities through a Permutation Algorithm

    Directory of Open Access Journals (Sweden)

    Sangyum Lee

    2013-01-01

    Full Text Available This paper presents a mathematical programming model for optimal pavement rehabilitation planning. The model maximized the rehabilitation area through a newly developed permutation algorithm, based on the procedures outlined in the harmony search (HS algorithm. Additionally, the proposed algorithm was based on an optimal solution method for the problem of multilocation rehabilitation activities on pavement structure, using empirical deterioration and rehabilitation effectiveness models, according to a limited maintenance budget. Thus, nonlinear pavement performance and rehabilitation activity decision models were used to maximize the objective functions of the rehabilitation area within a limited budget, through the permutation algorithm. Our results showed that the heuristic permutation algorithm provided a good optimum in terms of maximizing the rehabilitation area, compared with a method of the worst-first maintenance currently used in Seoul.

  11. The Alignment of the CMS Silicon Tracker

    CERN Document Server

    Lampen, Pekka Tapio

    2013-01-01

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

  12. A fast and efficient algorithm for Slater determinant updates in quantum Monte Carlo simulations.

    Science.gov (United States)

    Nukala, Phani K V V; Kent, P R C

    2009-05-28

    We present an efficient low-rank updating algorithm for updating the trial wave functions used in quantum Monte Carlo (QMC) simulations. The algorithm is based on low-rank updating of the Slater determinants. In particular, the computational complexity of the algorithm is O(kN) during the kth step compared to traditional algorithms that require O(N(2)) computations, where N is the system size. For single determinant trial wave functions the new algorithm is faster than the traditional O(N(2)) Sherman-Morrison algorithm for up to O(N) updates. For multideterminant configuration-interaction-type trial wave functions of M+1 determinants, the new algorithm is significantly more efficient, saving both O(MN(2)) work and O(MN(2)) storage. The algorithm enables more accurate and significantly more efficient QMC calculations using configuration-interaction-type wave functions.

  13. Mechanism in determining pretilt angle of liquid crystals aligned on fluorinated copolymer films

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Hsin-Ying; Wang, Chih-Yu; Lin, Chia-Jen; Pan, Ru-Pin [Department of Electrophysics, National Chiao Tung University, Hsinchu, Taiwan 30010 (China); Lin, Song-Shiang; Lee, Chein-Dhau [Material and Chemical Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan 31040 (China); Kou, Chwung-Shan, E-mail: rpchao@mail.nctu.edu.t [Department of Physics, National Tsing Hua University, Hsinchu, Taiwan 30013 (China)

    2009-08-07

    This work explores the surface treatment of copolymer materials with fluorinated carbonyl groups in various mole fractions by ultraviolet irradiation and ion-beam (IB) bombardment and its effect on liquid crystal (LC) surface alignments. X-ray photoemission spectroscopic analysis confirms that the content of the grafted CF{sub 2} side chains dominates the pretilt angle. A significant increase in oxygen content is responsible for the increase in the polar surface energy during IB treatment. Finally, the polar component of the surface energy dominates the pretilt angle of the LCs.

  14. 一种汉藏双语句子对齐算法%Chinese -Tibetan Bilingual Sentence Alignment Algorithm

    Institute of Scientific and Technical Information of China (English)

    安见才让; 王玲玲

    2011-01-01

    双语语料库建设及其自动对齐研究对计算语言学的发展具有重要意义.双语对齐技术是加工双语文本的核心,对齐效果的好坏直接影响了以后工作的进行.基于汉藏双语的实际情况,提出了一种利用句子长度、相似度和锚点信息的汉藏双语句子对齐方法,该方法用相似度找到句子的锚点,用锚点将双语文本分割成几个分块,在对应双语分块中用基于长度的对齐实现句子的对齐.通过测试数据进行的实验结果显示,这种方法有着良好的准确率,有效地解决了汉藏双语真实文本的句子对齐问题.%Bilingual corpus and its automatic alignment are of great significance to the development of computational linguistics. As the key technology during the course of building corpus, bilingual alignment technology has a direct impact on the future work process. Based on the actual situation of Chinese -Tibetan bilingual, a Chinese- Tibetan bilingual sentence aligning method is proposed in this paper,taking advantage of the length and similarity of sentences as well as the anchor information. In this method, after identifying the anchor of a sentence with the similarity measure, the lingual text will be separated into several fragments with the anchor information. Eventually, these text fragments could be aligned to response their counterparts based upon the length of sentences. According to experiments on plenty of testing data, this method manages to tackle the problem about aligning real Chinese - Tibetan bilingual texts effectively with high standard of accuracy.

  15. String Match Algorithms and Applications in DNA Sequence Alignment%字符串匹配算法在 DNA 序列比对中的应用

    Institute of Scientific and Technical Information of China (English)

    陈建平

    2015-01-01

    The advancement of high-throughput sequencing technologies has led bioinformatics research into the big data era.New technologies generate huge amounts of biological genetic data,which pose significant challenges to data analysis. DNA sequence alignment is one critical step of the bioinformatics analysis flow,providing mapping information for the following variants calling processes.Question B of 201 5 “Shenzhen Cup ”Summer Camp of Mathematical Modeling discusses about DNA sequence alignment problem,requiring students to provide the best solution for fast sequence alignment.Here,we give a brief review on the students’work,then we introduce algorithms implemented in common DNA sequence alignment programs.%高通量测序技术的飞速发展让生物信息领域迎来了大数据时代。新技术在提供海量生物遗传信息的同时,也给分析这些数据带来了新的挑战。DNA 序列比对是信息分析流程中的关键步骤,为后续的变异检测提供序列比对信息。2015“深圳杯”数学建模夏令营 B 题以 DNA 序列比对为研究课题,希望参赛学生给出序列快速比对的最佳方案。本文简要点评了各参赛队伍的解答情况,然后介绍了现有 DNA 序列比对软件中用到的算法和数据结构。

  16. Semiautomatic beam-based LHC collimator alignment

    CERN Document Server

    Valentino, Gianluca; Bruce, Roderik; Wollmann, Daniel; Sammut, Nicholas; Rossi, Adriana; Redaelli, Stefano

    2012-01-01

    Full beam-based alignment of the LHC collimation system was a time-consuming procedure (up to 28 hours) as the collimators were set up manually. A yearly alignment campaign has been sufficient for now, although in the future due to tighter tolerances this may lead to a decrease in the cleaning efficiency if machine parameters such as the beam orbit drift over time. Automating the collimator setup procedure can reduce the beam time for collimator setup and allow for more frequent alignments, therefore reducing the risk of performance degradation. This article describes the design and testing of a semiautomatic algorithm as a first step towards a fully automatic setup procedure. The parameters used to measure the accuracy and performance of the alignment are defined and determined from experimental data. A comparison of these measured parameters at 450 GeV and 3.5 TeV with manual and semiautomatic alignment is provided.

  17. Determination of Optimal Double Sampling Plan using Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Sampath Sundaram

    2012-03-01

    Full Text Available Normal 0 false false false EN-US X-NONE X-NONE MicrosoftInternetExplorer4 Designing double sampling plan requires identification of sample sizes and acceptance numbers. In this paper a genetic algorithm has been designed for the selection of optimal acceptance numbers and sample sizes for the specified producer’s risk and consumer’s risk. Implementation of the algorithm has been illustrated numerically for different choices of quantities involved in a double sampling plan   

  1. Fast alignment algorithm of inertial fixed frame in quasi-static environment%伪静态环境凝固惯性系快速对准算法

    Institute of Scientific and Technical Information of China (English)

    刘学俊; 李永涛

    2014-01-01

    惯性导航系统在开始工作时需要进行初始对准从而确定初始姿态。提出了一种与经典的对准算法如陀螺罗经或卡尔曼滤波技术不同的凝固惯性系快速(IF3)对准算法。可在任意初始误差条件下进行对准,且能适应高频扰动环境。将姿态矩阵分解成地球自转、惯性速率和对准矩阵三个部分。对准矩阵依靠两组分别处于不同惯性系里的观测向量确定。通过采用前置平滑滤波、层叠采样和二重积分技术,对准精度显著改善。在载车发动机怠速运行和人员上下车扰动条件下,60 s对准误差优于1 mil (1),180 s对准误差优于0.6 mil(1),300 s对准误差优于0.4 mil(1)。实验结果证明了IF3对准算法的快速性、准确性和鲁棒性。%An initial alignment is needed to determine the initial attitude when inertial navigation system(INS) start to work. In this paper, an inertial fixed frame fast(IF3) alignment algorithm is devised, in contrast to the classic alignment algorithms, such as gyrocompassing and Kalman filtering techniques. Unlike classic techniques, the IF3 alignment is effective with any initial attitude error, as well as high frequency vibrations. The estimator is based on decomposing the attitude matrix into separate earth motion, inertial rate, and alignment matrix. And the alignment matrix is determined by two sets of observation vectors in different inertial fixed frames. By smooth pre-filtering, interleaved sampling and double integrating the observation vectors, it is shown that the precision of attitude estimates is improved. The IF3 alignment heading error is less than 1 mil(1) within 60 s, 0.6 mil(1) within 180 s, and 0.4 mil(1) within 300 s under the condition that the vehicle engine is running at idle and intended introducing the perturbation caused by a person’s getting on and off the vehicle. Experiment tests favorably demonstrate its rapidness, accuracy and

  2. Determining the Cost-Savings Threshold and Alignment Accuracy of Patient-Specific Instrumentation in Total Ankle Replacements.

    Science.gov (United States)

    Hamid, Kamran S; Matson, Andrew P; Nwachukwu, Benedict U; Scott, Daniel J; Mather, Richard C; DeOrio, James K

    2017-01-01

    Traditional intraoperative referencing for total ankle replacements (TARs) involves multiple steps and fluoroscopic guidance to determine mechanical alignment. Recent adoption of patient-specific instrumentation (PSI) allows for referencing to be determined preoperatively, resulting in less steps and potentially decreased operative time. We hypothesized that usage of PSI would result in decreased operating room time that would offset the additional cost of PSI compared with standard referencing (SR). In addition, we aimed to compare postoperative radiographic alignment between PSI and SR. Between August 2014 and September 2015, 87 patients undergoing TAR were enrolled in a prospectively collected TAR database. Patients were divided into cohorts based on PSI vs SR, and operative times were reviewed. Radiographic alignment parameters were retrospectively measured at 6 weeks postoperatively. Time-driven activity-based costing (TDABC) was used to derive direct costs. Cost vs operative time-savings were examined via 2-way sensitivity analysis to determine cost-saving thresholds for PSI applicable to a range of institution types. Cost-saving thresholds defined the price of PSI below which PSI would be cost-saving. A total of 35 PSI and 52 SR cases were evaluated with no significant differences identified in patient characteristics. Operative time from incision to completion of casting in cases without adjunct procedures was 127 minutes with PSI and 161 minutes with SR ( P cost-savings threshold range at our institution of $863 below which PSI pricing would provide net cost-savings. Two-way sensitivity analysis generated a globally applicable cost-savings threshold model based on institution-specific costs and surgeon-specific time-savings. This study demonstrated equivalent postoperative TAR alignment with PSI and SR referencing systems but with a significant decrease in operative time with PSI. Based on TDABC and associated sensitivity analysis, a cost-savings threshold

  3. Metabolic network alignment in large scale by network compression

    Directory of Open Access Journals (Sweden)

    Ay Ferhat

    2012-03-01

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

  4. Algorithm for Triangulating Visual Landmarks and Determining Their Covariance

    Science.gov (United States)

    2012-01-01

    gyroscopes ........................................ 22 1 1. INTRODUCTION The work described in this report has to do with the problem of vision...IMUs. Because of the small magnitude of random Euler angle errors from even inexpensive gyroscopes , the presented algorithm for triangulation is...gyroscopes9. Silicon-Vibratory MEMs Tactical-grade IFOGs Aviation-Grade Spinning Mass Random gyro rate noise 1 hr/ 0.1 hr/ 0.002 hr/ Random

  5. A computational algorithm for crack determination: The multiple crack case

    Science.gov (United States)

    Bryan, Kurt; Vogelius, Michael

    1992-01-01

    An algorithm for recovering a collection of linear cracks in a homogeneous electrical conductor from boundary measurements of voltages induced by specified current fluxes is developed. The technique is a variation of Newton's method and is based on taking weighted averages of the boundary data. The method also adaptively changes the applied current flux at each iteration to maintain maximum sensitivity to the estimated locations of the cracks.

  6. A Model for Aligning Self-Determination and General Curriculum Standards

    Science.gov (United States)

    Konrad, Moira; Walker, Allison R.; Fowler, Catherine H.; Test, David W.; Wood, Wendy M.

    2008-01-01

    Researchers and practitioners have emphasized the importance of teaching self-determination skills to students with disabilities for more than a decade. One major barrier to teaching self-determination in recent years has been teachers' not knowing how to focus on reading, writing, and mathematics and simultaneously teach self-determination…

  7. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez.

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

  8. An Iterative Fingerprint Enhancement Algorithm Based on Accurate Determination of Orientation Flow

    CERN Document Server

    Dube, Simant

    2009-01-01

    We describe an algorithm to enhance and binarize a fingerprint image. The algorithm is based on accurate determination of orientation flow of the ridges of the fingerprint image by computing variance of the neighborhood pixels around a pixel in different directions. We show that an iterative algorithm which captures the mutual interdependence of orientation flow computation, enhancement and binarization gives very good results on poor quality images.

  9. Robust Interference Alignment Algorithm Based on QR Decomposition%一种基于QR分解的稳健干扰对齐算法

    Institute of Scientific and Technical Information of China (English)

    2015-01-01

    Most interference alignment algorithms assume that the senders know perfect Channel State Information (CSI), but in practical communication systems, due to the channel estimation error, the delayed feedback and so on, the CSI often exists the error. Therefore, a robust interference alignment algorithm is presented based on the QR decomposition. Firstly, the QR is used to preprocess the jointly received signal with the of error for eliminating half of the interference terms. Then this paper minimizes the interference power from the sender to the other receivers to design the pre-coding matrix, and utilizes Minimum Mean Square Error (MMSE) criterion to design the interference suppression matrix. Finally, under the conditions of perfect CSI and error CSI, the simulation results verify that the proposed algorithm improves effectively the performance of the system.%大多数干扰对齐算法都假定发送端可以获得理想的信道状态信息(CSI),由于信道估计误差、反馈延迟等原因,实际通信系统中CSI往往是有误差的。为此,该文提出一种基于QR分解的稳健干扰对齐算法。对含有误差的联合接收信号进行基于 QR 分解的预处理,消除一半有误差的干扰;然后在有误差的等效信道联合矩阵下,充分考虑信道误差和干扰的影响,通过最小化发送端泄漏到非目标接收端的干扰信号功率来设计预编码矩阵,并基于最小均方误差(MMSE)准则来设计干扰抑制矩阵。最后,在理想CSI和误差CSI的情况下,通过实验仿真,证明了该算法有效地提高了系统性能。

  10. Finding local structural similarities among families of unrelated protein structures: a generic non-linear alignment algorithm.

    Science.gov (United States)

    Lehtonen, J V; Denessiouk, K; May, A C; Johnson, M S

    1999-02-15

    We have developed a generic tool for the automatic identification of regions of local structural similarity in unrelated proteins having different folds, as well as for defining more global similarities that result from homologous protein structures. The computer program GENFIT has evolved from the genetic algorithm-based three-dimensional protein structure comparison program GA_FIT. GENFIT, however, can locate and superimpose regions of local structural homology regardless of their position in a pair of structures, the fold topology, or the chain direction. Furthermore, it is possible to restrict the search to a volume centered about a region of interest (e.g., catalytic site, ligand-binding site) in two protein structures. We present a number of examples to illustrate the function of the program, which is a parallel processing implementation designed for distribution to multiple machines over a local network or to run on a single multiprocessor computer.

  11. Alignment of flexible protein structures.

    Science.gov (United States)

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

    2000-01-01

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

  12. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez

    Since December, the muon alignment community has focused on analyzing the data recorded so far in order to produce new DT and CSC Alignment Records for the second reprocessing of CRAFT data. Two independent algorithms were developed which align the DT chambers using global tracks, thus providing, for the first time, a relative alignment of the barrel with respect to the tracker. These results are an important ingredient for the second CRAFT reprocessing and allow, for example, a more detailed study of any possible mis-modelling of the magnetic field in the muon spectrometer. Both algorithms are constructed in such a way that the resulting alignment constants are not affected, to first order, by any such mis-modelling. The CSC chambers have not yet been included in this global track-based alignment due to a lack of statistics, since only a few cosmics go through the tracker and the CSCs. A strategy exists to align the CSCs using the barrel as a reference until collision tracks become available. Aligning the ...

  13. Robust Floor Determination Algorithm for Indoor Wireless Localization Systems under Reference Node Failure

    Directory of Open Access Journals (Sweden)

    Kriangkrai Maneerat

    2016-01-01

    Full Text Available One of the challenging problems for indoor wireless multifloor positioning systems is the presence of reference node (RN failures, which cause the values of received signal strength (RSS to be missed during the online positioning phase of the location fingerprinting technique. This leads to performance degradation in terms of floor accuracy, which in turn affects other localization procedures. This paper presents a robust floor determination algorithm called Robust Mean of Sum-RSS (RMoS, which can accurately determine the floor on which mobile objects are located and can work under either the fault-free scenario or the RN-failure scenarios. The proposed fault tolerance floor algorithm is based on the mean of the summation of the strongest RSSs obtained from the IEEE 802.15.4 Wireless Sensor Networks (WSNs during the online phase. The performance of the proposed algorithm is compared with those of different floor determination algorithms in literature. The experimental results show that the proposed robust floor determination algorithm outperformed the other floor algorithms and can achieve the highest percentage of floor determination accuracy in all scenarios tested. Specifically, the proposed algorithm can achieve greater than 95% correct floor determination under the scenario in which 40% of RNs failed.

  14. An Algorithm for Determining Database Consistency Under the Coles World Assumption

    Institute of Scientific and Technical Information of China (English)

    沈一栋

    1992-01-01

    It is well-known that there are circumstances where applying Reiter's closed world assumption(CWA)will lead to logical inconsistencies.In this paper,a new characterization of the CA consistency is pesented and an algorithm is proposed for determining whether a datalase without function symbols is consistent with the CWA.The algorithm is shown to be efficient.

  15. Determining the Number of Signals in MUSIC Algorithm by CFAR Technique

    Institute of Scientific and Technical Information of China (English)

    XIAGuangrong; LIUXingzhao

    2004-01-01

    A new algorithm based on the CFAR detection technique is proposed to estimate the number of signals in MUSIC method. This algorithm is described in detail and analyzed theoretically in signal detection aspect. Based on the theoretical analysis and Gaussianity test, it is pointed out that the eigenvalues of estimated white noise covariance matrix are Gaussian, and the number of signals in MUSIC algorithm can be determined by an asymptotic CFAR technique. Monte Carlo experiments show that it is efficient. Contrasted to the Minimum description length (MDL) and Akaike information criterion (AIC) algorithms, it is flexible and can describe the detection performance exactly via the false alarm rate.

  16. Direct determination of resonance energy transfer in photolyase: structural alignment for the functional state.

    Science.gov (United States)

    Tan, Chuang; Guo, Lijun; Ai, Yuejie; Li, Jiang; Wang, Lijuan; Sancar, Aziz; Luo, Yi; Zhong, Dongping

    2014-11-13

    Photoantenna is essential to energy transduction in photoinduced biological machinery. A photoenzyme, photolyase, has a light-harvesting pigment of methenyltetrahydrofolate (MTHF) that transfers its excitation energy to the catalytic flavin cofactor FADH¯ to enhance DNA-repair efficiency. Here we report our systematic characterization and direct determination of the ultrafast dynamics of resonance energy transfer from excited MTHF to three flavin redox states in E. coli photolyase by capturing the intermediates formed through the energy transfer and thus excluding the electron-transfer quenching pathway. We observed 170 ps for excitation energy transferring to the fully reduced hydroquinone FADH¯, 20 ps to the fully oxidized FAD, and 18 ps to the neutral semiquinone FADH(•), and the corresponding orientation factors (κ(2)) were determined to be 2.84, 1.53 and 1.26, respectively, perfectly matching with our calculated theoretical values. Thus, under physiological conditions and over the course of evolution, photolyase has adopted the optimized orientation of its photopigment to efficiently convert solar energy for repair of damaged DNA.

  17. Determination of Selection Method in Genetic Algorithm for Land Suitability

    Directory of Open Access Journals (Sweden)

    Irfianti Asti Dwi

    2016-01-01

    Full Text Available Genetic Algoirthm is one alternative solution in the field of modeling optimization, automatic programming and machine learning. The purpose of the study was to compare some type of selection methods in Genetic Algorithm for land suitability. Contribution of this research applies the best method to develop region based horticultural commodities. This testing is done by comparing the three methods on the method of selection, the Roulette Wheel, Tournament Selection and Stochastic Universal Sampling. Parameters of the locations used in the test scenarios include Temperature = 27°C, Rainfall = 1200 mm, hummidity = 30%, Cluster fruit = 4, Crossover Probabiitiy (Pc = 0.6, Mutation Probabilty (Pm = 0.2 and Epoch = 10. The second test epoch incluides location parameters consist of Temperature = 30°C, Rainfall = 2000 mm, Humidity = 35%, Cluster fruit = 5, Crossover Probability (Pc = 0.7, Mutation Probability (Pm = 0.3 and Epoch 10. The conclusion of this study shows that the Roulette Wheel is the best method because it produces more stable and fitness value than the other two methods.

  18. MULTIFREQUENCY ALGORITHMS FOR DETERMINING THE MOISTURE CONTENT OF LIQUID EMULSIONS BY THE METHOD OF RESONANCE DIELCOMETRY

    Directory of Open Access Journals (Sweden)

    A. A. Korobko

    2017-06-01

    Full Text Available Purpose. The main attention is paid to the development and investigation of multifrequency algorithms for the realization of the method of resonance dielcometric measurement of the humidity of emulsions of the type «nonpolar liquid dielectric-water». Multifrequency algorithms take into account the problem of «uncertainty of varieties» and increase the sensitivity of the dielcometric method. Methodology. Multifrequency algorithms are proposed to solve the problem of «uncertainty of varieties» and improve the metrological characteristics of the resonance dielcometric method. The essence of the algorithms is to use a mathematical model of the emulsion and to determine the permittivity of the dehydrated liquid and the emulsion. The task of developing algorithms is to determine and take into account the influence of the parasitic electrical capacitance of the measuring oscillator and the measuring transducer. The essence of the method consists in alternately determining the resonance frequency of the oscillatory circuit with various configurations, which allows to take into account errors from parasitic parameters. The problem of «uncertainty of varieties» is formulated and solved. The metrological characteristics of the resonance dielcometric method are determined using algorithms. Results. Frequency domains of application of mathematical model of an emulsion are defined. An algorithm in a general form with four frequencies suitable for practical implementation in dielcometric resonance measurements is developed. Partial algorithms with three and two frequencies are developed. The systematic values of simulation errors in the emulsion in the microwave range are determined. Generalized metrological characteristics are obtained. The ways of increasing the sensitivity of the dielcometric method are determined. The problem of «uncertainty of varieties» was solved. Experimental data on determination of humidity for the developed algorithms are

  19. CORE: Common Region Extension Based Multiple Protein Structure Alignment for Producing Multiple Solution

    Institute of Scientific and Technical Information of China (English)

    Woo-Cheol Kim; Sanghyun Park; Jung-Im Won

    2013-01-01

    Over the past several decades,biologists have conducted numerous studies examining both general and specific functions of proteins.Generally,if similarities in either the structure or sequence of amino acids exist for two proteins,then a common biological function is expected.Protein function is determined primarily based on the structure rather than the sequence of amino acids.The algorithm for protein structure alignment is an essential tool for the research.The quality of the algorithm depends on the quality of the similarity measure that is used,and the similarity measure is an objective function used to determine the best alignment.However,none of existing similarity measures became golden standard because of their individual strength and weakness.They require excessive filtering to find a single alignment.In this paper,we introduce a new strategy that finds not a single alignment,but multiple alignments with different lengths.This method has obvious benefits of high quality alignment.However,this novel method leads to a new problem that the running time for this method is considerably longer than that for methods that find only a single alignment.To address this problem,we propose algorithms that can locate a common region (CORE) of multiple alignment candidates,and can then extend the CORE into multiple alignments.Because the CORE can be defined from a final alignment,we introduce CORE* that is similar to CORE and propose an algorithm to identify the CORE*.By adopting CORE* and dynamic programming,our proposed method produces multiple alignments of various lengths with higher accuracy than previous methods.In the experiments,the alignments identified by our algorithm are longer than those obtained by TM-align by 17% and 15.48%,on average,when the comparison is conducted at the level of super-family and fold,respectively.

  20. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    Z. Szillasi and G. Gomez.

    2013-01-01

    When CMS is opened up, major components of the Link and Barrel Alignment systems will be removed. This operation, besides allowing for maintenance of the detector underneath, is needed for making interventions that will reinforce the alignment measurements and make the operation of the alignment system more reliable. For that purpose and also for their general maintenance and recalibration, the alignment components will be transferred to the Alignment Lab situated in the ISR area. For the track-based alignment, attention is focused on the determination of systematic uncertainties, which have become dominant, since now there is a large statistics of muon tracks. This will allow for an improved Monte Carlo misalignment scenario and updated alignment position errors, crucial for high-momentum muon analysis such as Z′ searches.

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

    Directory of Open Access Journals (Sweden)

    M. Mueller

    2016-06-01

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

  2. Determination of Steering Wheel Angles during CAR Alignment by Image Analysis Methods

    Science.gov (United States)

    Mueller, M.; Voegtle, T.

    2016-06-01

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

  3. Factors determining cervical spine sagittal balance in asymptomatic adults: correlation with spinopelvic balance and thoracic inlet alignment.

    Science.gov (United States)

    Lee, Sang-Hun; Son, Eun-Seok; Seo, Eun-Min; Suk, Kyung-Soo; Kim, Ki-Tack

    2015-04-01

    Based on the previous studies, cervical lordosis (CL) is a parameter influenced by thoracic kyphosis (TK); however, the correlations still remain unclear. Few studies have analyzed the correlations between the cervical spine lordosis and global spinopelvic balance. To date, there has been no study focused on the factors determining cervical spine sagittal balance. Seventy-seven asymptomatic volunteers without the history of symptoms related to whole spine. Statistical significance of correlations of radiographic parameters on cervical spine and whole-spine standing lateral radiograph. To analyze the factors determining cervical spine sagittal balance, including global spinopelvic balance and thoracic inlet (TI) alignment in asymptomatic adults. A prospective radiographic study. Cervical and whole-spine standing lateral radiographs were taken to analyze the following parameters: spinopelvic parameters pelvic incidence (PI), sacral slope (SS), lumbar lordosis (LL), and TK; TI parameters thoracic inlet angle (TIA) and T1 slope; and cervical spine parameters C0-C2, C2-C7, and C0-C7 angles and cervical tilting. Statistical analysis was performed using the Pearson correlation coefficients and multiple regression analysis. All the parameters showed a normal distribution. There was a significant sequential linkage between PI and SS (r=0.653), SS and LL (r=0.807), LL and TK (r=-0.516), and TK and C0-C7 angle (r=-0.322). There was a significant relationship between TK and T1 slope (r=0.351) but no significant relationship between TK and TIA. There were significant sequential relationships between TIA and T1 slope (r=0.694), T1 slope and C2-C7 angle (r=-0.624), and C2-C7 and C0-C2 angles (r=-0.547). T1 slope was the only parameter that demonstrated a significant correlation with both SP and TI parameters. A linear regression model showed that T1 slope had a stronger relationship with TIA (r=0.694) than TK (r=0.351). T1 slope was a key factor determining cervical spine

  4. Local Linear Embedding Algorithm with Adaptively Determining Neighborhood

    Directory of Open Access Journals (Sweden)

    Zhenduo Wang

    2014-06-01

    Full Text Available Local linear embedding is a kind of very competitive nonlinear dimensionality reduction technique with good representational capacity for a broader range of manifolds and high computational efficiency. However, it is based on the assumption that the whole data manifolds are evenly distributed so that it determines the neighborhood for all points with the same neighborhood size. Accordingly, it fails to nicely deal with most real problems that are unevenly distributed. This paper presents a new approach that takes the general conceptual framework of Hessian locally linear embedding so as to guarantee its correctness in the setting of local isometry for an open connected subset, but dynamically determines the local neighborhood size for each point. This approach estimates the approximate geodesic distance between any two points by the shortest path in the local neighborhood graph, and then determines the neighborhood size for each point by using the relationship between its local estimated geodesic distance matrix and local Euclidean distance matrix. This approach has clear geometry intuition as well as the better performance and stability. It deals with the sparsely sampled or noise contaminated data sets that are often unevenly distributed. The conducted experiments on benchmark data sets validate the proposed approach

  5. RNA Structural Alignments, Part I

    DEFF Research Database (Denmark)

    Havgaard, Jakob Hull; Gorodkin, Jan

    2014-01-01

    Simultaneous alignment and secondary structure prediction of RNA sequences is often referred to as "RNA structural alignment." A class of the methods for structural alignment is based on the principles proposed by Sankoff more than 25 years ago. The Sankoff algorithm simultaneously folds and alig...... the methods based on the Sankoff algorithm. All the practical implementations of the algorithm use heuristics to make them run in reasonable time and memory. These heuristics are also described in this chapter.......Simultaneous alignment and secondary structure prediction of RNA sequences is often referred to as "RNA structural alignment." A class of the methods for structural alignment is based on the principles proposed by Sankoff more than 25 years ago. The Sankoff algorithm simultaneously folds and aligns...... two or more sequences. The advantage of this algorithm over those that separate the folding and alignment steps is that it makes better predictions. The disadvantage is that it is slower and requires more computer memory to run. The amount of computational resources needed to run the Sankoff algorithm...

  6. Mobile and replicated alignment of arrays in data-parallel programs

    Science.gov (United States)

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

    1993-01-01

    When a data-parallel language like FORTRAN 90 is compiled for a distributed-memory machine, aggregate data objects (such as arrays) are distributed across the processor memories. The mapping determines the amount of residual communication needed to bring operands of parallel operations into alignment with each other. A common approach is to break the mapping into two stages: first, an alignment that maps all the objects to an abstract template, and then a distribution that maps the template to the processors. We solve two facets of the problem of finding alignments that reduce residual communication: we determine alignments that vary in loops, and objects that should have replicated alignments. We show that loop-dependent mobile alignment is sometimes necessary for optimum performance, and we provide algorithms with which a compiler can determine good mobile alignments for objects within do loops. We also identify situations in which replicated alignment is either required by the program itself (via spread operations) or can be used to improve performance. We propose an algorithm based on network flow that determines which objects to replicate so as to minimize the total amount of broadcast communication in replication. This work on mobile and replicated alignment extends our earlier work on determining static alignment.

  7. Determining competency in the sexually assaulted patient: a decision algorithm.

    Science.gov (United States)

    Martin, Sharolyn; Housley, Connie; Raup, Glenn

    2010-07-01

    The determination of competency for decisions regarding one's care is of great individual importance as it represents a basic human right. Often, in Emergency Nursing, we are presented with situations that require difficult decisions that must be made in a brief time frame. The role of the Sexual Assault Nurse Examiner (SANE) in providing assessment and care to victims of assault is crucial to initiating the restoration of health and dignity of the patient in a tragic set of circumstances. Patients who present for SANE examination may have issues surrounding their capacity to make competent decisions regarding their assessment and care, further complicating an already tenuous situation. SANE nurses should be knowledgeable concerning competency and care issues and utilize a methodical process to guide their decision-making.

  8. 基于联邦网络的传递对准滤波补偿算法%Transfer Alignment Filtering Compensating Algorithm Based on Federal Neural Network

    Institute of Scientific and Technical Information of China (English)

    赵剡; 王纪南; 解春明

    2012-01-01

    针对空中环境各种干扰因素对空空导弹传递对准(TA)滤波的影响,提出一种基于联邦网络的补偿算法.将干扰误差考虑为量测输入纳入滤波系统,改进标准Kalman滤波结构.将补偿神经网络设计成联邦结构,两个子系统分别用于训练量测输入估计误差、输出层权值误差和隐层权值误差.推导了联邦网络的训练算法并对算法进行了稳定性证明,保证了网络在结构上计算量小,系统反馈能力强,能够对干扰误差进行有效在线预测,辅助改进Kalman滤波器对失准角进行精确估计.仿真比较实验验证了该算法能够在不需任何先验信息的条件下,及时适应对准环境,预测校正干扰误差,滤波收敛快、精度高,适合空空导弹在具体设备和环境条件下的快速精确传递对准.%Focusing on the influence of various disturbing sources under air environment on transfer alignment (TA), a compensating algorithm based on federal neural network was put forward. Firstly, standard Kalman filtering structure was improved by regarding disturbing errors as measurement input. Then, the neural network was designed to form federal structure with two subsystems, which were used to train measurement input estimating error, output layer weight error and hidden layer weight error. Further, the training algorithm of the federal neural network was deduced and its stability was proved, which ensured low computing load and strong feedback capability. The online disturbing errors were efficiently predicted and aided to modified Kalman filter for accurate estimation of misalignment. Results of simulation experiments validate that, without knowing any priori information, the proposed algorithm could timely adapt to TA environment, predict and rectify disturbing errors, achieve fast convergence and high accuracy. It is feasible for air-to-air missile to implement rapid and high accuracy TA under hard air environment with different apparatus.

  9. Improved Collision Detection Algorithm Based on Axis- Aligned Bounding Box%基于改进轴向包围盒的碰撞检测算法

    Institute of Scientific and Technical Information of China (English)

    孙毅刚; 段晓晔; 张红颖

    2011-01-01

    Airport emergency rescue is an important field of civil aviation, and the emergency rescue in the virtual scene can save resources largely.In order to improve the authenticity and accuracy of collision detection in the virtual scene, this paper proposed a collision deteetion algorithm based on feature - triangle.By adding the feature elements of vertex, edges and face in the triangle, feature -triangle was formed to solve the issue of queries in the triangulated model; then axis - aligned bounding box combined with feature - triangle was used to complete collision detection,and accurate intersection calculation was performed in the final stage of the algorithm to provide more collision informarion for the collision response.Experimental results show that the proposed algorithm can save time and has better performance.%研究机场应急救援是民航领域的问题.为防止机场地面车辆拥堵,要求在虚拟场景下的应急演练可全方位测试系统.为增强虚拟演练场景中碰撞检测的真实性与精确性,提出了一种基于特征三角形的碰撞检测算法.在基于三角形的模型中,通过在三角形中添加特征元素(点、边、面)形成特征三角形,利用特征三角形可以有效解决重复查询;通过轴向包围盒结合特征三角形,更好地完成碰撞检测,最后进行精确求交计算,为碰撞响应提供更多的碰撞信息.实验结果表明,算法可以缩短计算时间,提高检测精度,具有实际指导价值.

  10. Software alignment of the LHCb inner tracker sensors

    Energy Technology Data Exchange (ETDEWEB)

    Maciuc, Florin

    2009-04-20

    This work uses the Millepede linear alignment method, which is essentially a {chi}{sup 2} minimization algorithm, to determine simultaneously between 76 and 476 alignment parameters and several million track parameters. For the case of non-linear alignment models, Millepede is embedded in a Newton-Raphson iterative procedure. If needed a more robust approach is provided by adding quasi-Newton steps which minimize the approximate {chi}{sup 2} model function. The alignment apparatus is applied to locally align the LHCb's Inner Tracker sensors in an a priori fixed system of coordinate. An analytic measurement model was derived as function of track parameters and alignment parameters, for the two cases: null and nonnull magnetic field. The alignment problem is equivalent to solving a linear system of equations, and usually a matrix inversion is required. In general, as consequence of global degrees of freedom or poorly constrained modes, the alignment matrix is singular or near-singular. The global degrees of freedom are obtained: directly from {chi}{sup 2} function invariant transformations, and in parallel by an alignment matrix diagonalization followed by an extraction of the least constrained modes. The procedure allows to properly de ne the local alignment of the Inner Tracker. Using Monte Carlo data, the outlined procedure reconstructs the position of the IT sensors within micrometer precision or better. For rotations equivalent precision was obtained. (orig.)

  11. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    Gervasio Gomez

    The main progress of the muon alignment group since March has been in the refinement of both the track-based alignment for the DTs and the hardware-based alignment for the CSCs. For DT track-based alignment, there has been significant improvement in the internal alignment of the superlayers inside the DTs. In particular, the distance between superlayers is now corrected, eliminating the residual dependence on track impact angles, and good agreement is found between survey and track-based corrections. The new internal geometry has been approved to be included in the forthcoming reprocessing of CRAFT samples. The alignment of DTs with respect to the tracker using global tracks has also improved significantly, since the algorithms use the latest B-field mapping, better run selection criteria, optimized momentum cuts, and an alignment is now obtained for all six degrees of freedom (three spatial coordinates and three rotations) of the aligned DTs. This work is ongoing and at a stage where we are trying to unders...

  12. Migration and alignment of spherical particles in sheared viscoelastic suspensions. A quantitative determination of the flow-induced self-assembly kinetics.

    Science.gov (United States)

    Pasquino, Rossana; Panariello, Daniele; Grizzuti, Nino

    2013-03-15

    Flow-Induced Self-Assembly (FISA) is the flow-driven formation of ordered structures in complex fluids. In this paper the effect of shear flow on the microstructure formation of dilute sphere suspensions in a viscoelastic fluid has been studied experimentally by optical microscopy techniques. The system is formed by Polymethylmethacrylate beads suspended in 20 wt.% aqueous solutions of Hydroxypropylcellulose at volume fractions ranging between 0.1% and 1.0%. Experiments show that, under the action of flow, beads migrate from the bulk to the shear walls, there forming strings aligned along the flow direction. Strings grow with time eventually reaching a steady-state final length. The alignment kinetics have been quantified by means of an alignment factor, which is a measure of the average length of the strings. The experimental results indicate that both shear rate and particle concentration are relevant factors in determining the alignment factor kinetics. In particular, it is shown that, upon increasing shear rate, strings grow both faster and longer. As a consequence, the characteristic time of the overall alignment process remains roughly constant. It is also shown that an increase in particle volume fraction determines effects similar to an increase of shear rate.

  13. SINS Alignment Algorithm for Marching Vehicles with the Aid of Distance-Transfer-Unit (DTU)%一种里程计辅助车载捷联惯导行进间对准方法

    Institute of Scientific and Technical Information of China (English)

    陈鸿跃; 孙谦; 刘宇航

    2013-01-01

    提出一种车载捷联惯导行进间对准方法。以里程计信息为辅助,将行进间对准过程分为粗对准和精对准,以惯性坐标系作为捷联惯导解算的参考基准并借助里程计信息进行粗对准,采用10状态Kalman滤波器进行精对准,观测量采用捷联惯导解算的速度与里程计解算得到的速度之差。进行仿真试验和实车试验,试验结果表明:该方法实现了行进间初始对准,兼容静基座及晃动基座初始对准,对行车路线及行进方式不做要求,捷联惯导在25 min内实现了和静基座对准相同的精度,对准精度与对准的时间正相关,对准时间越长对准精度越高。%A SINS alignment algorithm for marching vehicles was presented. Alignment process was parted into coarse alignment and precise alignment. Coarse alignment was achieved in the inertial coordinate system with the aid of distance-transfer-unit. Precise alignment was achieved through Kalman filter with ten states. Then the difference between the velocities obtained respectively from the inertial coordinate system and the DTU was observed. By simulation experiments and real vehicle tests, alignment for marching vehicles was realized both in the static and swaying base conditions. When driving route or mode is not limited, SINS achieved an alignment precision same as static base alignment in twenty-five minutes. Precision of alignment was positively relevant to the time of alignment. The longer the alignment took, the higher the precision was.

  14. Performance comparison of attitude determination, attitude estimation, and nonlinear observers algorithms

    Science.gov (United States)

    MOHAMMED, M. A. SI; BOUSSADIA, H.; BELLAR, A.; ADNANE, A.

    2017-01-01

    This paper presents a brief synthesis and useful performance analysis of different attitude filtering algorithms (attitude determination algorithms, attitude estimation algorithms, and nonlinear observers) applied to Low Earth Orbit Satellite in terms of accuracy, convergence time, amount of memory, and computation time. This latter is calculated in two ways, using a personal computer and also using On-board computer 750 (OBC 750) that is being used in many SSTL Earth observation missions. The use of this comparative study could be an aided design tool to the designer to choose from an attitude determination or attitude estimation or attitude observer algorithms. The simulation results clearly indicate that the nonlinear Observer is the more logical choice.

  15. Biased Random-Key Genetic Algorithms for the Winner Determination Problem in Combinatorial Auctions.

    Science.gov (United States)

    de Andrade, Carlos Eduardo; Toso, Rodrigo Franco; Resende, Mauricio G C; Miyazawa, Flávio Keidi

    2015-01-01

    In this paper we address the problem of picking a subset of bids in a general combinatorial auction so as to maximize the overall profit using the first-price model. This winner determination problem assumes that a single bidding round is held to determine both the winners and prices to be paid. We introduce six variants of biased random-key genetic algorithms for this problem. Three of them use a novel initialization technique that makes use of solutions of intermediate linear programming relaxations of an exact mixed integer linear programming model as initial chromosomes of the population. An experimental evaluation compares the effectiveness of the proposed algorithms with the standard mixed linear integer programming formulation, a specialized exact algorithm, and the best-performing heuristics proposed for this problem. The proposed algorithms are competitive and offer strong results, mainly for large-scale auctions.

  16. Software alignment of the LHCb Outer Tracker chambers

    Energy Technology Data Exchange (ETDEWEB)

    Deissenroth, Marc

    2010-04-21

    This work presents an alignment algorithm that was developed to precisely determine the positions of the LHCb Outer Tracker detector elements. The algorithm is based on the reconstruction of tracks and exploits that misalignments of the detector change the residual between a measured hit and the reconstructed track. It considers different levels of granularities of the Outer Tracker geometry and fully accounts for correlations of all elements which are imposed by particle trajectories. In extensive tests, simulated shifts and rotations for different levels of the detector granularity have been used as input to the track reconstruction and alignment procedure. With about 260 000 tracks the misalignments are recovered with a statistical precision of O(10 - 100 {mu}m) for the translational degrees of freedom and of O(10{sup -2} - 10{sup -1} mrad) for rotations. A study has been performed to determine the impact of Outer Tracker misalignments on the performance of the track reconstruction algorithms. It shows that the achieved statistical precision does not decrease the track reconstruction performance in a significant way. During the commissioning of the LHCb detector, cosmic ray muon events have been collected. The events have been analysed and used for the first alignment of the 216 Outer Tracker modules. The module positions have been determined within {proportional_to} 90 {mu}m. The developed track based alignment algorithm has demonstrated its reliability and is one of the core algorithms which are used for the precise determination of the positions of the LHCb Outer Tracker elements. (orig.)

  17. A New Hybrid Algorithm to Solve Winner Determination Problem in Multiunit Double Internet Auction

    OpenAIRE

    Mourad Ykhlef; Reem Alqifari

    2015-01-01

    Solving winner determination problem in multiunit double auction has become an important E-business task. The main issue in double auction is to improve the reward in order to match the ideal prices and quantity and make the best profit for sellers and buyers according to their bids and predefined quantities. There are many algorithms introduced for solving winner in multiunit double auction. Conventional algorithms can find the optimal solution but they take a long time, particularly when th...

  18. [Effect of algorithms for calibration set selection on quantitatively determining asiaticoside content in Centella total glucosides by near infrared spectroscopy].

    Science.gov (United States)

    Zhan, Xue-yan; Zhao, Na; Lin, Zhao-zhou; Wu, Zhi-sheng; Yuan, Rui-juan; Qiao, Yan-jiang

    2014-12-01

    The appropriate algorithm for calibration set selection was one of the key technologies for a good NIR quantitative model. There are different algorithms for calibration set selection, such as Random Sampling (RS) algorithm, Conventional Selection (CS) algorithm, Kennard-Stone(KS) algorithm and Sample set Portioning based on joint x-y distance (SPXY) algorithm, et al. However, there lack systematic comparisons between two algorithms of the above algorithms. The NIR quantitative models to determine the asiaticoside content in Centella total glucosides were established in the present paper, of which 7 indexes were classified and selected, and the effects of CS algorithm, KS algorithm and SPXY algorithm for calibration set selection on the accuracy and robustness of NIR quantitative models were investigated. The accuracy indexes of NIR quantitative models with calibration set selected by SPXY algorithm were significantly different from that with calibration set selected by CS algorithm or KS algorithm, while the robustness indexes, such as RMSECV and |RMSEP-RMSEC|, were not significantly different. Therefore, SPXY algorithm for calibration set selection could improve the predicative accuracy of NIR quantitative models to determine asiaticoside content in Centella total glucosides, and have no significant effect on the robustness of the models, which provides a reference to determine the appropriate algorithm for calibration set selection when NIR quantitative models are established for the solid system of traditional Chinese medcine.

  19. Real-time Imaging Orientation Determination System to Verify Imaging Polarization Navigation Algorithm

    Directory of Open Access Journals (Sweden)

    Hao Lu

    2016-01-01

    Full Text Available Bio-inspired imaging polarization navigation which can provide navigation information and is capable of sensing polarization information has advantages of high-precision and anti-interference over polarization navigation sensors that use photodiodes. Although all types of imaging polarimeters exist, they may not qualify for the research on the imaging polarization navigation algorithm. To verify the algorithm, a real-time imaging orientation determination system was designed and implemented. Essential calibration procedures for the type of system that contained camera parameter calibration and the inconsistency of complementary metal oxide semiconductor calibration were discussed, designed, and implemented. Calibration results were used to undistort and rectify the multi-camera system. An orientation determination experiment was conducted. The results indicated that the system could acquire and compute the polarized skylight images throughout the calibrations and resolve orientation by the algorithm to verify in real-time. An orientation determination algorithm based on image processing was tested on the system. The performance and properties of the algorithm were evaluated. The rate of the algorithm was over 1 Hz, the error was over 0.313°, and the population standard deviation was 0.148° without any data filter.

  20. Comparison between summing-up algorithms to determine areas of small peaks on high baselines

    Science.gov (United States)

    Shi, Quanlin; Zhang, Jiamei; Chang, Yongfu; Qian, Shaojun

    2005-12-01

    It is found that the minimum detectable activity (MDA) has a same tendency as the relative standard deviation (RSD) and a particular application is characteristic of the ratio of the peak area to the baseline height. Different applications need different algorithms to reduce the RSD of peak areas or the MDA of potential peaks. A model of Gaussian peaks superposed on linear baselines is established to simulate the multichannel spectrum and summing-up algorithms such as total peak area (TPA), and Covell and Sterlinski are compared to find the most appropriate algorithm for different applications. The results show that optimal Covell and Sterlinski algorithms will yield MDA or RSD half lower than TPA when the areas of small peaks on high baselines are to be determined. The conclusion is proved by experiment.

  1. Algorithm to determine electrical submersible pump performance considering temperature changes for viscous crude oils

    Energy Technology Data Exchange (ETDEWEB)

    Valderrama, A. [Petroleos de Venezuela, S.A., Distrito Socialista Tecnologico (Venezuela); Valencia, F. [Petroleos de Venezuela, S.A., Instituto de Tecnologia Venezolana para el Petroleo (Venezuela)

    2011-07-01

    In the heavy oil industry, electrical submersible pumps (ESPs) are used to transfer energy to fluids through stages made up of one impeller and one diffuser. Since liquid temperature increases through the different stages, viscosity might change between the inlet and outlet of the pump, thus affecting performance. The aim of this research was to create an algorithm to determine ESPs' performance curves considering temperature changes through the stages. A computational algorithm was developed and then compared with data collected in a laboratory with a CG2900 ESP. Results confirmed that when the fluid's viscosity is affected by the temperature changes, the stages of multistage pump systems do not have the same performance. Thus the developed algorithm could help production engineers to take viscosity changes into account and optimize the ESP design. This study developed an algorithm to take into account the fluid viscosity changes through pump stages.

  2. Distributed Interference Alignment with Low Overhead

    CERN Document Server

    Ma, Yanjun; Chen, Rui

    2011-01-01

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

  3. GraphAlignment: Bayesian pairwise alignment of biological networks

    Directory of Open Access Journals (Sweden)

    Kolář Michal

    2012-11-01

    Full Text Available Abstract Background With increased experimental availability and accuracy of bio-molecular networks, tools for their comparative and evolutionary analysis are needed. A key component for such studies is the alignment of networks. Results We introduce the Bioconductor package GraphAlignment for pairwise alignment of bio-molecular networks. The alignment incorporates information both from network vertices and network edges and is based on an explicit evolutionary model, allowing inference of all scoring parameters directly from empirical data. We compare the performance of our algorithm to an alternative algorithm, Græmlin 2.0. On simulated data, GraphAlignment outperforms Græmlin 2.0 in several benchmarks except for computational complexity. When there is little or no noise in the data, GraphAlignment is slower than Græmlin 2.0. It is faster than Græmlin 2.0 when processing noisy data containing spurious vertex associations. Its typical case complexity grows approximately as O(N2.6. On empirical bacterial protein-protein interaction networks (PIN and gene co-expression networks, GraphAlignment outperforms Græmlin 2.0 with respect to coverage and specificity, albeit by a small margin. On large eukaryotic PIN, Græmlin 2.0 outperforms GraphAlignment. Conclusions The GraphAlignment algorithm is robust to spurious vertex associations, correctly resolves paralogs, and shows very good performance in identification of homologous vertices defined by high vertex and/or interaction similarity. The simplicity and generality of GraphAlignment edge scoring makes the algorithm an appropriate choice for global alignment of networks.

  4. Low-cost attitude determination system using an extended Kalman filter (EKF) algorithm

    Science.gov (United States)

    Esteves, Fernando M.; Nehmetallah, Georges; Abot, Jandro L.

    2016-05-01

    Attitude determination is one of the most important subsystems in spacecraft, satellite, or scientific balloon mission s, since it can be combined with actuators to provide rate stabilization and pointing accuracy for payloads. In this paper, a low-cost attitude determination system with a precision in the order of arc-seconds that uses low-cost commercial sensors is presented including a set of uncorrelated MEMS gyroscopes, two clinometers, and a magnetometer in a hierarchical manner. The faster and less precise sensors are updated by the slower, but more precise ones through an Extended Kalman Filter (EKF)-based data fusion algorithm. A revision of the EKF algorithm fundamentals and its implementation to the current application, are presented along with an analysis of sensors noise. Finally, the results from the data fusion algorithm implementation are discussed in detail.

  5. Determination of Activation Functions in A Feedforward Neural Network by using Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Oğuz ÜSTÜN

    2009-03-01

    Full Text Available In this study, activation functions of all layers of the multilayered feedforward neural network have been determined by using genetic algorithm. The main criteria that show the efficiency of the neural network is to approximate to the desired output with the same number nodes and connection weights. One of the important parameter to determine this performance is to choose a proper activation function. In the classical neural network designing, a network is designed by choosing one of the generally known activation function. In the presented study, a table has been generated for the activation functions. The ideal activation function for each node has been chosen from this table by using the genetic algorithm. Two dimensional regression problem clusters has been used to compare the performance of the classical static neural network and the genetic algorithm based neural network. Test results reveal that the proposed method has a high level approximation capacity.

  6. Determination of components of mixed color solutions by fluorescence spectroscopy combined with calibration algorithms.

    Science.gov (United States)

    Zhu, Chun; Li, Run; Que, Li-Zhi; Zhu, Tuo; Chen, Guo-Qing

    2014-07-01

    The three-dimensional spectra of mixed solutions of allure red, sunset yellow and brilliant blue were obtained. Then the three synthetic food colors were determined by parallel factor analysis (PARAFAC) and alternating trilinear decomposition (ATLD) algorithms, respectively. The component number of model is three by core-consistency diagnostic. The average recoveries of allure red, sunset yellow and brilliant blue obtained by PARAFAC were 98.75% +/- 8.9%, 97.22% +/- 2.9% and 99.00% +/- 2.9% and those by ATLD algorithm were 99.78% +/- 5.9%, 92.52% +/- 5.5% and 97.23% +/- 5.8%, respectively. Results show that both of the algorithms can be used in direct and rapid determination of multi-components of mixtures. From further comparison, the PARAFAC is more stable and advantageous.

  7. A Distributed Algorithm for Determining Minimal Covers of Acyclic Database Schemes

    Institute of Scientific and Technical Information of China (English)

    叶新铭

    1994-01-01

    Acyclic databases possess several desirable properties for their design and use.A distributed algorithm is proposed for determining a minimal cover of an alpha-,beta-,gamma-,or Berge-acyclic database scheme over a set of attributes in a distributed environment.

  8. First Attempt of Orbit Determination of SLR Satellites and Space Debris Using Genetic Algorithms

    Science.gov (United States)

    Deleflie, F.; Coulot, D.; Descosta, R.; Fernier, A.; Richard, P.

    2013-08-01

    We present an orbit determination method based on genetic algorithms. Contrary to usual estimation methods mainly based on least-squares methods, these algorithms do not require any a priori knowledge of the initial state vector to be estimated. These algorithms can be applied when a new satellite is launched or for uncatalogued objects that appear in images obtained from robotic telescopes such as the TAROT ones. We show in this paper preliminary results obtained from an SLR satellite, for which tracking data acquired by the ILRS network enable to build accurate orbital arcs at a few centimeter level, which can be used as a reference orbit ; in this case, the basic observations are made up of time series of ranges, obtained from various tracking stations. We show as well the results obtained from the observations acquired by the two TAROT telescopes on the Telecom-2D satellite operated by CNES ; in that case, the observations are made up of time series of azimuths and elevations, seen from the two TAROT telescopes. The method is carried out in several steps: (i) an analytical propagation of the equations of motion, (ii) an estimation kernel based on genetic algorithms, which follows the usual steps of such approaches: initialization and evolution of a selected population, so as to determine the best parameters. Each parameter to be estimated, namely each initial keplerian element, has to be searched among an interval that is preliminary chosen. The algorithm is supposed to converge towards an optimum over a reasonable computational time.

  9. Derivation and Testing of Computer Algorithms for Automatic Real-Time Determination of Space Vehicle Potentials in Various Plasma Environments

    Science.gov (United States)

    1988-05-31

    COMPUTER ALGORITHMS FOR AUTOMATIC REAL-TIME DETERMINATION OF SPACE VEHICLE POTENTIALS IN VARIOUS PLASMA ENVIRONMENTS May 31, 1988 Stanley L. Spiegel...crrnaion DiviSiofl 838 12 2 DERIVATION AND TESTING OF COMPUTER ALGORITHMS FOR AUTOMATIC REAL-TIME DETERMINATION OF SPACE VEHICLE POTENTIALS IN VARIOUS...S.L., "Derivation and testing of computer algorithms for automatic real time determination of space vehicle poteuatials in various plasma

  10. Orbit IMU alignment: Error analysis

    Science.gov (United States)

    Corson, R. W.

    1980-01-01

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

  11. Group Based Interference Alignment

    CERN Document Server

    Ma, Yanjun; Chen, Rui; Yao, Junliang

    2010-01-01

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

  12. Improved Monkey-King Genetic Algorithm for Solving Large Winner Determination in Combinatorial Auction

    Science.gov (United States)

    Li, Yuzhong

    Using GA solve the winner determination problem (WDP) with large bids and items, run under different distribution, because the search space is large, constraint complex and it may easy to produce infeasible solution, would affect the efficiency and quality of algorithm. This paper present improved MKGA, including three operator: preprocessing, insert bid and exchange recombination, and use Monkey-king elite preservation strategy. Experimental results show that improved MKGA is better than SGA in population size and computation. The problem that traditional branch and bound algorithm hard to solve, improved MKGA can solve and achieve better effect.

  13. Determination of the effective Young's modulus of vertically aligned carbon nanotube arrays: a simple nanotube-based varactor

    Energy Technology Data Exchange (ETDEWEB)

    Olofsson, Niklas; Eriksson, Anders [Department of Physics, Goeteborg University, SE-41296 Goeteborg (Sweden); Ek-Weis, Johan; Campbell, Eleanor E B [School of Chemistry, Edinburgh University, West Mains Road, Edinburgh EH9 3JJ (United Kingdom); Idda, Tonio, E-mail: eleanor.campbell@ed.ac.u [LAAS-CNRS, 7 Avenue du Colonel Roche, 31077 Toulouse Cedex (France)

    2009-09-23

    The electromechanical properties of arrays of vertically aligned multiwalled carbon nanotubes were studied in a parallel plate capacitor geometry. The electrostatic actuation was visualized using both optical microscopy and scanning electron microscopy, and highly reproducible behaviour was achieved for actuation voltages below the pull-in voltage. The walls of vertically aligned carbon nanotubes behave as solid cohesive units. The effective Young's modulus for the carbon nanotube arrays was determined by comparing the actuation results with the results of electrostatic simulations and was found to be exceptionally low, of the order of 1-10 MPa. The capacitance change and Q-factor were determined by measuring the frequency dependence of the radio-frequency transmission. Capacitance changes of over 20% and Q-factors in the range 100-10 were achieved for a frequency range of 0.2-1.5 GHz.

  14. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    S. Szillasi

    2013-01-01

    The CMS detector has been gradually opened and whenever a wheel became exposed the first operation was the removal of the MABs, the sensor structures of the Hardware Barrel Alignment System. By the last days of June all 36 MABs have arrived at the Alignment Lab at the ISR where, as part of the Alignment Upgrade Project, they are refurbished with new Survey target holders. Their electronic checkout is on the way and finally they will be recalibrated. During LS1 the alignment system will be upgraded in order to allow more precise reconstruction of the MB4 chambers in Sector 10 and Sector 4. This requires new sensor components, so called MiniMABs (pictured below), that have already been assembled and calibrated. Image 6: Calibrated MiniMABs are ready for installation For the track-based alignment, the systematic uncertainties of the algorithm are under scrutiny: this study will enable the production of an improved Monte Carlo misalignment scenario and to update alignment position errors eventually, crucial...

  15. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez

    2012-01-01

      A new muon alignment has been produced for 2012 A+B data reconstruction. It uses the latest Tracker alignment and single-muon data samples to align both DTs and CSCs. Physics validation has been performed and shows a modest improvement in stand-alone muon momentum resolution in the barrel, where the alignment is essentially unchanged from the previous version. The reference-target track-based algorithm using only collision muons is employed for the first time to align the CSCs, and a substantial improvement in resolution is observed in the endcap and overlap regions for stand-alone muons. This new alignment is undergoing the approval process and is expected to be deployed as part of a new global tag in the beginning of December. The pT dependence of the φ-bias in curvature observed in Monte Carlo was traced to a relative vertical misalignment between the Tracker and barrel muon systems. Moving the barrel as a whole to match the Tracker cures this pT dependence, leaving only the &phi...

  16. A Self-Adaptive Fuzzy c-Means Algorithm for Determining the Optimal Number of Clusters

    Science.gov (United States)

    Wang, Zhihao; Yi, Jing

    2016-01-01

    For the shortcoming of fuzzy c-means algorithm (FCM) needing to know the number of clusters in advance, this paper proposed a new self-adaptive method to determine the optimal number of clusters. Firstly, a density-based algorithm was put forward. The algorithm, according to the characteristics of the dataset, automatically determined the possible maximum number of clusters instead of using the empirical rule n and obtained the optimal initial cluster centroids, improving the limitation of FCM that randomly selected cluster centroids lead the convergence result to the local minimum. Secondly, this paper, by introducing a penalty function, proposed a new fuzzy clustering validity index based on fuzzy compactness and separation, which ensured that when the number of clusters verged on that of objects in the dataset, the value of clustering validity index did not monotonically decrease and was close to zero, so that the optimal number of clusters lost robustness and decision function. Then, based on these studies, a self-adaptive FCM algorithm was put forward to estimate the optimal number of clusters by the iterative trial-and-error process. At last, experiments were done on the UCI, KDD Cup 1999, and synthetic datasets, which showed that the method not only effectively determined the optimal number of clusters, but also reduced the iteration of FCM with the stable clustering result. PMID:28042291

  17. Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

    Directory of Open Access Journals (Sweden)

    Skolnick Jeffrey

    2008-12-01

    Full Text Available Abstract Background Protein tertiary structure comparisons are employed in various fields of contemporary structural biology. Most structure comparison methods involve generation of an initial seed alignment, which is extended and/or refined to provide the best structural superposition between a pair of protein structures as assessed by a structure comparison metric. One such metric, the TM-score, was recently introduced to provide a combined structure quality measure of the coordinate root mean square deviation between a pair of structures and coverage. Using the TM-score, the TM-align structure alignment algorithm was developed that was often found to have better accuracy and coverage than the most commonly used structural alignment programs; however, there were a number of situations when this was not true. Results To further improve structure alignment quality, the Fr-TM-align algorithm has been developed where aligned fragment pairs are used to generate the initial seed alignments that are then refined using dynamic programming to maximize the TM-score. For the assessment of the structural alignment quality from Fr-TM-align in comparison to other programs such as CE and TM-align, we examined various alignment quality assessment scores such as PSI and TM-score. The assessment showed that the structural alignment quality from Fr-TM-align is better in comparison to both CE and TM-align. On average, the structural alignments generated using Fr-TM-align have a higher TM-score (~9% and coverage (~7% in comparison to those generated by TM-align. Fr-TM-align uses an exhaustive procedure to generate initial seed alignments. Hence, the algorithm is computationally more expensive than TM-align. Conclusion Fr-TM-align, a new algorithm that employs fragment alignment and assembly provides better structural alignments in comparison to TM-align. The source code and executables of Fr-TM-align are freely downloadable at: http://cssb.biology.gatech.edu/skolnick/files/FrTMalign/.

  18. An Algorithm to Determine Stable Connected Dominating Sets for Mobile Ad hoc Networks using Strong Neighborhoods

    Directory of Open Access Journals (Sweden)

    Natarajan Meghanathan

    2012-05-01

    Full Text Available We propose an algorithm to determine stable connected dominating sets (CDS for mobile ad hoc networks using the notion of strong neighborhood (SN. The SN-CDS algorithm takes an input parameter called the Threshold Neighborhood Distance Ratio (TNDR; for an edge to be part of a strong neighborhood-based topology, the ratio of the physical Euclidean distance between the end nodes of the edge to that of the transmission range per node has to be less than or equal to the TNDR. The algorithm prefers to include nodes (into the SN-CDS in the decreasing order of the number of uncovered strong neighbors until all nodes in the network are covered. We observe the SN-CDS (TNDR < 1 to have a significantly longer lifetime than a maximum density-based CDS (MaxD-CDS with TNDR = 1.0; the tradeoff being a slightly larger CDS Node Size and hop count per path.

  19. Testing of the on-board attitude determination and control algorithms for SAMPEX

    Science.gov (United States)

    McCullough, Jon D.; Flatley, Thomas W.; Henretty, Debra A.; Markley, F. Landis; San, Josephine K.

    1993-02-01

    Algorithms for on-board attitude determination and control of the Solar, Anomalous, and Magnetospheric Particle Explorer (SAMPEX) have been expanded to include a constant gain Kalman filter for the spacecraft angular momentum, pulse width modulation for the reaction wheel command, an algorithm to avoid pointing the Heavy Ion Large Telescope (HILT) instrument boresight along the spacecraft velocity vector, and the addition of digital sun sensor (DSS) failure detection logic. These improved algorithms were tested in a closed-loop environment for three orbit geometries, one with the sun perpendicular to the orbit plane, and two with the sun near the orbit plane - at Autumnal Equinox and at Winter Solstice. The closed-loop simulator was enhanced and used as a truth model for the control systems' performance evaluation and sensor/actuator contingency analysis. The simulations were performed on a VAX 8830 using a prototype version of the on-board software.

  20. A Fast Algorithm for Determining the Existence and Value of Integer Roots of N

    CERN Document Server

    Libby, Vibeke

    2010-01-01

    We show that all perfect odd integer squares not divisible by 3, can be usefully written as sqrt(N) = a + 18p, where the constant a is determined by the basic properties of N. The equation can be solved deterministically by an efficient four step algorithm that is solely based on integer arithmetic. There is no required multiplication or division by multiple digit integers, nor does the algorithm need a seed value. It finds the integer p when N is a perfect square, and certifies N as a non-square when the algorithm terminates without a solution. The number of iterations scales approximately as log(sqrt(N)/2) for square roots. The paper also outlines how one of the methods discussed for squares can be extended to finding an arbitrary root of N. Finally, we present a rule that distinguishes products of twin primes from squares.

  1. Thickness determination in textile material design: dynamic modeling and numerical algorithms

    Science.gov (United States)

    Xu, Dinghua; Ge, Meibao

    2012-03-01

    Textile material design is of paramount importance in the study of functional clothing design. It is therefore important to determine the dynamic heat and moisture transfer characteristics in the human body-clothing-environment system, which directly determine the heat-moisture comfort level of the human body. Based on a model of dynamic heat and moisture transfer with condensation in porous fabric at low temperature, this paper presents a new inverse problem of textile thickness determination (IPTTD). Adopting the idea of the least-squares method, we formulate the IPTTD into a function minimization problem. By means of the finite-difference method, quasi-solution method and direct search method for one-dimensional minimization problems, we construct iterative algorithms of the approximated solution for the IPTTD. Numerical simulation results validate the formulation of the IPTTD and demonstrate the effectiveness of the proposed numerical algorithms.

  2. Determining the Effectiveness of Incorporating Geographic Information Into Vehicle Performance Algorithms

    Energy Technology Data Exchange (ETDEWEB)

    Sera White

    2012-04-01

    This thesis presents a research study using one year of driving data obtained from plug-in hybrid electric vehicles (PHEV) located in Sacramento and San Francisco, California to determine the effectiveness of incorporating geographic information into vehicle performance algorithms. Sacramento and San Francisco were chosen because of the availability of high resolution (1/9 arc second) digital elevation data. First, I present a method for obtaining instantaneous road slope, given a latitude and longitude, and introduce its use into common driving intensity algorithms. I show that for trips characterized by >40m of net elevation change (from key on to key off), the use of instantaneous road slope significantly changes the results of driving intensity calculations. For trips exhibiting elevation loss, algorithms ignoring road slope overestimated driving intensity by as much as 211 Wh/mile, while for trips exhibiting elevation gain these algorithms underestimated driving intensity by as much as 333 Wh/mile. Second, I describe and test an algorithm that incorporates vehicle route type into computations of city and highway fuel economy. Route type was determined by intersecting trip GPS points with ESRI StreetMap road types and assigning each trip as either city or highway route type according to whichever road type comprised the largest distance traveled. The fuel economy results produced by the geographic classification were compared to the fuel economy results produced by algorithms that assign route type based on average speed or driving style. Most results were within 1 mile per gallon ({approx}3%) of one another; the largest difference was 1.4 miles per gallon for charge depleting highway trips. The methods for acquiring and using geographic data introduced in this thesis will enable other vehicle technology researchers to incorporate geographic data into their research problems.

  3. Parallel algorithm for determining motion vectors in ice floe images by matching edge features

    Science.gov (United States)

    Manohar, M.; Ramapriyan, H. K.; Strong, J. P.

    1988-01-01

    A parallel algorithm is described to determine motion vectors of ice floes using time sequences of images of the Arctic ocean obtained from the Synthetic Aperture Radar (SAR) instrument flown on-board the SEASAT spacecraft. Researchers describe a parallel algorithm which is implemented on the MPP for locating corresponding objects based on their translationally and rotationally invariant features. The algorithm first approximates the edges in the images by polygons or sets of connected straight-line segments. Each such edge structure is then reduced to a seed point. Associated with each seed point are the descriptions (lengths, orientations and sequence numbers) of the lines constituting the corresponding edge structure. A parallel matching algorithm is used to match packed arrays of such descriptions to identify corresponding seed points in the two images. The matching algorithm is designed such that fragmentation and merging of ice floes are taken into account by accepting partial matches. The technique has been demonstrated to work on synthetic test patterns and real image pairs from SEASAT in times ranging from .5 to 0.7 seconds for 128 x 128 images.

  4. An Algorithm for Efficient Maximum Likelihood Estimation and Confidence Interval Determination in Nonlinear Estimation Problems

    Science.gov (United States)

    Murphy, Patrick Charles

    1985-01-01

    An algorithm for maximum likelihood (ML) estimation is developed with an efficient method for approximating the sensitivities. The algorithm was developed for airplane parameter estimation problems but is well suited for most nonlinear, multivariable, dynamic systems. The ML algorithm relies on a new optimization method referred to as a modified Newton-Raphson with estimated sensitivities (MNRES). MNRES determines sensitivities by using slope information from local surface approximations of each output variable in parameter space. The fitted surface allows sensitivity information to be updated at each iteration with a significant reduction in computational effort. MNRES determines the sensitivities with less computational effort than using either a finite-difference method or integrating the analytically determined sensitivity equations. MNRES eliminates the need to derive sensitivity equations for each new model, thus eliminating algorithm reformulation with each new model and providing flexibility to use model equations in any format that is convenient. A random search technique for determining the confidence limits of ML parameter estimates is applied to nonlinear estimation problems for airplanes. The confidence intervals obtained by the search are compared with Cramer-Rao (CR) bounds at the same confidence level. It is observed that the degree of nonlinearity in the estimation problem is an important factor in the relationship between CR bounds and the error bounds determined by the search technique. The CR bounds were found to be close to the bounds determined by the search when the degree of nonlinearity was small. Beale's measure of nonlinearity is developed in this study for airplane identification problems; it is used to empirically correct confidence levels for the parameter confidence limits. The primary utility of the measure, however, was found to be in predicting the degree of agreement between Cramer-Rao bounds and search estimates.

  5. SAS-Pro: simultaneous residue assignment and structure superposition for protein structure alignment.

    Science.gov (United States)

    Shah, Shweta B; Sahinidis, Nikolaos V

    2012-01-01

    Protein structure alignment is the problem of determining an assignment between the amino-acid residues of two given proteins in a way that maximizes a measure of similarity between the two superimposed protein structures. By identifying geometric similarities, structure alignment algorithms provide critical insights into protein functional similarities. Existing structure alignment tools adopt a two-stage approach to structure alignment by decoupling and iterating between the assignment evaluation and structure superposition problems. We introduce a novel approach, SAS-Pro, which addresses the assignment evaluation and structure superposition simultaneously by formulating the alignment problem as a single bilevel optimization problem. The new formulation does not require the sequentiality constraints, thus generalizing the scope of the alignment methodology to include non-sequential protein alignments. We employ derivative-free optimization methodologies for searching for the global optimum of the highly nonlinear and non-differentiable RMSD function encountered in the proposed model. Alignments obtained with SAS-Pro have better RMSD values and larger lengths than those obtained from other alignment tools. For non-sequential alignment problems, SAS-Pro leads to alignments with high degree of similarity with known reference alignments. The source code of SAS-Pro is available for download at http://eudoxus.cheme.cmu.edu/saspro/SAS-Pro.html.

  6. Alignment validation

    Energy Technology Data Exchange (ETDEWEB)

    ALICE; ATLAS; CMS; LHCb; Golling, Tobias

    2008-09-06

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

  7. Dynamic windowing algorithm for the fast and accurate determination of luminescence lifetimes.

    Science.gov (United States)

    Collier, Bradley B; McShane, Michael J

    2012-06-05

    An algorithm for the accurate calculation of luminescence lifetimes in near-real-time is described. The dynamic rapid lifetime determination (DRLD) method uses a window-summing technique and dynamically selects the appropriate window width for each lifetime decay such that a large range of lifetimes can be accurately calculated. The selection of window width is based on an optimal range of window-sum ratios. The algorithm was compared to alternative approaches for rapid lifetime determination as well as nonlinear least-squares (NLLS) fitting in both simulated and real experimental conditions. A palladium porphyrin was used as a model luminophore to quantitatively evaluate the algorithm in a dynamic situation, where oxygen concentration was modulated to induce a change in lifetime. Unlike other window-summing techniques, the new algorithm calculates lifetimes that are not significantly different than the slower, traditional NLLS. In addition, the computation time required to calculate the lifetime is 4 orders of magnitude less than NLLS and 2 orders less than other iterative methods. This advance will improve the accuracy of real-time measurements that must be made on samples that are expected to exhibit widely varying lifetimes, such as sensors and biosensors.

  8. An Overview of Multiple Sequence Alignment Systems

    CERN Document Server

    Saeed, Fahad

    2009-01-01

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

  9. A cross-species alignment tool (CAT)

    DEFF Research Database (Denmark)

    Li, Heng; Guan, Liang; Liu, Tao;

    2007-01-01

    sensitive methods which are usually applied in aligning inter-species sequences. RESULTS: Here we present a new algorithm called CAT (for Cross-species Alignment Tool). It is designed to align mRNA sequences to mammalian-sized genomes. CAT is implemented using C scripts and is freely available on the web...

  10. Inferring comprehensible business/ICT alignment rules

    NARCIS (Netherlands)

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

    2009-01-01

    We inferred business rules for business/ICT alignment by applying a novel rule induction algorithm on a data set containing rich alignment information polled from 641 organisations in 7 European countries. The alignment rule set was created using AntMiner+, a rule induction technique with a reputati

  11. Kernel Contraction and Consolidation of Alignment under Ontology Change

    Directory of Open Access Journals (Sweden)

    Ahmed ZAHAF

    2016-08-01

    Full Text Available Alignment overcomes divergence in the specification of the semantics of vocabularies by different but overlapping ontologies. Therefore, it enhances semantic interoperability for many web based applications. However, ontology change following applications new requirements or new perception of domain knowledges can leads to undesirable knowledge such as inconsistent and therefore to a useless alignment. Ontologies and alignments are encoded in knowledge bases allowing applications to store only some explicit knowledge while they derive implicit ones by applying reasoning services on these knowledge bases. This underlying representation of ontologies and alignments leads us to follow base revision theory to deal with alignment revision under ontology change. For that purpose, we adapt kernel contraction framework to design rational operators and to formulate the set of postulates that characterize each class of these operators. We demonstrate the connection between each class of operators and the set of postulates that characterize them. Finally, we present algorithms to compute alignment kernels and incision functions. Kernels are sets of correspondences responsible of undesirable knowledge following alignment semantics. Incision functions determine the sets of correspondences to eliminate in order to restore alignment consistency or to realize a successful contraction.

  12. [Determination of Virtual Surgery Mass Point Spring Model Parameters Based on Genetic Algorithms].

    Science.gov (United States)

    Chen, Ying; Hu, Xuyi; Zhu, Qiguang

    2015-12-01

    Mass point-spring model is one of the commonly used models in virtual surgery. However, its model parameters have no clear physical meaning, and it is hard to set the parameter conveniently. We, therefore, proposed a method based on genetic algorithm to determine the mass-spring model parameters. Computer-aided tomography (CAT) data were used to determine the mass value of the particle, and stiffness and damping coefficient were obtained by genetic algorithm. We used the difference between the reference deformation and virtual deformation as the fitness function to get the approximate optimal solution of the model parameters. Experimental results showed that this method could obtain an approximate optimal solution of spring parameters with lower cost, and could accurately reproduce the effect of the actual deformation model as well.

  13. [Hyperspectral technology combined with CARS algorithm to quantitatively determine the SSC in Korla fragrant pear].

    Science.gov (United States)

    Zhan, Bai-Shao; Ni, Jun-Hui; Li, Jun

    2014-10-01

    Hyperspectral imaging has large data volume and high dimensionality, and original spectra data includes a lot of noises and severe scattering. And, quality of acquired hyperspectral data can be influenced by non-monochromatic light, external stray light and temperature, which resulted in having some non-linear relationship between the acquired hyperspectral data and the predicted quality index. Therefore, the present study proposed that competitive adaptive reweighted sampling (CARS) algorithm is used to select the key variables from visible and near infrared hyperspectral data. The performance of CARS was compared with full spectra, successive projections algorithm (SPA), Monte Carlo-uninformative variable elimination (MC-UVE), genetic algorithm (GA) and GA-SPA (genetic algorithm-successive projections algorithm). Two hundred Korla fragrant pears were used as research object. SPXY algorithm was used to divided sample set to correction set with 150 samples and prediction set with 50 samples, respectively. Based on variables selected by different methods, linear PLS and nonlinear LS-SVM models were developed, respectively, and the performance of models was assessed using parameters r2, RMSEP and RPD. A comprehensive comparison found that GA, GA-SPA and CARS can effectively select the variables with strong and useful information. These methods can be used for selection of Vis-NIR hyperspectral data variables, particularly for CARS. LS-SVM model can obtain the best results for SSC prediction of Korla fragrant pear based on variables obtained from CARS method. r2, RMSEP and RPD were 0.851 2, 0.291 3 and 2.592 4, respectively. The study showed that CARS is an effectively hyperspectral variable selection method, and nonlinear LS-SVM model is more suitable than linear PLS model for quantitatively determining the quality of fra- grant pear based on hyperspectral information.

  14. Confocal Microscopy for Process Monitoring and Wide-Area Height Determination of Vertically-Aligned Carbon Nanotube Forests

    Directory of Open Access Journals (Sweden)

    Markus Piwko

    2015-08-01

    Full Text Available Confocal microscopy is introduced as a new and generally applicable method for the characterization of the vertically-aligned carbon nanotubes (VACNT forest height. With this technique process control is significantly intensified. The topography of the substrate and VACNT can be mapped with a height resolution down to 15 nm. The advantages of confocal microscopy, compared to scanning electron microscopy (SEM, are demonstrated by investigating the growth kinetics of VACNT using Al2O3 buffer layers with varying thicknesses. A process optimization using confocal microscopy for fast VACNT forest height evaluation is presented.

  15. Pareto optimal pairwise sequence alignment.

    Science.gov (United States)

    DeRonne, Kevin W; Karypis, George

    2013-01-01

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

  16. Determining Relative Importance and Effective Settings for Genetic Algorithm Control Parameters.

    Science.gov (United States)

    Mills, K L; Filliben, J J; Haines, A L

    2015-01-01

    Setting the control parameters of a genetic algorithm to obtain good results is a long-standing problem. We define an experiment design and analysis method to determine relative importance and effective settings for control parameters of any evolutionary algorithm, and we apply this method to a classic binary-encoded genetic algorithm (GA). Subsequently, as reported elsewhere, we applied the GA, with the control parameter settings determined here, to steer a population of cloud-computing simulators toward behaviors that reveal degraded performance and system collapse. GA-steered simulators could serve as a design tool, empowering system engineers to identify and mitigate low-probability, costly failure scenarios. In the existing GA literature, we uncovered conflicting opinions and evidence regarding key GA control parameters and effective settings to adopt. Consequently, we designed and executed an experiment to determine relative importance and effective settings for seven GA control parameters, when applied across a set of numerical optimization problems drawn from the literature. This paper describes our experiment design, analysis, and results. We found that crossover most significantly influenced GA success, followed by mutation rate and population size and then by rerandomization point and elite selection. Selection method and the precision used within the chromosome to represent numerical values had least influence. Our findings are robust over 60 numerical optimization problems.

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

    Directory of Open Access Journals (Sweden)

    Che-Lun Hung

    2013-01-01

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

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

    Science.gov (United States)

    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. PMID:23671842

  19. SINS anti-interference self-alignment algorithm for the swaying base%晃动基座下捷联惯导的抗干扰自对准算法

    Institute of Scientific and Technical Information of China (English)

    王跃钢; 杨家胜

    2014-01-01

    针对捷联惯导(SINS)晃动基座下, SINS难以快速实现自对准的问题,提出SINS的抗干扰自对准算法。该算法通过将初始对准问题转化为Wahba求解问题来消除角运动干扰的影响;利用惯性坐标系重力矢量和晃动干扰加速度的频率特点,通过设计低通滤波器对比力在惯性坐标下的投影进行滤波来消除线振动干扰的影响。仿真结果表明,该算法不需要进行粗对准,能够在角运动干扰和线振动干扰同时存在的情况下快速实现自对准。%The conventional methods are difficult to achieve alignment rapidly when the strapdown inertial navigation system(SINS) under swaying base. Therefore, an anti-interference self-alignment algorithm for the swaying base is presented, which transforms the alignment problem into the Wahba problem to remove the angular interrupting, and uses the low-pass filter to filter the special force in inertial reference frame to remove the linear vibration interrupting according to the different frequency characteristics of gravity vector in inertial reference frame and the disturbance. The simulation results show that the presented method can accomplish alignment quickly even in the presence of angular motion and linear vibration interference without the coarse alignment process.

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

    Directory of Open Access Journals (Sweden)

    Daniels Noah M

    2012-10-01

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

  1. MUON DETECTORS: ALIGNMENT

    CERN Document Server

    M. Dallavalle

    2013-01-01

    A new Muon misalignment scenario for 2011 (7 TeV) Monte Carlo re-processing was re-leased. The scenario is based on running of standard track-based reference-target algorithm (exactly as in data) using single-muon simulated sample (with the transverse-momentum spectrum matching data). It used statistics similar to what was used for alignment with 2011 data, starting from an initially misaligned Muon geometry from uncertainties of hardware measurements and using the latest Tracker misalignment geometry. Validation of the scenario (with muons from Z decay and high-pT simulated muons) shows that it describes data well. The study of systematic uncertainties (dominant by now due to huge amount of data collected by CMS and used for muon alignment) is finalised. Realistic alignment position errors are being obtained from the estimated uncertainties and are expected to improve the muon reconstruction performance. Concerning the Hardware Alignment System, the upgrade of the Barrel Alignment is in progress. By now, d...

  2. Mineral crystal alignment in mineralized fracture callus determined by 3D small-angle X-ray scattering

    Energy Technology Data Exchange (ETDEWEB)

    Liu Yifei; Manjubala, Inderchand; Fratzl, Peter [Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam (Germany); Roschger, Paul [4th Medical Department, Ludwig Boltzmann Institute of Osteology at Hanusch Hospital of WGKK and AUVA Trauma Centre Meidling, 1140 Vienna (Austria); Schell, Hanna; Duda, Georg N, E-mail: fratzl@mpikg.mpg.d [Julius Wolff Institut and Center for Musculoskeletal Surgery, Charite- University Medicine Berlin, Augustenburger Platz 1, 13353 Berlin (Germany)

    2010-10-01

    Callus tissue formed during bone fracture healing is a mixture of different tissue types as revealed by histological analysis. But the structural characteristics of mineral crystals within the healing callus are not well known. Since two-dimensional (2D) scanning small-angle X-ray scattering (sSAXS) patterns showed that the size and orientation of callus crystals vary both spatially and temporally [1] and 2D electron microscopic analysis implies an anisotropic property of the callus morphology, the mineral crystals within the callus are also expected to vary in size and orientation in 3D. Three-dimensional small-angle X-ray scattering (3D SAXS), which combines 2D SAXS patterns collected at different angles of sample tilting, has been previously applied to investigate bone minerals in horse radius [2] and oim/oim mouse femur/tibia [3]. We implement a similar 3D SAXS method but with a different way of data analysis to gather information on the mineral alignment in fracture callus. With the proposed accurate yet fast assessment of 3D SAXS information, it was shown that the plate shaped mineral particles in the healing callus were aligned in groups with their predominant orientations occurring as a fiber texture.

  3. Detailed protein sequence alignment based on Spectral Similarity Score (SSS

    Directory of Open Access Journals (Sweden)

    Thomas Dina

    2005-04-01

    Full Text Available Abstract Background The chemical property and biological function of a protein is a direct consequence of its primary structure. Several algorithms have been developed which determine alignment and similarity of primary protein sequences. However, character based similarity cannot provide insight into the structural aspects of a protein. We present a method based on spectral similarity to compare subsequences of amino acids that behave similarly but are not aligned well by considering amino acids as mere characters. This approach finds a similarity score between sequences based on any given attribute, like hydrophobicity of amino acids, on the basis of spectral information after partial conversion to the frequency domain. Results Distance matrices of various branches of the human kinome, that is the full complement of human kinases, were developed that matched the phylogenetic tree of the human kinome establishing the efficacy of the global alignment of the algorithm. PKCd and PKCe kinases share close biological properties and structural similarities but do not give high scores with character based alignments. Detailed comparison established close similarities between subsequences that do not have any significant character identity. We compared their known 3D structures to establish that the algorithm is able to pick subsequences that are not considered similar by character based matching algorithms but share structural similarities. Similarly many subsequences with low character identity were picked between xyna-theau and xyna-clotm F/10 xylanases. Comparison of 3D structures of the subsequences confirmed the claim of similarity in structure. Conclusion An algorithm is developed which is inspired by successful application of spectral similarity applied to music sequences. The method captures subsequences that do not align by traditional character based alignment tools but give rise to similar secondary and tertiary structures. The Spectral

  4. Optimization of Determinant Factors of Satellite Electrical Power System with Particle Swarm Optimization (PSO Algorithm

    Directory of Open Access Journals (Sweden)

    Mojtaba Biglarahmadi

    2014-03-01

    Full Text Available Weight and dimension, cost, and performance are determinant factors for design, fabrication, and launch the satellites which are related to the mission type of the satellites. Each satellite includes several subsystems such as Electrical Power Subsystem (EPS, Navigation Subsystem, Thermal Subsystem, etc. The purpose of this paper is to optimize these determinant factors by Particle Swarm Optimization (PSO algorithm, for Electrical Power Subsystem. This paper considers the effects of selecting various types of Photovoltaic (PV cells and batteries on weight and dimension, cost, and performance of the satellite. We have used two various types of PVs and two various type of batteries in optimization of the Electrical Power Subsystem (EPS

  5. A Genetic Algorithm for Simultaneous Determination of Thin Films Thermal Transport Properties and Contact Resistance

    Institute of Scientific and Technical Information of China (English)

    Zhengxing HUANG; Zhen'an TANG; Ziqiang XU; Haitao DING; Yuqin GU

    2006-01-01

    A genetic algorithm (GA) was studied to simultaneously determine the thermal transport properties and the contact resistance of thin films deposited on a thick substrate. A pulsed photothermal reflectance (PPR) system was employed for the measurements. The GA was used to extract the thermal properties. Measurements were performed on SiO2 thin films of different thicknesses on silicon substrate. The results show that the GA accompanied with the PPR system is useful for the simultaneous determination of thermal properties of thin films on a substrate.

  6. Lord-Wingersky Algorithm Version 2.0 for Hierarchical Item Factor Models with Applications in Test Scoring, Scale Alignment, and Model Fit Testing. CRESST Report 830

    Science.gov (United States)

    Cai, Li

    2013-01-01

    Lord and Wingersky's (1984) recursive algorithm for creating summed score based likelihoods and posteriors has a proven track record in unidimensional item response theory (IRT) applications. Extending the recursive algorithm to handle multidimensionality is relatively simple, especially with fixed quadrature because the recursions can be defined…

  7. Determining the Optimal Placement of Sensors on a Concrete Arch Dam Using a Quantum Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Kai Zhu

    2016-01-01

    Full Text Available Structural modal identification has become increasingly important in health monitoring, fault diagnosis, vibration control, and dynamic analysis of engineering structures in recent years. Based on an analysis of traditional optimization algorithms, this paper proposes a novel sensor optimization criterion that combines the effective independence (EFI method with the modal strain energy (MSE method. Considering the complex structure and enormous degrees of freedom (DOFs of modern concrete arch dam, a quantum genetic algorithm (QGA is used to optimize the corresponding sensor network on the upstream surface of a dam. Finally, this study uses a specific concrete arch dam as an example and determines the optimal sensor placement using the proposed method. By comparing the results with the traditional optimization methods, the proposed method is shown to maximize the spatial intersection angle among the modal vectors of sensor network and can effectively resist ambient perturbations, which will make the identified modal parameters more precise.

  8. A new colour constancy algorithm based on automatic determination of gray framework parameters using neural network

    Indian Academy of Sciences (India)

    Mohammad Mehdi Faghih; Zeynab Khosravinia; Mohsen Ebrahimi Moghaddam

    2014-04-01

    Colour constancy is defined as the ability to estimate the actual colours of objects in an acquired image disregarding the colour of scene illuminant. Despite large variety of existing methods, no colour constancy algorithm can be considered as universal. Among the methods, the gray framework is one of the best-known and most used approaches. This framework has some parameters that should be set with appropriate values to achieve the best performance for each image. In this article, we propose a neural network-based algorithm that aims to automatically determine the best value of gray framework parameters for each image. It is a multi-level approach that estimates the optimal values for the gray framework parameters based on relevant features extracted from the input image. Experimental results on two popular colour constancy datasets show an acceptable improvement over state-of-the-art methods.

  9. Determining Optimal Replacement Policy with an Availability Constraint via Genetic Algorithms

    Directory of Open Access Journals (Sweden)

    Shengliang Zong

    2017-01-01

    Full Text Available We develop a model and a genetic algorithm for determining an optimal replacement policy for power equipment subject to Poisson shocks. If the time interval of two consecutive shocks is less than a threshold value, the failed equipment can be repaired. We assume that the operating time after repair is stochastically nonincreasing and the repair time is exponentially distributed with a geometric increasing mean. Our objective is to minimize the expected average cost under an availability requirement. Based on this average cost function, we propose the genetic algorithm to locate the optimal replacement policy N to minimize the average cost rate. The results show that the GA is effective and efficient in finding the optimal solutions. The availability of equipment has significance effect on the optimal replacement policy. Many practical systems fit the model developed in this paper.

  10. An improved quaternion Gauss–Newton algorithm for attitude determination using magnetometer and accelerometer

    Directory of Open Access Journals (Sweden)

    Liu Fei

    2014-08-01

    Full Text Available For the vector attitude determination, the traditional optimal algorithms which are based on quaternion estimator (QUEST measurement noise model are complicated for just two observations. In our application, the magnetometer and accelerometer are not two comparable kinds of sensors and both are not small field-of-view sensors as well. So in this paper a new unit measurement model is derived. According to the Wahba problem, the optimal weights for each measurement are obtained by the error variance researches. Then an improved quaternion Gauss–Newton method is presented and adopted to acquire attitude. Eventually, simulation results and experimental validation employed to test the proposed method demonstrate the usefulness of the improved algorithm.

  11. An improved quaternion Gauss-Newton algorithm for attitude determination using magnetometer and accelerometer

    Institute of Scientific and Technical Information of China (English)

    Liu Fei; Li Jie; Wang Haifu; Liu Chang

    2014-01-01

    For the vector attitude determination, the traditional optimal algorithms which are based on quaternion estimator (QUEST) measurement noise model are complicated for just two observa-tions. In our application, the magnetometer and accelerometer are not two comparable kinds of sen-sors and both are not small field-of-view sensors as well. So in this paper a new unit measurement model is derived. According to the Wahba problem, the optimal weights for each measurement are obtained by the error variance researches. Then an improved quaternion Gauss-Newton method is presented and adopted to acquire attitude. Eventually, simulation results and experimental valida-tion employed to test the proposed method demonstrate the usefulness of the improved algorithm.

  12. Algorithm based on the Thomson problem for determination of equilibrium structures of metal nanoclusters

    Science.gov (United States)

    Arias, E.; Florez, E.; Pérez-Torres, J. F.

    2017-06-01

    A new algorithm for the determination of equilibrium structures suitable for metal nanoclusters is proposed. The algorithm performs a stochastic search of the minima associated with the nuclear potential energy function restricted to a sphere (similar to the Thomson problem), in order to guess configurations of the nuclear positions. Subsequently, the guessed configurations are further optimized driven by the total energy function using the conventional gradient descent method. This methodology is equivalent to using the valence shell electron pair repulsion model in guessing initial configurations in the traditional molecular quantum chemistry. The framework is illustrated in several clusters of increasing complexity: Cu7, Cu9, and Cu11 as benchmark systems, and Cu38 and Ni9 as novel systems. New equilibrium structures for Cu9, Cu11, Cu38, and Ni9 are reported.

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

    Directory of Open Access Journals (Sweden)

    Trung Nghia Vu

    2013-04-01

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

  14. Optimization and improvement of FOA corner cube algorithm

    Science.gov (United States)

    McClay, Wilbert A., III; Awwal, Abdul A. S.; Burkhart, Scott C.; Candy, James V.

    2004-11-01

    Alignment of laser beams based on video images is a crucial task necessary to automate operation of the 192 beams at the National Ignition Facility (NIF). The final optics assembly (FOA) is the optical element that aligns the beam into the target chamber. This work presents an algorithm for determining the position of a corner cube alignment image in the final optics assembly. The improved algorithm was compared to the existing FOA algorithm on 900 noise-simulated images. While the existing FOA algorithm based on correlation with a synthetic template has a radial standard deviation of 1 pixel, the new algorithm based on classical matched filtering (CMF) and polynomial fit to the correlation peak improves the radial standard deviation performance to less than 0.3 pixels. In the new algorithm the templates are designed from real data stored during a year of actual operation.

  15. Optimization and Improvement of FOA Corner Cube Algorithm

    Energy Technology Data Exchange (ETDEWEB)

    McClay, W A; Awwal, A S; Burkhart, S C; Candy, J V

    2004-10-01

    Alignment of laser beams based on video images is a crucial task necessary to automate operation of the 192 beams at the National Ignition Facility (NIF). The final optics assembly (FOA) is the optical element that aligns the beam into the target chamber. This work presents an algorithm for determining the position of a corner cube alignment image in the final optics assembly. The improved algorithm was compared to the existing FOA algorithm on 900 noise-simulated images. While the existing FOA algorithm based on correlation with a synthetic template has a radial standard deviation of 1 pixel, the new algorithm based on classical matched filtering (CMF) and polynomial fit to the correlation peak improves the radial standard deviation performance to less than 0.3 pixels. In the new algorithm the templates are designed from real data stored during a year of actual operation.

  16. Validating determinants for an alternate foot placement selection algorithm during human locomotion in cluttered terrain.

    Science.gov (United States)

    Moraes, Renato; Allard, Fran; Patla, Aftab E

    2007-10-01

    The goal of this study was to validate dynamic stability and forward progression determinants for the alternate foot placement selection algorithm. Participants were asked to walk on level ground and avoid stepping, when present, on a virtual white planar obstacle. They had a one-step duration to select an alternate foot placement, with the task performed under two conditions: free (participants chose the alternate foot placement that was appropriate) and forced (a green arrow projected over the white planar obstacle cued the alternate foot placement). To validate the dynamic stability determinant, the distance between the extrapolated center of mass (COM) position, which incorporates the dynamics of the body, and the limits of the base of support was calculated in both anteroposterior (AP) and mediolateral (ML) directions in the double support phase. To address the second determinant, COM deviation from straight ahead was measured between adaptive and subsequent steps. The results of this study showed that long and lateral choices were dominant in the free condition, and these adjustments did not compromise stability in both adaptive and subsequent steps compared with the short and medial adjustments, which were infrequent and adversely affected stability. Therefore stability is critical when selecting an alternate foot placement in a cluttered terrain. In addition, changes in the plane of progression resulted in small deviations of COM from the endpoint goal. Forward progression of COM was maintained even for foot placement changes in the frontal plane, validating this determinant as part of the selection algorithm.

  17. Determination of best-fit potential parameters for a reactive force field using a genetic algorithm.

    Science.gov (United States)

    Pahari, Poonam; Chaturvedi, Shashank

    2012-03-01

    The ReaxFF interatomic potential, used for organic materials, involves more than 600 adjustable parameters, the best-fit values of which must be determined for different materials. A new method of determining the set of best-fit parameters for specific molecules containing carbon, hydrogen, nitrogen and oxygen is presented, based on a parameter reduction technique followed by genetic algorithm (GA) minimization. This work has two novel features. The first is the use of a parameter reduction technique to determine which subset of parameters plays a significant role for the species of interest; this is necessary to reduce the optimization space to manageable levels. The second is the application of the GA technique to a complex potential (ReaxFF) with a very large number of adjustable parameters, which implies a large parameter space for optimization. In this work, GA has been used to optimize the parameter set to determine best-fit parameters that can reproduce molecular properties to within a given accuracy. As a test problem, the use of the algorithm has been demonstrated for nitromethane and its decomposition products.

  18. Beyond Alignment

    DEFF Research Database (Denmark)

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

  19. Performance Analysis of Alignment Process of MEMS IMU

    Directory of Open Access Journals (Sweden)

    Vadim Bistrov

    2012-01-01

    Full Text Available The procedure of determining the initial values of the attitude angles (pitch, roll, and heading is known as the alignment. Also, it is essential to align an inertial system before the start of navigation. Unless the inertial system is not aligned with the vehicle, the information provided by MEMS (microelectromechanical system sensors is not useful for navigating the vehicle. At the moment MEMS gyroscopes have poor characteristics and it’s necessary to develop specific algorithms in order to obtain the attitude information of the object. Most of the standard algorithms for the attitude estimation are not suitable when using MEMS inertial sensors. The wavelet technique, the Kalman filter, and the quaternion are not new in navigation data processing. But the joint use of those techniques for MEMS sensor data processing can give some new results. In this paper the performance of a developed algorithm for the attitude estimation using MEMS IMU (inertial measurement unit is tested. The obtained results are compared with the attitude output of another commercial GPS/IMU device by Xsens. The impact of MEMS sensor measurement noises on an alignment process is analysed. Some recommendations for the Kalman filter algorithm tuning to decrease standard deviation of the attitude estimation are given.

  20. The CMS Silicon Tracker Alignment

    CERN Document Server

    Castello, R

    2008-01-01

    The alignment of the Strip and Pixel Tracker of the Compact Muon Solenoid experiment, with its large number of independent silicon sensors and its excellent spatial resolution, is a complex and challenging task. Besides high precision mounting, survey measurements and the Laser Alignment System, track-based alignment is needed to reach the envisaged precision.\\\\ Three different algorithms for track-based alignment were successfully tested on a sample of cosmic-ray data collected at the Tracker Integration Facility, where 15\\% of the Tracker was tested. These results, together with those coming from the CMS global run, will provide the basis for the full-scale alignment of the Tracker, which will be carried out with the first \\emph{p-p} collisions.

  1. [Application of successive projections algorithm to nondestructive determination of total amino acids in oilseed rape leaves].

    Science.gov (United States)

    Liu, Fei; Zhang, Fan; Fang, Hui; Jin, Zong-Lai; Zhou, Wei-Jun; He, Yong

    2009-11-01

    Near infrared (NIR) spectroscopy combined with successive projections algorithm (SPA) was investigated for the fast and nondestructive determination of total amino acids (TAA) in oilseed rape leaves. Total amino acids are important indices of the growing status of oilseed rape. A total of 150 leave samples were scanned, the calibration set was composed of 80 samples, the validation set was composed of 40 samples and the prediction set was composed of 30 samples. The optimal partial least squares (PLS) model was developed for the prediction of total amino acids in oilseed rape leaves after the performance comparison of different pretreatments, including smoothing method, standard normal variate (SNV), the first derivative and second derivative. Simultaneously, successive projections algorithm was applied for the extraction of effective wavelengths (EWs), which were thought to have least collinearity and redundancies in the spectral data. The selected effective wavelengths were used as the inputs of multiple linear regression (MLR), partial least squares (PLS) and least square-support vector machine (LS-SVM). Then the SPA-MLR, SPA-PLS and SPA-LS-SVM models were developed for performance comparison. The determination coefficient (R2) and root mean square error (RMSE) were used as the model evaluation indices. The results indicated that both SPA-MLR and SPA-PLS models were better than full-spectrum PLS model, and the best performance was achieved by SPA-LS-SVM model with R2 = 0.983 0 and RMSEP = 0.396 4. An excellent prediction precision was achieved. In conclusion, successive projections algorithm is a powerful way for effective wavelength selection, and it is feasible to determine the total amino acids in oil-seed rape leaves using near infrared spectroscopy and SPA-LS-SVM, and an excellent prediction precision was obtained. This study supplied a new and alternative approach to the further application of near infrared spectroscopy in the response of stress and on

  2. An analytical algorithm to determine allowable ampacities of horizontally installed rectangular bus bars

    Directory of Open Access Journals (Sweden)

    Klimenta Dardan O.

    2016-01-01

    Full Text Available The main objective of this paper is to propose an algorithm for the determination of the allowable ampacities of single rectangular-section bus bars without the occurrence of correction factors. Without correction factors, the ampacity computation of the copper and aluminium bus bars is fully automatized. The analytical algorithm has been implemented in a computer program code that along with the allowable ampacity can compute the bus bar temperature and the individual heat transfer coefficient for each side of the bus bar, as well as their corresponding power losses. Natural and forced convection correlations for rectangular bus bars are applied. Effects of the solar radiation and radiation heat losses from the bus bar surface are taken into consideration as well. The finite element method (FEM has been used for the linear/non-linear steady-state thermal analysis, i.e. for validation of the analytical algorithm. All FEM-based numerical computations were carried out using the COMSOL Heat Transfer Module. [Projekat Ministarstva nauke Republike Srbije, br. TR33046

  3. Novel algorithm for determining optimal blankholder forces in deep drawing of aluminum alloy sheet

    Institute of Scientific and Technical Information of China (English)

    孙成智; 陈关龙; 林忠钦; 赵亦希

    2004-01-01

    Wrinkling and fracture are main defects in sheet metal forming of aluminum alloy sheet, which can be reduced or even eliminated by manipulating a suitable blank-holder forces (BHF). But, it is difficult to attain the optimum BHF during sheet metal forming. A new optimization algorithm integrating the finite element method (FEM)and adaptive response surface method is presented to determinate the optimal BHFs in deep drawing of aluminum rectangular box. To assure convergence, the trust region modes management strategies are used to adjust the move limit of design spaces. Finally, the optimum results of rectangular box deep drawing are given. Verification experiments are performed to verify the optimal result.

  4. Mirror alignment control for COMPASS RICH-1 detector

    Energy Technology Data Exchange (ETDEWEB)

    Alexeev, M. [INFN, Sezione di Torino and University of East Piemonte, Alessandria (Italy); Birsa, R. [INFN, Sezione di Trieste, Trieste (Italy); Bradamante, F.; Bressan, A. [INFN, Sezione di Trieste and University of Trieste, Trieste (Italy); Chiosso, M. [INFN, Sezione di Torino and University of Torino, Torino (Italy); Ciliberti, P. [INFN, Sezione di Trieste and University of Trieste, Trieste (Italy); Dalla Torre, S. [INFN, Sezione di Trieste, Trieste (Italy); Denisov, O. [INFN, Sezione di Torino, Torino (Italy); Duic, V. [INFN, Sezione di Trieste and University of Trieste, Trieste (Italy); Ferrero, A. [INFN, Sezione di Torino and University of Torino, Torino (Italy); Finger, M.; Finger, M. [Charles University, Praga (Czech Republic); JINR, Dubna (Russian Federation); Giorgi, M. [INFN, Sezione di Trieste and University of Trieste, Trieste (Italy); Gobbo, B. [INFN, Sezione di Trieste, Trieste (Italy); Levorato, S. [INFN, Sezione di Trieste and University of Trieste, Trieste (Italy); Maggiora, A. [INFN, Sezione di Torino, Torino (Italy); Martin, A. [INFN, Sezione di Trieste and University of Trieste, Trieste (Italy); Menon, G. [INFN, Sezione di Trieste, Trieste (Italy); Panzieri, D. [INFN, Sezione di Torino and University of East Piemonte, Alessandria (Italy); Pesaro, G. [INFN, Sezione di Trieste and University of Trieste, Trieste (Italy)

    2011-05-21

    The focusing system of the COMPASS RICH-1 detector consists of two segmented spherical mirror surfaces, formed by 68 hexagonal and 48 pentagonal individual elements. All individual mirrors have two degrees of freedom to adjust the angular alignment in order to obtain a continuous spherical surface. Relative angular misalignments can be monitored on-line by the CLAM method, based on the optical reconstruction of line images. Complementing the CLAM measurements with photogrammetry, the absolute mirror orientation and position in space can be determined too. The method is described, as well as the algorithms used to access the relative and absolute mirror alignment.

  5. The GLAS Algorithm Theoretical Basis Document for Precision Orbit Determination (POD)

    Science.gov (United States)

    Rim, Hyung Jin; Yoon, S. P.; Schultz, Bob E.

    2013-01-01

    The Geoscience Laser Altimeter System (GLAS) was the sole instrument for NASA's Ice, Cloud and land Elevation Satellite (ICESat) laser altimetry mission. The primary purpose of the ICESat mission was to make ice sheet elevation measurements of the polar regions. Additional goals were to measure the global distribution of clouds and aerosols and to map sea ice, land topography and vegetation. ICESat was the benchmark Earth Observing System (EOS) mission to be used to determine the mass balance of the ice sheets, as well as for providing cloud property information, especially for stratospheric clouds common over polar areas. The GLAS instrument operated from 2003 to 2009 and provided multi-year elevation data needed to determine changes in sea ice freeboard, land topography and vegetation around the globe, in addition to elevation changes of the Greenland and Antarctic ice sheets. This document describes the Precision Orbit Determination (POD) algorithm for the ICESat mission. The problem of determining an accurate ephemeris for an orbiting satellite involves estimating the position and velocity of the satellite from a sequence of observations. The ICESatGLAS elevation measurements must be very accurately geolocated, combining precise orbit information with precision pointing information. The ICESat mission POD requirement states that the position of the instrument should be determined with an accuracy of 5 and 20 cm (1-s) in radial and horizontal components, respectively, to meet the science requirements for determining elevation change.

  6. A statistical physics perspective on alignment-independent protein sequence comparison.

    Science.gov (United States)

    Chattopadhyay, Amit K; Nasiev, Diar; Flower, Darren R

    2015-08-01

    Within bioinformatics, the textual alignment of amino acid sequences has long dominated the determination of similarity between proteins, with all that implies for shared structure, function and evolutionary descent. Despite the relative success of modern-day sequence alignment algorithms, so-called alignment-free approaches offer a complementary means of determining and expressing similarity, with potential benefits in certain key applications, such as regression analysis of protein structure-function studies, where alignment-base similarity has performed poorly. Here, we offer a fresh, statistical physics-based perspective focusing on the question of alignment-free comparison, in the process adapting results from 'first passage probability distribution' to summarize statistics of ensemble averaged amino acid propensity values. In this article, we introduce and elaborate this approach. © The Author 2015. Published by Oxford University Press.

  7. An Algorithm for Chinese Plagiarism Detection Based on Left Align Word Frequency Vector Space Model%基于左归词频向量空间模型的中文文本抄袭检测算法

    Institute of Scientific and Technical Information of China (English)

    谢松山; 唐雁

    2015-01-01

    提出一种基于左归词频向量空间模型的抄袭检测算法 .通过左归处理将抄袭文本的指代还原 ,借助同义词链对所有同义词统一左对齐于同义词链首词 ,然后以直接统计词频构造文本词频特征 ,抛弃词频统计抄袭检测算法中以TF-IDF多步计算相对词频的处理 ,最后以词频特征构造向量空间模型 ,用余弦相似计算文本相似度 .实验表明 ,算法在各种抄袭类型的数据集上综合性能更优、稳定性更好、效率更高 .%In this paper ,an algorithm for plagiarism detection based on left align word frequency vector space model is proposed .First ,left align treatment is made to recover the reference in the copied text . Next ,all synonyms are unified with the synonym chain by left-justifying them with the first word at their synonym chain .Then ,a text word frequency features are constructed directly with statistical method ,a-bandoning the multi-step process of TF-IDF to calculate the relative word frequency in other word frequen-cy plagiarism detection algorithms .Finally ,a vector space model is constructed ,using the word frequency features ,and the text similarity is calculated using the cosine similarity .Experimental results show that this algorithm on various types of plagiarism data sets has better overall performance ,better stability and greater efficiency .

  8. Lord-Wingersky Algorithm Version 2.0 for Hierarchical Item Factor Models with Applications in Test Scoring, Scale Alignment, and Model Fit Testing.

    Science.gov (United States)

    Cai, Li

    2015-06-01

    Lord and Wingersky's (Appl Psychol Meas 8:453-461, 1984) recursive algorithm for creating summed score based likelihoods and posteriors has a proven track record in unidimensional item response theory (IRT) applications. Extending the recursive algorithm to handle multidimensionality is relatively simple, especially with fixed quadrature because the recursions can be defined on a grid formed by direct products of quadrature points. However, the increase in computational burden remains exponential in the number of dimensions, making the implementation of the recursive algorithm cumbersome for truly high-dimensional models. In this paper, a dimension reduction method that is specific to the Lord-Wingersky recursions is developed. This method can take advantage of the restrictions implied by hierarchical item factor models, e.g., the bifactor model, the testlet model, or the two-tier model, such that a version of the Lord-Wingersky recursive algorithm can operate on a dramatically reduced set of quadrature points. For instance, in a bifactor model, the dimension of integration is always equal to 2, regardless of the number of factors. The new algorithm not only provides an effective mechanism to produce summed score to IRT scaled score translation tables properly adjusted for residual dependence, but leads to new applications in test scoring, linking, and model fit checking as well. Simulated and empirical examples are used to illustrate the new applications.

  9. Digital Image Analysis Algorithm For Determination of Particle Size Distributions In Diesel Engines

    Science.gov (United States)

    Armas, O.; Ballesteros, R.; Gomez, A.

    One of the most serious problems associated to Diesel engines is pollutant emissions, standing out nitrogen oxides and particulate matter. However, although current emis- sions standards in Europe and America with regard to light vehicles and heavy duty engines refer the particulate limit in mass units, concern for knowing size and number of particles emitted by engines is being increased recently. This interest is promoted by last studies about particle harmful effects on health and is enhanced by recent changes in internal combustion engines technology. This study is focused on the implementation of a method to determine the particle size distribution made up in current methodology for vehicles certification in Europe. It will use an automated Digital Image Analysis Algorithm (DIAA) to determine particle size trends from Scanning Electron Microscope (SEM) images of filters charged in a dilution system used for measuring specific particulate emissions. The experimental work was performed on a steady state direct injection Diesel en- gine with 0.5 MW rated power, being considered as a typical engine in middle power industries. Particulate size distributions obtained using DIAA and a Scanning Mobil- ity Particle Sizer (SMPS), nowadays considered as the most reliable technique, were compared. Although number concentration detected by this method does not repre- sent real flowing particle concentration, this algorithm fairly reproduces the trends observed with SMPS when the engine load is varied.

  10. An Accurate de novo Algorithm for Glycan Topology Determination from Mass Spectra.

    Science.gov (United States)

    Dong, Liang; Shi, Bing; Tian, Guangdong; Li, YanBo; Wang, Bing; Zhou, MengChu

    2015-01-01

    Determining the glycan topology automatically from mass spectra represents a great challenge. Existing methods fall into approximate and exact ones. The former including greedy and heuristic ones can reduce the computational complexity, but suffer from information lost in the procedure of glycan interpretation. The latter including dynamic programming and exhaustive enumeration are much slower than the former. In the past years, nearly all emerging methods adopted a tree structure to represent a glycan. They share such problems as repetitive peak counting in reconstructing a candidate structure. Besides, tree-based glycan representation methods often have to give different computational formulas for binary and ternary glycans. We propose a new directed acyclic graph structure for glycan representation. Based on it, this work develops a de novo algorithm to accurately reconstruct the tree structure iteratively from mass spectra with logical constraints and some known biosynthesis rules, by a single computational formula. The experiments on multiple complex glycans extracted from human serum show that the proposed algorithm can achieve higher accuracy to determine a glycan topology than prior methods without increasing computational burden.

  11. Momentum bias determination in the tracker alignment and first differential t anti t cross section measurement at CMS

    Energy Technology Data Exchange (ETDEWEB)

    Enderle, Holger

    2012-01-15

    This thesis is prepared within the framework of the CMS experiment at the Large Hadron Collider. It is divided into a technical topic and an analysis. In the technical part, a method is developed to validate the alignment of the tracker geometry concerning biases in the momentum measurement. The method is based on the comparison of the measured momentum of isolated tracks and the corresponding energy deposited in the calorimeter. Comparing positively and negatively charged hadrons, the twist of the tracker is constrained with a precision of ({delta}{phi})/({delta}z)=12 ({mu}rad)/(m). The analysis deals with cross section measurements in events containing an isolated muon and jets. The complete dataset of proton-proton collisions at a centre-of-mass energy of 7 TeV taken in 2010 is investigated. This corresponds to an integrated luminosity of 35.9 pb{sup -1}. Cross sections including different physics processes with an isolated muon and jets in the final state are measured for different jet multiplicities (N{sub jets} {>=}1;2;3;4). With increasing jet multiplicity, the transition from a W {yields} l{nu} dominated to a strongly t anti t enriched phase space becomes evident. The inclusive cross section for t anti t production derived from the four jet sample is measured to be {sigma}=172{+-}15(stat.){+-}41(syst.){+-}7(lumi.) pb. Cross sections differentially in kinematic quantities of the muon, (d{sigma})/(d{sub PT}), (d{sigma})/(d{eta}) are measured as well and compared to theoretical predictions.

  12. Progressive multiple sequence alignments from triplets

    Directory of Open Access Journals (Sweden)

    Stadler Peter F

    2007-07-01

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

  13. Comparison of Two Forced Alignment Systems for Aligning Bribri Speech

    Directory of Open Access Journals (Sweden)

    Rolando Coto-Solano

    2017-04-01

    Full Text Available Forced alignment provides drastic savings in time when aligning speech recordings and is particularly useful for the study of Indigenous languages, which are severely under-resourced in corpora and models. Here we compare two forced alignment systems, FAVE-align and EasyAlign, to determine which one provides more precision when processing running speech in the Chibchan language Bribri. We aligned a segment of a story narrated in Bribri and compared the errors in finding the center of the words and the edges of phonemes when compared with the manual correction. FAVE-align showed better performance: It has an error of 7% compared to 24% with EasyAlign when finding the center of words, and errors of 22~24 ms when finding the edges of phonemes, compared to errors of 86~130 ms with EasyAlign. In addition to this, EasyAlign failed to detect 7% of phonemes, while also inserting 58 spurious phones into the transcription. Future research includes verifying these results for other genres and other Chibchan languages. Finally, these results provide additional evidence for the applicability of natural language processing methods to Chibchan languages and point to future work such as the construction of corpora and the training of automated speech recognition systems.

  14. CATO: The Clone Alignment Tool.

    Directory of Open Access Journals (Sweden)

    Peter V Henstock

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

  15. CATO: The Clone Alignment Tool.

    Science.gov (United States)

    Henstock, Peter V; LaPan, Peter

    2016-01-01

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

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

    OpenAIRE

    Krishnadev Oruganty; Srinivasan Narayanaswamy

    2011-01-01

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

  17. Algorithms for Autonomous GPS Orbit Determination and Formation Flying: Investigation of Initialization Approaches and Orbit Determination for HEO

    Science.gov (United States)

    Axelrad, Penina; Speed, Eden; Leitner, Jesse A. (Technical Monitor)

    2002-01-01

    This report summarizes the efforts to date in processing GPS measurements in High Earth Orbit (HEO) applications by the Colorado Center for Astrodynamics Research (CCAR). Two specific projects were conducted; initialization of the orbit propagation software, GEODE, using nominal orbital elements for the IMEX orbit, and processing of actual and simulated GPS data from the AMSAT satellite using a Doppler-only batch filter. CCAR has investigated a number of approaches for initialization of the GEODE orbit estimator with little a priori information. This document describes a batch solution approach that uses pseudorange or Doppler measurements collected over an orbital arc to compute an epoch state estimate. The algorithm is based on limited orbital element knowledge from which a coarse estimate of satellite position and velocity can be determined and used to initialize GEODE. This algorithm assumes knowledge of nominal orbital elements, (a, e, i, omega, omega) and uses a search on time of perigee passage (tau(sub p)) to estimate the host satellite position within the orbit and the approximate receiver clock bias. Results of the method are shown for a simulation including large orbital uncertainties and measurement errors. In addition, CCAR has attempted to process GPS data from the AMSAT satellite to obtain an initial estimation of the orbit. Limited GPS data have been received to date, with few satellites tracked and no computed point solutions. Unknown variables in the received data have made computations of a precise orbit using the recovered pseudorange difficult. This document describes the Doppler-only batch approach used to compute the AMSAT orbit. Both actual flight data from AMSAT, and simulated data generated using the Satellite Tool Kit and Goddard Space Flight Center's Flight Simulator, were processed. Results for each case and conclusion are presented.

  18. Self-alignment algorithm without latitude for SINS based on gravitational apparent motion and wavelet denoising%未知纬度条件下基于重力视运动与小波去噪的SINS自对准方法

    Institute of Scientific and Technical Information of China (English)

    刘锡祥; 杨燕; 黄永江; 宋清

    2016-01-01

    Double-vector attitude determination algorithm in inertial frame takes two gravitational apparent motion vectors as non-collinear vectors. Although this method solve the traditional algorithm’s problem that the information is susceptible to angular motion disturbance on swinging base, it still needs accurate latitude information to participate in alignment calculation. Aiming to fulfill the alignment for strapdown inertial navigation system without aided latitude information, a self-alignment method with three gravitational apparent motion vectors is designed. In this method, the alignment problem is attributed to solving the attitude matrix between current navigation frame and initial body frame and is solved with vector operation. Simulation results indicate that those random noises in the accelerator will be projected in gravitation apparent motion vectors and decrease the alignment accuracy, and even cause alignment failure when with large noise. For denoising, the daubechies (db4) wavelet is introduced to decompose gravitational apparent motions with 5 layers, and three denoised apparent motion vectors are selected to participate in the alignment. Simulation results indicate that the db4 owns excellent denoising effects and the alignment method with three apparent motion vectors and db4 in inertial frame can fulfill the alignment without aided latitude information.%基于惯性系的双矢量定姿方法选择惯性系中的两个重力视运动向量作为不共线矢量,解决了传统双矢量定姿方法在晃动基座条件下易受载体角运动干扰而无法实现对准的问题,但该方法仍需要精确的地理纬度信息以参与对准计算。针对未知纬度条件下的SINS抗晃动自对准问题,提出了一种基于重力视运动的三矢量自对准方法。该方法将初始对准问题归结为求解当前时刻导航系相对于初始时刻载体系的姿态矩阵问题,并利用矢量运算进行求解,仿真结果表

  19. A Vondrak low pass filter for IMU sensor initial alignment on a disturbed base.

    Science.gov (United States)

    Li, Zengke; Wang, Jian; Gao, Jingxiang; Li, Binghao; Zhou, Feng

    2014-12-10

    The initial alignment of the Inertial Measurement Unit (IMU) is an important process of INS to determine the coordinate transformation matrix which is used in the integration of Global Positioning Systems (GPS) with Inertial Navigation Systems (INS). In this paper a novel alignment method for a disturbed base, such as a vehicle disturbed by wind outdoors, implemented with the aid of a Vondrak low pass filter, is proposed. The basic principle of initial alignment including coarse alignment and fine alignment is introduced first. The spectral analysis is processed to compare the differences between the characteristic error of INS force observation on a stationary base and on disturbed bases. In order to reduce the high frequency noise in the force observation more accurately and more easily, a Vondrak low pass filter is constructed based on the spectral analysis result. The genetic algorithms method is introduced to choose the smoothing factor in the Vondrak filter and the corresponding objective condition is built. The architecture of the proposed alignment method with the Vondrak low pass filter is shown. Furthermore, simulated experiments and actual experiments were performed to validate the new algorithm. The results indicate that, compared with the conventional alignment method, the Vondrak filter could eliminate the high frequency noise in the force observation and the proposed alignment method could improve the attitude accuracy. At the same time, only one parameter needs to be set, which makes the proposed method easier to implement than other low-pass filter methods.

  20. A Vondrak Low Pass Filter for IMU Sensor Initial Alignment on a Disturbed Base

    Directory of Open Access Journals (Sweden)

    Zengke Li

    2014-12-01

    Full Text Available The initial alignment of the Inertial Measurement Unit (IMU is an important process of INS to determine the coordinate transformation matrix which is used in the integration of Global Positioning Systems (GPS with Inertial Navigation Systems (INS. In this paper a novel alignment method for a disturbed base, such as a vehicle disturbed by wind outdoors, implemented with the aid of a Vondrak low pass filter, is proposed. The basic principle of initial alignment including coarse alignment and fine alignment is introduced first. The spectral analysis is processed to compare the differences between the characteristic error of INS force observation on a stationary base and on disturbed bases. In order to reduce the high frequency noise in the force observation more accurately and more easily, a Vondrak low pass filter is constructed based on the spectral analysis result. The genetic algorithms method is introduced to choose the smoothing factor in the Vondrak filter and the corresponding objective condition is built. The architecture of the proposed alignment method with the Vondrak low pass filter is shown. Furthermore, simulated experiments and actual experiments were performed to validate the new algorithm. The results indicate that, compared with the conventional alignment method, the Vondrak filter could eliminate the high frequency noise in the force observation and the proposed alignment method could improve the attitude accuracy. At the same time, only one parameter needs to be set, which makes the proposed method easier to implement than other low-pass filter methods.

  1. Onorbit IMU alignment error budget

    Science.gov (United States)

    Corson, R. W.

    1980-01-01

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

  2. Determining molecular structures and conformations directly from electron diffraction using a genetic algorithm.

    Science.gov (United States)

    Habershon, Scott; Zewail, Ahmed H

    2006-02-13

    A global optimization strategy, based upon application of a genetic algorithm (GA), is demonstrated as an approach for determining the structures of molecules possessing significant conformational flexibility directly from gas-phase electron diffraction data. In contrast to the common approach to molecular structure determination, based on trial-and-error assessment of structures available from quantum chemical calculations, the GA approach described here does not require expensive quantum mechanical calculations or manual searching of the potential energy surface of the sample molecule, relying instead upon simple comparison between the experimental and calculated diffraction pattern derived from a proposed trial molecular structure. Structures as complex as all-trans retinal and p-coumaric acid, both important chromophores in photosensing processes, may be determined by this approach. In the examples presented here, we find that the GA approach can determine the correct conformation of a flexible molecule described by 11 independent torsion angles. We also demonstrate applications to samples comprising a mixture of two distinct molecular conformations. With these results we conclude that applications of this approach are very promising in elucidating the structures of large molecules directly from electron diffraction data.

  3. ATLAS Inner Detector Alignment

    CERN Document Server

    Bocci, A

    2008-01-01

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

  4. The Application of Multiobjective Genetic Algorithm to the Parameter Optimization of Single-Well Potential Stochastic Resonance Algorithm Aimed at Simultaneous Determination of Multiple Weak Chromatographic Peaks

    Directory of Open Access Journals (Sweden)

    Haishan Deng

    2014-01-01

    Full Text Available Simultaneous determination of multiple weak chromatographic peaks via stochastic resonance algorithm attracts much attention in recent years. However, the optimization of the parameters is complicated and time consuming, although the single-well potential stochastic resonance algorithm (SSRA has already reduced the number of parameters to only one and simplified the process significantly. Even worse, it is often difficult to keep amplified peaks with beautiful peak shape. Therefore, multiobjective genetic algorithm was employed to optimize the parameter of SSRA for multiple optimization objectives (i.e., S/N and peak shape and multiple chromatographic peaks. The applicability of the proposed method was evaluated with an experimental data set of Sudan dyes, and the results showed an excellent quantitative relationship between different concentrations and responses.

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

    Science.gov (United States)

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

    2017-09-01

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

  6. Alignment of Sexuality Education with Self Determination for People with Significant Disabilities: A Review of Research and Future Directions

    Science.gov (United States)

    Travers, Jason; Tincani, Matt; Whitby, Peggy Schaefer; Boutot, E. Amanda

    2014-01-01

    Sexual development is a complex but vital part of the human experience. People with significant disabilities are not excluded from this principle, but often may be prevented from receiving high-quality and comprehensive instruction necessary for a healthy sexual life. The functional model of self-determination emphasizes increasing knowledge,…

  7. Alignment of Sexuality Education with Self Determination for People with Significant Disabilities: A Review of Research and Future Directions

    Science.gov (United States)

    Travers, Jason; Tincani, Matt; Whitby, Peggy Schaefer; Boutot, E. Amanda

    2014-01-01

    Sexual development is a complex but vital part of the human experience. People with significant disabilities are not excluded from this principle, but often may be prevented from receiving high-quality and comprehensive instruction necessary for a healthy sexual life. The functional model of self-determination emphasizes increasing knowledge,…

  8. An algorithm for determining use of trauma-focused cognitive-behavioral therapy.

    Science.gov (United States)

    Lang, Jason M; Ford, Julian D; Fitzgerald, Monica M

    2010-12-01

    The shift toward dissemination of evidence-based practices has led to many questions about who is appropriate for a particular treatment model, particularly with complex clients, in diverse community settings, and when multiple evidence-based models have overlapping target populations. Few research-based tools exist to facilitate these clinical decisions. The research on trauma-focused cognitive-behavioral therapy (TF-CBT), an evidence-based treatment for children suffering from posttraumatic stress reactions, is reviewed to inform development of an algorithm to assist clinicians in determining whether a particular client is appropriate for TF-CBT. Recommendations are made for future research that will facilitate matching TF-CBT and other evidence-based practices to particular child clients.

  9. Intercomparison of Numerical Inversion Algorithms for Particle Size Determination of Polystyrene Suspensions Using Spectral Turbidimetry

    Directory of Open Access Journals (Sweden)

    Benjamin Glasse

    2015-01-01

    Full Text Available The continuous monitoring of the particle size distribution in particulate processes with suspensions or emulsions requires measurement techniques that can be used as in situ devices in contrast to ex situ or laboratory methods. In this context, for the evaluation of turbidimetric spectral measurements, the application of different numerical inversion algorithms is investigated with respect to the particle size distribution determination of polystyrene suspensions. A modified regularization concept consisting of a Twomey-Phillips-Regularization with an integrated nonnegative constraint and a modified L-curve criterion for the selection of the regularization parameter is used. The particle size (i.e., particle diameter of polystyrene suspensions in the range x=0.03–3 µm was validated via dynamic light scattering and differential centrifugal sedimentation and compared to the retrieved particle size distribution from the inverted turbidimetry measurements.

  10. Analysis of a distributed algorithm to determine multiple routes with path diversity in ad hoc networks.

    Energy Technology Data Exchange (ETDEWEB)

    Ghosal, Dipak (University of California, Davis, CA); Mueller, Stephen Ng

    2005-04-01

    With multipath routing in mobile ad hoc networks (MANETs), a source can establish multiple routes to a destination for routing data. In MANETs, mulitpath routing can be used to provide route resilience, smaller end-to-end delay, and better load balancing. However, when the multiple paths are close together, transmissions of different paths may interfere with each other, causing degradation in performance. Besides interference, the physical diversity of paths also improves fault tolerance. We present a purely distributed multipath protocol based on the AODV-Multipath (AODVM) protocol called AODVM with Path Diversity (AODVM/PD) that finds multiple paths with a desired degree of correlation between paths specified as an input parameter to the algorithm. We demonstrate through detailed simulation analysis that multiple paths with low degree of correlation determined by AODVM/PD provides both smaller end-to-end delay than AODVM in networks with low mobility and better route resilience in the presence of correlated node failures.

  11. ANALYZING THE DETERMINANTS OF THE VOTING BEHAVIOR USING A GENETIC ALGORITHM

    Directory of Open Access Journals (Sweden)

    Vizcaino-Gonzalez, Marcos

    2016-09-01

    Full Text Available Using data about votes emitted by funds in meetings held by United States banks from 2003 to 2013, we apply a genetic algorithm to a set of financial variables in order to detect the determinants of the vote direction. Our findings indicate that there are three main explanatory factors: the market value of the firm, the shareholder activism measured as the total number of funds voting, and the temporal context, which reflects the influence of recent critical events affecting the banking industry, including bankruptcies, reputational failures, and mergers and acquisitions. As a result, considering that voting behavior has been empirically linked to reputational harms, these findings can be considered as a useful insight about the keys that should be taken into account in order to achieve an effective reputational risk management strategy.

  12. A tomographic algorithm to determine tip-tilt information from laser guide stars

    Science.gov (United States)

    Reeves, A. P.; Morris, T. J.; Myers, R. M.; Bharmal, N. A.; Osborn, J.

    2016-06-01

    Laser Guide Stars (LGS) have greatly increased the sky-coverage of Adaptive Optics (AO) systems. Due to the up-link turbulence experienced by LGSs, a Natural Guide Star (NGS) is still required, preventing full sky-coverage. We present a method of obtaining partial tip-tilt information from LGSs alone in multi-LGS tomographic LGS AO systems. The method of LGS up-link tip-tilt determination is derived using a geometric approach, then an alteration to the Learn and Apply algorithm for tomographic AO is made to accommodate up-link tip-tilt. Simulation results are presented, verifying that the technique shows good performance in correcting high altitude tip-tilt, but not that from low altitudes. We suggest that the method is combined with multiple far off-axis tip-tilt NGSs to provide gains in performance and sky-coverage over current tomographic AO systems.

  13. A tomographic algorithm to determine tip-tilt information from laser guide stars

    CERN Document Server

    Reeves, A P; Myers, R M; Bharmal, N A; Osborn, J

    2016-01-01

    Laser Guide Stars (LGS) have greatly increased the sky-coverage of Adaptive Optics (AO) systems. Due to the up-link turbulence experienced by LGSs, a Natural Guide Star (NGS) is still required, preventing full sky-coverage. We present a method of obtaining tip-tilt information from LGSs alone in multi-LGS tomographic LGS AO systems. The method of LGS up-link tip-tilt determination is derived using a geometric approach, then an alteration to the Learn and Apply algorithm for tomographic AO is made to accommodate up-link tip-tilt. Simulation results are presented, verifying that the technique shows good performance in correcting high altitude tip-tilt, but not that from low altitudes. We suggest that the method is combined with far off-axis tip-tilt NGS to provide gains in performance and sky-coverage over current tomographic AO systems.

  14. Horizon Acquisition for Attitude Determination Using Image Processing Algorithms- Results of HORACE on REXUS 16

    Science.gov (United States)

    Barf, J.; Rapp, T.; Bergmann, M.; Geiger, S.; Scharf, A.; Wolz, F.

    2015-09-01

    The aim of the Horizon Acquisition Experiment (HORACE) was to prove a new concept for a two-axis horizon sensor using algorithms processing ordinary images, which is also operable at high spinning rates occurring during emergencies. The difficulty to cope with image distortions, which is avoided by conventional horizon sensors, was introduced on purpose as we envision a system being capable of using any optical data. During the flight on REXUS1 16, which provided a suitable platform similar to the future application scenario, a malfunction of the payload cameras caused severe degradation of the collected scientific data. Nevertheless, with the aid of simulations we could show that the concept is accurate (±0.6°), fast (~ lOOms/frame) and robust enough for coarse attitude determination during emergencies and also applicable for small satellites. Besides, technical knowledge regarding the design of REXUS-experiments, including the detection of interferences between SATA and GPS, was gained.

  15. NOTE: An algorithm for automatic determination of the respiratory phases in four-dimensional computed tomography

    Science.gov (United States)

    Kleshneva, T.; Muzik, J.; Alber, M.

    2006-08-01

    Recently, several techniques have been developed to improve the quality of computed tomography (CT) images of the thoracic and abdominal region that are degraded by the interference of the scanning process and respiration. Several devices for respiratory-correlated CT are available for clinical usage. They are based on the synchronization of the acquired CT image data with the respiratory motion using a signal from an external respiratory monitoring system. In this work, some practical aspects of clinical implementation of the multi-slice 4D CT scanner Somatom Sensation Open (Siemens Medical Solutions, Erlangen, Germany) equipped with a respiratory gating system (RGS) AZ-733V (Anzai Medical, Tokyo, Japan) are discussed. A new algorithm developed for automatic respiratory phase determination needed for the reconstruction of the 4D CT images is presented.

  16. Preliminary results of algorithms to determine horizontal and vertical underwater visibilities of coastal waters

    Digital Repository Service at National Institute of Oceanography (India)

    Suresh, T.; Joshi, Shreya; Talaulikar, M.; Desa, E.J.

    Algorithms developed for underwater horizontal and vertical visibilities are presented. The algorithms have been developed to derive the underwater visibilities based on the contrast theory using the in-situ and Hydrolight derived optical parameters...

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

    Energy Technology Data Exchange (ETDEWEB)

    Mohammadi, Shahin [Purdue Univ., West Lafayette, IN (United States); Gleich, David F. [Purdue Univ., West Lafayette, IN (United States); Kolda, Tamara G. [Sandia National Laboratories (SNL-CA), Livermore, CA (United States); Grama, Ananth [Purdue Univ., West Lafayette, IN (United States)

    2015-11-01

    Network alignment is an important tool with extensive applications in comparative interactomics. Traditional approaches aim to simultaneously maximize the number of conserved edges and the underlying similarity of aligned entities. We propose a novel formulation of the network alignment problem that extends topological similarity to higher-order structures and provide a new objective function that maximizes the number of aligned substructures. This objective function corresponds to an integer programming problem, which is NP-hard. Consequently, we approximate this objective function as a surrogate function whose maximization results in a tensor eigenvalue problem. Based on this formulation, we present an algorithm called Triangular AlignMEnt (TAME), which attempts to maximize the number of aligned triangles across networks. We focus on alignment of triangles because of their enrichment in complex networks; however, our formulation and resulting algorithms can be applied to general motifs. Using a case study on the NAPABench dataset, we show that TAME is capable of producing alignments with up to 99% accuracy in terms of aligned nodes. We further evaluate our method by aligning yeast and human interactomes. Our results indicate that TAME outperforms the state-of-art alignment methods both in terms of biological and topological quality of the alignments.

  18. Validation of the TES algorithm for emissivity determination using field measurements

    Science.gov (United States)

    Schmugge, T.; Ogawa, K.; French, A.; Ritchie, J.; Rango, A.

    2009-04-01

    Knowledge of the surface emissivity is important for determining the radiation balance at the land surface. This is especially true for arid regions with sparse vegetation, where the emissivity of the exposed soils and rocks is highly variable. The multispectral thermal infrared data obtained from the Advanced Spaceborne Thermal Emission and Reflection (ASTER) radiometer on NASA's Terra satellite have been shown to be of good quality and provide a unique new tool for studying the emissivity of the land surface. ASTER has 5 channels in the 8 to 12 micrometer waveband with 90 m spatial resolution, when the data are combined with the Temperature Emissivity Separation (TES) algorithm the surface emissivity over this wavelength region can be determined along with surface temperature. To overcome the problem of having too many unknowns, i.e. 5 emissivities and the surface temperature, TES makes use of an empirical relation between the minimum emissivity and the range of values for the 5 ASTER channels. The TES algorithm was validated using measurements with a multispectral thermal infrared field radiometer (CIMEL 312) which has essentially the same 5 bands as ASTER. The measurements were made on several soils in the Jornada Experimental Range (JER) and the White Sands National Monument in southern New Mexico, USA. The JER is a long-term ecological reserve (LTER) site located at the northern end of the Chihuahuan desert. The site is typical of desert grassland where the main vegetation components are grass and shrubs. At the White Sands National Monument dunes of gypsum sand cover about 700 km2 (275 square miles). Since gypsum has a unique emissivity spectra with a pronounced minimum at the 8.6 micrometer wavelength it is a good target for satellite observations of emissivity. The observed emissivity spectra for these sites in New Mexico show good agreement ( <0.02) with values calculated from the laboratory spectra for the soil samples when the difference of physical

  19. EM-CDKF algorithm and its applications on SINS′initial alignment%EM-CDKF算法及其SINS初始对准应用

    Institute of Scientific and Technical Information of China (English)

    丁国强; 徐洁; 周卫东; 张志艳

    2014-01-01

    针对非线性捷联惯导系统噪声先验统计信息未知问题,基于中心差分卡尔曼滤波基本算法,采用极大似然准则构造极大期望最速下降梯度算法展开系统未知噪声统计特性在线估计计算研究,构建一类捷联惯导系统初始对准极大期望自适应中心差分最优滤波算法。该算法利用极大似然准则构造系统噪声统计特性对数似然函数,采用极大期望最速下降梯度法把系统噪声统计特性估计转化为对数似然函数期望最大值计算,获得系统过程噪声和观测噪声在线递推估计的自适应极大期望中心差分卡尔曼算法。经过大方位失准角捷联惯导系统初始对准仿真实验,与中心差分卡尔曼滤波基本算法相比,自适应极大期望中心差分卡尔曼算法能够有效解决基本算法在系统噪声先验知识未知情形下的滤波精度下降甚至发散问题,并且能够实现系统噪声统计特性的在线递推估计。%As the unknow n priori statistical properties of the nonlinear strap-dow n inertial navigation system (SINS) noises ,based on the central divided Kalman filtering (CDKF) algorithm ,the expecta-tion maximum steepest descent method was presented to develop the adaptive expectation maximum based central divided Kalman filtering (EM-CDKF) algorithm with maximum likelihood criterion ,to evaluate on-line the system noise’s statistical properties .The EM-CDKF algorithm constructs the Log-likelihood function of system noises statistical properties with maximum likelihood criterion ,and transforms the estimation evaluation of system noise statistical properties into the maximum evalua-tion of Log-likelihood function with the expectation maximum steepest descent method ,and with the EM-CDKF algorithm ,the process and measurement noises can be evaluated by online recursive pat-tern .T he simulink experiments of SINS’ large azimuth misalignment angle indicate that ,compared to

  20. Pin-Align: a new dynamic programming approach to align protein-protein interaction networks.

    Science.gov (United States)

    Amir-Ghiasvand, Farid; Nowzari-Dalini, Abbas; Momenzadeh, Vida

    2014-01-01

    To date, few tools for aligning protein-protein interaction networks have been suggested. These tools typically find conserved interaction patterns using various local or global alignment algorithms. However, the improvement of the speed, scalability, simplification, and accuracy of network alignment tools is still the target of new researches. In this paper, we introduce Pin-Align, a new tool for local alignment of protein-protein interaction networks. Pin-Align accuracy is tested on protein interaction networks from IntAct, DIP, and the Stanford Network Database and the results are compared with other well-known algorithms. It is shown that Pin-Align has higher sensitivity and specificity in terms of KEGG Ortholog groups.

  1. Pin-Align: A New Dynamic Programming Approach to Align Protein-Protein Interaction Networks

    Directory of Open Access Journals (Sweden)

    Farid Amir-Ghiasvand

    2014-01-01

    Full Text Available To date, few tools for aligning protein-protein interaction networks have been suggested. These tools typically find conserved interaction patterns using various local or global alignment algorithms. However, the improvement of the speed, scalability, simplification, and accuracy of network alignment tools is still the target of new researches. In this paper, we introduce Pin-Align, a new tool for local alignment of protein-protein interaction networks. Pin-Align accuracy is tested on protein interaction networks from IntAct, DIP, and the Stanford Network Database and the results are compared with other well-known algorithms. It is shown that Pin-Align has higher sensitivity and specificity in terms of KEGG Ortholog groups.

  2. Robust and Efficient Parametric Face Alignment

    NARCIS (Netherlands)

    Tzimiropoulos, Georgios; Zafeiriou, Stefanos; Pantic, Maja

    2011-01-01

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

  3. Locally converging algorithms for determining the critical temperature in Ising systems

    Science.gov (United States)

    Faraggi, Eshel; Robb, Daniel T.

    2008-10-01

    We introduce a class of algorithms that converge to criticality automatically, in a way similar to the invaded cluster algorithm. Unlike the invaded cluster algorithm which uses global percolation as a test for criticality, these local algorithms use an average over local observables, specifically the number of satisfied bonds, in a feedback loop which drives the system toward criticality. Two specific algorithms are introduced, the average algorithm and the locally converging Wolff algorithm. We apply these algorithms to study the Ising square lattice and the Ising Bethe lattice. We find reasonable convergence to the critical temperature for both systems under the locally converging Wolff algorithm. We also re-examine the phase diagram of the dilute two-dimensional (2D) Ising model and find results supporting our previously reported conclusions regarding the existence of a local regime of magnetization below the percolations threshold. In addition, the presented algorithms are computationally more efficient than the invaded cluster algorithm, requiring less CPU time and memory.

  4. 方位捷联平台重力仪分布式Kalman滤波初始对准算法%Distributed Kalman filter initial alignment algorithm for azimuth strapdown platform gravimeter

    Institute of Scientific and Technical Information of China (English)

    杨晔; 毋兴涛; 杨建林; 高巍; 裴志

    2014-01-01

    为充分利用分布式架构重力仪各处理器并行计算的能力,解决单个处理器运行整体式 Kalman滤波所遇到的非实时性问题,设计了一种分布式 Kalman 滤波对准算法。首先,给出了方位捷联平台重力仪的误差方程,建立了系统的状态方程和观测方程。然后,用协方差分析法对系统初始对准滤波方程进行处理,将原系统分解成维数相同的两个子系统,得到由两个子滤波器构成的初始对准滤波器。最后,利用Matlab建立了方位捷联平台惯导模型,分别应用整体式滤波和分布式滤波进行静基座初始对准。仿真结果表明,分布式滤波算法与整体式滤波算法具有相同的滤波精度,并且分布式滤波用时只有整体式滤波的60%,更有利于保证滤波算法的实时性。%A distributed Kalman filter alignment algorithm is developed in order to use the parallel computing ability of the distributed architecture gravimeter to solve the non real-time implementation of filtering based on one single processor. Firstly, the error equations of the azimuth strapdown platform gravimeter are deduced, and the state equations and observation equations are built. Secondly, an error covariance analytical method is applied to the filtering equations, and the system is decentralised into two subsystems with the same dimension. In this way we get the initial alignment filter formed by the two subfilters. Finally, the azimuth strapdown platform model is built by using Matlab, and stationary base alignment is implemented by using global Kalman filter and distributed Kalman filter separately. The simulation results show that the distributed filter has the same filtering accuracy and costs only 60%of time compared with the global one, which is favorable to ensure the real-time performance of the algorithm.

  5. Two algorithms for auto alignment in rocking base of SINS%捷联惯导晃动基座自对准算法比较

    Institute of Scientific and Technical Information of China (English)

    黄春梅; 孙晓慧; 许永龙; 于硕

    2013-01-01

    为了提高晃动载体的初始对准精度,分别采用了卡尔曼滤波法和 H∞滤波法。高斯白噪声和随机晃动的条件下进行两种算法的仿真研究,结果表明,高斯白噪声条件下,两者的滤波效果都很好,但在加入基座周期性晃动时,卡尔曼滤波出现了明显的发散现象,H∞滤波表现出了更好的稳定性。%Both Kalman Filter and H ∞ Filter are applied to improve the initial alignment accuracy .The two filters are simulated under conditions of white Gaussian noise and periodic rocking base respectively .The results show that both filters work well under white Gaussian noise but there is a obvious divergence phenomenon in Kalman Filter w hile H ∞ Filter remains stable w hen periodic rocking base noise is added .

  6. Aligning Sequences by Minimum Description Length

    Directory of Open Access Journals (Sweden)

    John S. Conery

    2008-01-01

    Full Text Available This paper presents a new information theoretic framework for aligning sequences in bioinformatics. A transmitter compresses a set of sequences by constructing a regular expression that describes the regions of similarity in the sequences. To retrieve the original set of sequences, a receiver generates all strings that match the expression. An alignment algorithm uses minimum description length to encode and explore alternative expressions; the expression with the shortest encoding provides the best overall alignment. When two substrings contain letters that are similar according to a substitution matrix, a code length function based on conditional probabilities defined by the matrix will encode the substrings with fewer bits. In one experiment, alignments produced with this new method were found to be comparable to alignments from CLUSTALW. A second experiment measured the accuracy of the new method on pairwise alignments of sequences from the BAliBASE alignment benchmark.

  7. Measurement methods and interpretation algorithms for the determination of the remaining lifetime of the electrical insulation

    Directory of Open Access Journals (Sweden)

    Engster F.

    2005-12-01

    Full Text Available The paper presents a set of on-line and off-line measuring methods for the dielectric parameters of the electric insulation as well as the method of results interpretation aimed to determine the occurence of a damage and to set up the its speed of evolution. These results lead finally to the determination of the life time under certain imposed safety conditions. The interpretation of the measurement results is done based on analytical algorithms allowing also the calculation of the index of correlation between the real results and the mathematical interpolation. It is performed a comparative analysis between different measuring and interpretation methods. There are considered certain events occurred during the measurement performance including their causes. The working-out of the analytical methods has been improved during the during the dielectric measurements performance for about 25 years at a number of 140 turbo and hydro power plants. Finally it is proposed a measurement program to be applied and which will allow the correlation of the on-line and off-line dielectric measurement obtaining thus a reliable technology of high accuracy level for the estimation of the available lifetime of electrical insulation.

  8. Genetic algorithms for determining the parameters of cellular automata in urban simulation

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    This paper demonstrates that cellular automata (CA) can be a useful tool for analyzing the process of many geographical phenomena. There are many studies on using CA to simulate the evolution of cites. Urban dynamics is determined by many spatial variables. The contribution of each spatial variable to the simulation is quantified by its parameter or weight. Calibration procedures are usually required for obtaining a suitable set of parameters so that the realistic urban forms can be simulated. Each parameter has a unique role in controlling urban morphology in the simulation. In this paper, these parameters for urban simulation are determined by using empirical data. Genetic algorithms are used to search for the optimal combination of these parameters. There are spatial variations for urban dynamics in a large region. Distinct sets of parameters can be used to represent the unique features of urban dynamics for various subregions. A further experiment is to evaluate each set of parameters based on the theories of compact cities. It is considered that the better set of parameters can be identified according to the utility function in terms of compact development. This set of parameters can be cloned to other regions to improve overall urban morphology. The original parameters can be also modified to produce more compact urban forms for planning purposes. This approach can provide a useful exploratory tool for testing various planning scenarios for urban development.

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

    Science.gov (United States)

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

    2010-01-01

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

  10. Aligned Layers of Silver Nano-Fibers

    Directory of Open Access Journals (Sweden)

    Andrii B. Golovin

    2012-02-01

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

  11. Algorithm for vertical ozone profile determination for the Nimbus-4 BUV data set

    Science.gov (United States)

    Bhartia, P. K.; Klenk, K. F.; Kaveeshwar, V. G.; Ahmad, S.; Fleig, A. J.; Mcpeters, R. D.; Mateer, C. L.

    1981-01-01

    A description is provided of the algorithm used by the Ozone Processing Team at NASA to process seven years of Backscatter Ultraviolet (BUV) ozone profile data. The algorithm is a modification of the original retrieval algorithm developed by Mateer (1972) to process some of the early data from the BUV experiment. Principal changes made are in the first guess selection scheme, the use of all wavelengths in the inversion, and the weighting of the various wavelengths according to the errors in the radiance estimation. It is found that the described BUV ozone profile algorithm is an extremely efficient algorithm for retrieving large amounts of satellite data. The algorithm makes full use of all the available information from the measured radiances including the longer wavelength radiances which previously had not been used.

  12. Determining hypocentral parameters for local earthquakes under ill conditions using genetic algorithm

    Science.gov (United States)

    Kim, Woohan; Hahm, In-Kyeong; Kim, Won-Young; Lee, Jung Mo

    2010-10-01

    We demonstrate that GA-MHYPO determines accurate hypocentral parameters for local earthquakes under ill conditions, such as limited number of stations (phase data), large azimuthal gap, and noisy data. The genetic algorithm (GA) in GA-MHYPO searches for the optimal 1-D velocity structure which provides the minimum traveltime differences between observed (true) and calculated P and S arrivals within prescribed ranges. GA-MHYPO is able to determine hypocentral parameters more accurately in many circumstances than conventional methods which rely on an a priori (and possibly incorrect) 1-D velocity model. In our synthetic tests, the accuracy of hypocentral parameters obtained by GA-MHYPO given ill conditions is improved by more than a factor of 20 for error-free data, and by a factor of five for data with errors, compared to that obtained by conventional methods such as HYPOINVERSE. In the case of error-free data, GA-MHYPO yields less than 0.1 km errors in focal depths and hypocenters without strong dependence on azimuthal coverage up to 45°. Errors are less than 1 km for data with errors of a 0.1-s standard deviation. To test the performance using real data, a well-recorded earthquake in the New Madrid seismic zone and earthquakes recorded under ill conditions in the High Himalaya are relocated by GA-MHYPO. The hypocentral parameters determined by GA-MHYPO under both good and ill conditions show similar computational results, which suggest that GA-MHYPO is robust and yields more reliable hypocentral parameters than standard methods under ill conditions for natural earthquakes.

  13. Efficient Algorithm Using a Broadband Approach to Determine the Complex Constants of Piezoelectric Ceramics

    Science.gov (United States)

    Buiochi, F.; Kiyono, C. Y.; Peréz, N.; Adamowski, J. C.; Silva, E. C. N.

    A new systematic and efficient algorithm to obtain the ten complex constants of piezoelectric materials belonging to the 6 mm symmetry class was developed. A finite element method routine was implemented in Matlab using eight-node axisymmetric elements. The algorithm raises the electrical conductance and resistance curves and calculates the quadratic difference between the experimental and numerical curves. Finally, to minimize the difference, an optimization algorithm based on the "Method of Moving Asymptotes" (MMA) is used. The algorithm is able to adjust the curves over a wide frequency range obtaining the real and imaginary parts of the material properties simultaneously.

  14. Low-Carbon Energy Development in Indonesia in Alignment with Intended Nationally Determined Contribution (INDC by 2030

    Directory of Open Access Journals (Sweden)

    Ucok W.R. Siagian

    2017-01-01

    Full Text Available This study analyzed the role of low-carbon energy technologies in reducing the greenhouse gas emissions of Indonesia’s energy sector by 2030. The aim of this study was to provide insights into the Indonesian government’s approach to developing a strategy and plan for mitigating emissions and achieving Indonesia’s emission reduction targets by 2030, as pledged in the country’s Intended Nationally Determined Contribution. The Asia-Pacific Integrated Model/Computable General Equilibrium (AIM/CGE model was used to quantify three scenarios that had the same socioeconomic assumptions: baseline, countermeasure (CM1, and CM2, which had a higher emission reduction target than that of CM1. Results of the study showed that an Indonesian low-carbon energy system could be achieved with two pillars, namely, energy efficiency measures and deployment of less carbon-intensive energy systems (i.e., the use of renewable energy in the power and transport sectors, and the use of natural gas in the power sector and in transport. Emission reductions would also be satisfied through the electrification of end-user consumption where the electricity supply becomes decarbonized by deploying renewables for power generation. Under CM1, Indonesia could achieve a 15.5% emission reduction target (compared to the baseline scenario. This reduction could be achieved using efficiency measures that reduce final energy demand by 4%; This would require the deployment of geothermal power plants at a rate six times greater than the baseline scenario and four times the use of hydropower than that used in the baseline scenario. Greater carbon reductions (CM2; i.e., a 27% reduction could be achieved with similar measures to CM1 but with more intensive penetration. Final energy demand would need to be cut by 13%, deployment of geothermal power plants would need to be seven times greater than at baseline, and hydropower use would need to be five times greater than the baseline case

  15. Fast algorithms for determining the linear complexities of sequences over GF(pm) with the period 3n

    Institute of Scientific and Technical Information of China (English)

    CHEN; Hao

    2006-01-01

    In this paper, for the the primes p such that 3 is a divisor of p - 1, we prove a result which reduces the computation of the linear complexity of a sequence over GF(pm)(any positive integer m) with the period 3n (n and pm - 1 are coprime) to the computation of the linear complexities of three sequences with the period n. Combined with some known algorithms such as generalized Games-Chan algorithm, Berlekamp-Massey algorithm and Xiao-Wei-Lam-lmamura algorithm, we can determine the linear complexity of any sequence over GF(pm) with the period 3n (n and pm - 1 are coprime) more efficiently.

  16. Cognitive Development Optimization Algorithm Based Support Vector Machines for Determining Diabetes

    Directory of Open Access Journals (Sweden)

    Utku Kose

    2016-03-01

    Full Text Available The definition, diagnosis and classification of Diabetes Mellitus and its complications are very important. First of all, the World Health Organization (WHO and other societies, as well as scientists have done lots of studies regarding this subject. One of the most important research interests of this subject is the computer supported decision systems for diagnosing diabetes. In such systems, Artificial Intelligence techniques are often used for several disease diagnostics to streamline the diagnostic process in daily routine and avoid misdiagnosis. In this study, a diabetes diagnosis system, which is formed via both Support Vector Machines (SVM and Cognitive Development Optimization Algorithm (CoDOA has been proposed. Along the training of SVM, CoDOA was used for determining the sigma parameter of the Gauss (RBF kernel function, and eventually, a classification process was made over the diabetes data set, which is related to Pima Indians. The proposed approach offers an alternative solution to the field of Artificial Intelligence-based diabetes diagnosis, and contributes to the related literature on diagnosis processes.

  17. An image segmentation based on a genetic algorithm for determining soil coverage by crop residues.

    Science.gov (United States)

    Ribeiro, Angela; Ranz, Juan; Burgos-Artizzu, Xavier P; Pajares, Gonzalo; del Arco, Maria J Sanchez; Navarrete, Luis

    2011-01-01

    Determination of the soil coverage by crop residues after ploughing is a fundamental element of Conservation Agriculture. This paper presents the application of genetic algorithms employed during the fine tuning of the segmentation process of a digital image with the aim of automatically quantifying the residue coverage. In other words, the objective is to achieve a segmentation that would permit the discrimination of the texture of the residue so that the output of the segmentation process is a binary image in which residue zones are isolated from the rest. The RGB images used come from a sample of images in which sections of terrain were photographed with a conventional camera positioned in zenith orientation atop a tripod. The images were taken outdoors under uncontrolled lighting conditions. Up to 92% similarity was achieved between the images obtained by the segmentation process proposed in this paper and the templates made by an elaborate manual tracing process. In addition to the proposed segmentation procedure and the fine tuning procedure that was developed, a global quantification of the soil coverage by residues for the sampled area was achieved that differed by only 0.85% from the quantification obtained using template images. Moreover, the proposed method does not depend on the type of residue present in the image. The study was conducted at the experimental farm "El Encín" in Alcalá de Henares (Madrid, Spain).

  18. An objective algorithm for the determination of bone mineral content using dichromatic absorptiometry

    Energy Technology Data Exchange (ETDEWEB)

    Appledorn, C.R.; Witt, R.M.; Wellman, H.N.; Johnston, C.C.

    1985-05-01

    The determination of vertebral column bone mineral content by dual photon absorptiometric methods is a problem of continued clinical interest. The more successful methods suffer from the frequent need of operator interaction in order to maintain good precision results. The authors have introduced a new objective algorithm that eliminates the subjectiveness of operator interaction without sacrificing reproducibility. The authors' system consists of a modified rectilinear scanner interfaced to a CAMAC acquisition device coupled to a PDP-11V03 minicomputer. The subject is scanned in the supine position with legs elevated to minimize lordosis. The source (Gd-153) and detector are collimated defining an area of 10mm x 10mm at the level of the spine. The transverse scan width is usually 120 mm. Scanning from the iliac crests toward the head, 50 transverses at 3mm y-increments are acquired at approximately 1mm increments. The data analysis begins with the calculation of R-value for each pixel in the scan. The calculations for bone mineral content are performed and various quantities are accumulated. In a reproducibility study of 116 patient studies, the authors achieved a bone mineral/bone area ratio precision (std dev/mean) of 1.37% without operator interaction nor vertebral body selection.

  19. Determination of thermal emission spectra maximizing thermophotovoltaic performance using a genetic algorithm

    CERN Document Server

    DeSutter, John; Francoeur, Mathieu

    2016-01-01

    Optimal radiator thermal emission spectra maximizing thermophotovoltaic (TPV) conversion efficiency and output power density are determined when temperature effects in the cell are considered. To do this, a framework is designed in which a TPV model that accounts for radiative, electrical and thermal losses is coupled with a genetic algorithm. The TPV device under study involves a spectrally selective radiator at a temperature of 2000 K, a gallium antimonide cell, and a cell thermal management system characterized by a fluid temperature and a heat transfer coefficient of 293 K and 600 Wm-2K-1. It is shown that a maximum conversion efficiency of 38.8% is achievable with an emission spectrum that has emissivity of unity between 0.719 eV and 0.763 eV and zero elsewhere. This optimal spectrum is less than half of the width of those when thermal losses are neglected. A maximum output power density of 41708 Wm-2 is achievable with a spectrum having emissivity values of unity between 0.684 eV and 1.082 eV and zero e...

  20. Cognitive Development Optimization Algorithm Based Support Vector Machines for Determining Diabetes

    Directory of Open Access Journals (Sweden)

    Utku Kose

    2016-03-01

    Full Text Available The definition, diagnosis and classification of Diabetes Mellitus and its complications are very important. First of all, the World Health Organization (WHO and other societies, as well as scientists have done lots of studies regarding this subject. One of the most important research interests of this subject is the computer supported decision systems for diagnosing diabetes. In such systems, Artificial Intelligence techniques are often used for several disease diagnostics to streamline the diagnostic process in daily routine and avoid misdiagnosis. In this study, a diabetes diagnosis system, which is formed via both Support Vector Machines (SVM and Cognitive Development Optimization Algorithm (CoDOA has been proposed. Along the training of SVM, CoDOA was used for determining the sigma parameter of the Gauss (RBF kernel function, and eventually, a classification process was made over the diabetes data set, which is related to Pima Indians. The proposed approach offers an alternative solution to the field of Artificial Intelligence-based diabetes diagnosis, and contributes to the related literature on diagnosis processes.

  1. A hybrid algorithm of BSC and QFD to determine the criteria affecting implementation of successful outsourcing

    Directory of Open Access Journals (Sweden)

    Mohammad Hemati

    2012-04-01

    Full Text Available Successful organizations share some identical factors that pave the way for their success. Among these factors, strategic management is the key to success for organizations to contribute more to the competitive world market of today. In this respect, the pivotal role of outsourcing cannot be denied. This research parallelizes the criteria affecting the outsourcing success as presented in Elmuti model with the Balanced score card method in the Tose'e Ta'avon Bank. In this research, questionnaires and interviews with experts helped determine the strategic goals at four perspectives of balanced score card method (at Tose'e Ta'avon Bank and the relative weights were computed for each of balance score card (BSC perspectives by using AHP method. As the next step, the indexes were prioritized by applying the quality function development(QFD technique and considering strategic goals at four perspectives in section "WHAT" and the outsourcing success criteria of Elmuti model in section "HOW". At the end of algorithm, the results are compared with the Elmuti method. Based on the results, the hybrid proposed technique seems to perform better than Elmuti.

  2. Multiple Whole Genome Alignments Without a Reference Organism

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-01-16

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

  3. Determination of multifractal dimensions of complex networks by means of the sandbox algorithm

    Science.gov (United States)

    Liu, Jin-Long; Yu, Zu-Guo; Anh, Vo

    2015-02-01

    Complex networks have attracted much attention in diverse areas of science and technology. Multifractal analysis (MFA) is a useful way to systematically describe the spatial heterogeneity of both theoretical and experimental fractal patterns. In this paper, we employ the sandbox (SB) algorithm proposed by Tél et al. (Physica A 159, 155-166 (1989)), for MFA of complex networks. First, we compare the SB algorithm with two existing algorithms of MFA for complex networks: the compact-box-burning algorithm proposed by Furuya and Yakubo (Phys. Rev. E 84, 036118 (2011)), and the improved box-counting algorithm proposed by Li et al. (J. Stat. Mech.: Theor. Exp. 2014, P02020 (2014)) by calculating the mass exponents τ(q) of some deterministic model networks. We make a detailed comparison between the numerical and theoretical results of these model networks. The comparison results show that the SB algorithm is the most effective and feasible algorithm to calculate the mass exponents τ(q) and to explore the multifractal behavior of complex networks. Then, we apply the SB algorithm to study the multifractal property of some classic model networks, such as scale-free networks, small-world networks, and random networks. Our results show that multifractality exists in scale-free networks, that of small-world networks is not obvious, and it almost does not exist in random networks.

  4. Probabilistic sequence alignment of stratigraphic records

    Science.gov (United States)

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

    2014-10-01

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

  5. Faster exon assembly by sparse spliced alignment

    CERN Document Server

    Tiskin, Alexander

    2007-01-01

    Assembling a gene from candidate exons is an important problem in computational biology. Among the most successful approaches to this problem is \\emph{spliced alignment}, proposed by Gelfand et al., which scores different candidate exon chains within a DNA sequence of length $m$ by comparing them to a known related gene sequence of length n, $m = \\Theta(n)$. Gelfand et al.\\ gave an algorithm for spliced alignment running in time O(n^3). Kent et al.\\ considered sparse spliced alignment, where the number of candidate exons is O(n), and proposed an algorithm for this problem running in time O(n^{2.5}). We improve on this result, by proposing an algorithm for sparse spliced alignment running in time O(n^{2.25}). Our approach is based on a new framework of \\emph{quasi-local string comparison}.

  6. Some aspects of SR beamline alignment

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-09-01

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

  7. A Multi-Agent Immune Network Algorithm and Its Application to Murphree Efficiency Determination for the Distillation Column

    Institute of Scientific and Technical Information of China (English)

    Xuhua Shi; Feng Qian

    2011-01-01

    Artificial Immune Network (aiNet) algorithms have become popular for global optimization in many modern industrial applications. However, high-dimensional systems using such models suffer from a potential premature convergence problem. In the existing aiNet algorithms, the premature convergence problem can be avoided by implementing various clonal selection methods, such as immune suppression and mutation approaches, both for single population and multi-population cases. This paper presents a new Multi-Agent Artificial Immune Network (Ma-aiNet) algorithm, which combines immune mechanics and multiagent technology, to overcome the premature convergence problem in high-dimensional systems and to efficiently use the agent ability of sensing and acting on the environment. Ma-aiNet integrates global and local search algorithms. The performance of the proposed method is evaluated using 10 benchmark problems, and the results are compared with other well-known intelligent algorithms. The study demonstrates that Ma-aiNet outperforms other algorithms tested. Ma-aiNet is also used to determine the Murphree efficiency of a distillation column with satisfactory results.

  8. DEMON-type algorithms for determination of hydro-acoustic signatures of surface ships and of divers

    Science.gov (United States)

    Slamnoiu, G.; Radu, O.; Rosca, V.; Pascu, C.; Damian, R.; Surdu, G.; Curca, E.; Radulescu, A.

    2016-08-01

    With the project “System for detection, localization, tracking and identification of risk factors for strategic importance in littoral areas”, developed in the National Programme II, the members of the research consortium intend to develop a functional model for a hydroacoustic passive subsystem for determination of acoustic signatures of targets such as fast boats and autonomous divers. This paper presents some of the results obtained in the area of hydroacoustic signal processing by using DEMON-type algorithms (Detection of Envelope Modulation On Noise). For evaluation of the performance of various algorithm variations we have used both audio recordings of the underwater noise generated by ships and divers in real situations and also simulated noises. We have analysed the results of processing these signals using four DEMON algorithm structures as presented in the reference literature and a fifth DEMON algorithm structure proposed by the authors of this paper. The algorithm proposed by the authors generates similar results to those obtained by applying the traditional algorithms but requires less computing resources than those and at the same time it has proven to be more resilient to random noise influence.

  9. deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns

    Science.gov (United States)

    Ekstrøm, Claus T.; Stadler, Peter F.; Hoffmann, Steve; Gorodkin, Jan

    2012-01-01

    Motivation: High-throughput sequencing methods allow whole transcriptomes to be sequenced fast and cost-effectively. Short RNA sequencing provides not only quantitative expression data but also an opportunity to identify novel coding and non-coding RNAs. Many long transcripts undergo post-transcriptional processing that generates short RNA sequence fragments. Mapped back to a reference genome, they form distinctive patterns that convey information on both the structure of the parent transcript and the modalities of its processing. The miR-miR* pattern from microRNA precursors is the best-known, but by no means singular, example. Results: deepBlockAlign introduces a two-step approach to align RNA-seq read patterns with the aim of quickly identifying RNAs that share similar processing footprints. Overlapping mapped reads are first merged to blocks and then closely spaced blocks are combined to block groups, each representing a locus of expression. In order to compare block groups, the constituent blocks are first compared using a modified sequence alignment algorithm to determine similarity scores for pairs of blocks. In the second stage, block patterns are compared by means of a modified Sankoff algorithm that takes both block similarities and similarities of pattern of distances within the block groups into account. Hierarchical clustering of block groups clearly separates most miRNA and tRNA, and also identifies about a dozen tRNAs clustering together with miRNA. Most of these putative Dicer-processed tRNAs, including eight cases reported to generate products with miRNA-like features in literature, exhibit read blocks distinguished by precise start position of reads. Availability: The program deepBlockAlign is available as source code from http://rth.dk/resources/dba/. Contact: gorodkin@rth.dk; studla@bioinf.uni-leipzig.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22053076

  10. Evaluation of alignment methods and data pretreatments on the determination of the most important peaks for the discrimination of coffee varieties Arabica and Robusta using gas chromatography-mass spectroscopy.

    Science.gov (United States)

    Hovell, A M C; Pereira, E J; Arruda, N P; Rezende, C M

    2010-09-30

    Coffee samples were analyzed by GC/MS in order to determine the most important peaks for the discrimination of the varieties Arabica and Robusta. The resulting peak tables from chromatographic analysis were aligned and pretreated before being submitted to multivariate analysis. A rapid and easy-to-perform peak alignment procedure, which does not require advanced programming skills to use, was compared with the tedious manual alignment procedure. The influence of three types of data pretreatment, normalization, logarithmic and square root transformations and their combinations, on the variables selected as most important by the regression coefficients of partial least squares-discriminant analysis (PLS-DA), are shown. Test samples different from those used in the calibration and comparison with the substances already known as being responsible for Arabica and Robusta coffees discrimination were used to determine the best pretreatments for both datasets. The data pretreatment consisting of square root transformation followed by normalization (RN) was chosen as being the most appropriate. The results obtained showed that the much quicker automated aligned method could be used as a substitute for the manually aligned method, allowing all the peaks in the chromatogram to be used for multivariate analysis. Copyright © 2010 Elsevier B.V. All rights reserved.

  11. Determining the band alignment of TbAs:GaAs and TbAs:In{sub 0.53}Ga{sub 0.47}As

    Energy Technology Data Exchange (ETDEWEB)

    Bomberger, Cory C.; Chase, D. Bruce; Zide, Joshua M. O., E-mail: zide@udel.edu [Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716 (United States); Vanderhoef, Laura R. [Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716 (United States); Rahman, Abdur [Physics and Technology Department, Edinboro University of Pennsylvania, Edinboro, Pennsylvania 16444 (United States); Shah, Deesha; Taylor, Antoinette J.; Azad, Abul K. [Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Doty, Matthew F. [Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716 (United States); Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716 (United States)

    2015-09-07

    We propose and systematically justify a band structure for TbAs nanoparticles in GaAs and In{sub 0.53}Ga{sub 0.47}As host matrices. Fluence-dependent optical-pump terahertz-probe measurements suggest the TbAs nanoparticles have a band gap and provide information on the carrier dynamics, which are determined by the band alignment. Spectrophotometry measurements provide the energy of optical transitions in the nanocomposite systems and reveal a large blue shift in the absorption energy when the host matrix is changed from In{sub 0.53}Ga{sub 0.47}As to GaAs. Finally, Hall data provides the approximate Fermi level in each system. From this data, we deduce that the TbAs:GaAs system forms a type I (straddling) heterojunction and the TbAs:In{sub 0.53}Ga{sub 0.47}As system forms a type II (staggered) heterojunction.

  12. Automatic determination of the arterial input function in dynamic susceptibility contrast MRI: comparison of different reproducible clustering algorithms

    Energy Technology Data Exchange (ETDEWEB)

    Yin, Jiandong; Yang, Jiawen; Guo, Qiyong [Shengjing Hospital of China Medical University, Department of Radiology, Shenyang (China)

    2015-05-01

    Arterial input function (AIF) plays an important role in the quantification of cerebral hemodynamics. The purpose of this study was to select the best reproducible clustering method for AIF detection by comparing three algorithms reported previously in terms of detection accuracy and computational complexity. First, three reproducible clustering methods, normalized cut (Ncut), hierarchy (HIER), and fast affine propagation (FastAP), were applied independently to simulated data which contained the true AIF. Next, a clinical verification was performed where 42 subjects participated in dynamic susceptibility contrast MRI (DSC-MRI) scanning. The manual AIF and AIFs based on the different algorithms were obtained. The performance of each algorithm was evaluated based on shape parameters of the estimated AIFs and the true or manual AIF. Moreover, the execution time of each algorithm was recorded to determine the algorithm that operated more rapidly in clinical practice. In terms of the detection accuracy, Ncut and HIER method produced similar AIF detection results, which were closer to the expected AIF and more accurate than those obtained using FastAP method; in terms of the computational efficiency, the Ncut method required the shortest execution time. Ncut clustering appears promising because it facilitates the automatic and robust determination of AIF with high accuracy and efficiency. (orig.)

  13. MULTIFREQUENCY ALGORITHMS FOR DETERMINING THE MOISTURE CONTENT OF LIQUID EMULSIONS BY THE METHOD OF RESONANCE DIELCOMETRY

    National Research Council Canada - National Science Library

    A. A. Korobko

    2017-01-01

    Purpose. The main attention is paid to the development and investigation of multifrequency algorithms for the realization of the method of resonance dielcometric measurement of the humidity of emulsions of the type...

  14. Algorithm of determining fingerprint rotation%指纹旋转情况判定

    Institute of Scientific and Technical Information of China (English)

    牛重

    2012-01-01

    指纹旋转对社保指纹自主识别系统的性能有负面影响.通过对旋转指纹的研究,采取基于细化二值指纹图像,直接根据录入的指纹图像就可以判定出指纹的旋转情况,而不需要与库存模板进行匹配.它们能给出提示,引导用户采集到不发生旋转的指纹图像.以此解决旋转指纹对指纹识别系统性能的负面影响.文中给出了提取指纹中心点的算法,提出了一种新的基于细化二值指纹图像的脊线跟踪提取算法.%Fingerprint rotation has negative impact on social security fingerprint self-recognition system. This paper uses the refinement of the binary fingerprint imag, based on the inputing fingerprint images, and determines the fingerprint rotation .does not match the inventory templates. They give tips and guide the users collecting the fingerpring, in which does not take place rotation,and solves the negative impact on rotating fingerprint to the system. It presents an algorithm of extracting fingerpint centre point,which is the new ridge line tracking extracting based on refinement of the binarg fingerprint image.

  15. Determining leaf trajectories for dynamic multileaf collimators with consideration of marker visibility: an algorithm study.

    Science.gov (United States)

    Zhao, Bo; Dai, Jianrong

    2014-09-01

    The purpose of this study was to develop a leaf-setting algorithm for Dynamic Multileaf Collimator-Intensity-Modulated Radiation Therapy (DMLC-IMRT) for optimal marker visibility. Here, a leaf-setting algorithm (called a Delta algorithm) was developed with the objective of maximizing marker visibility so as to improve the tracking effectiveness of fiducial markers during treatment delivery. The initial leaf trajectories were generated using a typical leaf-setting algorithm, then the leaf trajectories were adjusted by Delta algorithm operations (analytical computations and a series of matrix calculations) to achieve the optimal solution. The performance of the Delta algorithm was evaluated with six test fields (with randomly generated intensity profiles) and 15 clinical fields from IMRT plans of three prostate cancer patients. Compared with the initial solution, the Delta algorithm kept the total delivered intensities (TDIs) constant (without increasing the beam delivery time), but improved marker visibility (the percentage ratio of marker visibility time to beam delivery time). For the artificial fields (with three markers), marker visibility increased from 68.00-72.00% for a small field (5 × 5), from 38.46-43.59% for a medium field (10 × 10), and from 28.57-37.14% for a large field (20 × 20). For the 15 clinical fields, marker visibility increased 6-30% for eight fields and > 50% for two fields but did not change for five fields. A Delta algorithm was proposed to maximize marker visibility for DMLC-IMRT without increasing beam delivery time, and this will provide theoretical fundamentals for future studies of 4D DMLC tracking radiotherapy. © The Author 2014. Published by Oxford University Press on behalf of The Japan Radiation Research Society and Japanese Society for Radiation Oncology.

  16. Interference Alignment Using Variational Mean Field Annealing

    DEFF Research Database (Denmark)

    Badiu, Mihai Alin; Guillaud, Maxime; Fleury, Bernard Henri

    2014-01-01

    We study the problem of interference alignment in the multiple-input multiple- output interference channel. Aiming at minimizing the interference leakage power relative to the receiver noise level, we use the deterministic annealing approach to solve the optimization problem. In the corresponding...... for interference alignment. We also show that the iterative leakage minimization algorithm by Gomadam et al. and the alternating minimization algorithm by Peters and Heath, Jr. are instances of our method. Finally, we assess the performance of the proposed algorithm through computer simulations....

  17. Transfer alignment of shipborne inertial-guided weapon systems

    Institute of Scientific and Technical Information of China (English)

    Sun Changyue; Deng Zhenglong

    2009-01-01

    The transfer alignment problem of the shipborne weapon inertial navigation system (INS) is addressed. Specifically, two transfer alignment algorithms subjected to the ship motions induced by the waves are discussed. To consider the limited maneuver level performed by the ship, a new filter algorithm for transfer alignment methods using velocity and angular rate matching is first derived. And then an improved method using integrated velocity and integrated angular rate matching is introduced to reduce the effect of the ship body flexure. The simulation results show the feasibility and validity of the proposed transfer alignment algorithms.

  18. Sparse alignment for robust tensor learning.

    Science.gov (United States)

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

    2014-10-01

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

  19. LHCb: Experience with LHCb alignment software on first data

    CERN Multimedia

    Deissenroth, M

    2009-01-01

    We report results obtained with different track-based algorithms for the alignment of the LHCb detector with first data. The large-area Muon Detector and Outer Tracker have been aligned with a large sample of tracks from cosmic rays. The three silicon detectors --- VELO, TT-station and Inner Tracker --- have been aligned with beam-induced events from the LHC injection line. We compare the results from the track-based alignment with expectations from detector survey.

  20. Fast Implementation of Matched Filter Based Automatic Alignment Image Processing

    Energy Technology Data Exchange (ETDEWEB)

    Awwal, A S; Rice, K; Taha, T

    2008-04-02

    Video images of laser beams imprinted with distinguishable features are used for alignment of 192 laser beams at the National Ignition Facility (NIF). Algorithms designed to determine the position of these beams enable the control system to perform the task of alignment. Centroiding is a common approach used for determining the position of beams. However, real world beam images suffer from intensity fluctuation or other distortions which make such an approach susceptible to higher position measurement variability. Matched filtering used for identifying the beam position results in greater stability of position measurement compared to that obtained using the centroiding technique. However, this gain is achieved at the expense of extra processing time required for each beam image. In this work we explore the possibility of using a field programmable logic array (FPGA) to speed up these computations. The results indicate a performance improvement of 20 using the FPGA relative to a 3 GHz Pentium 4 processor.

  1. Yield-determination uncertainties using the strong-shock algorithm. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Pound, M.J.; Kent, G.I.

    1990-03-26

    Data from forty explosions were reduced by the CORRTEX algorithmic method to give a yield and the resultant error of measurement. The yield uncertainty turned out to be roughly 26% for yields over 40kt. In the course of this analysis the constraints for the algorithmic equation were rederived. The yield uncertainties for tests below 50kt was postulated. The uncertainty went up considerably if the cable was close enough to be affected by ENP. For example the uncertainty, using the best methodology, was 33% at 10kt, 37% at 5kt, 46% at 2kt, and 57% at 1 kt.

  2. An Algorithm for Determining Minimal Reduced—Coverings of Acyclic Database Schemes

    Institute of Scientific and Technical Information of China (English)

    刘铁英; 叶新铭

    1996-01-01

    This paper reports an algoritm(DTV)for deermining the minimal reducedcovering of an acyclic database scheme over a specified subset of attributes.The output of this algotithm contains not only minimum number of attributes but also minimum number of partial relation schemes.The algorithm has complexity O(|N|·|E|2),where|N| is the number of attributes and |E|the number of relation schemes.It is also proved that for Berge,γ or β acyclic database schemes,the output of algorithm DTV maintains the acyclicity correspondence.

  3. Determining reaction pathways and spin-orbit populations in the photodissociation of HBr and HI using velocity-aligned Doppler spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

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

    1988-09-22

    The technique of velocity-aligned Doppler spectroscopy (VADS) is used to investigate the photodissociation of HBr (193 nm) and HI (193 and 248 nm). Doppler profiles at Lyman-..cap alpha.. for the H-atom photofragment are reported, and the corresponding populations of the halogen atom /sup 2/P/sub 3/2/ and /sup 2/P/sub 1/2/ spin-orbit states are determined. The VADS technique facilitates measurement of spatial anisotropy (..beta..'s) for each spin-orbit state. For HI photolyzed at 248 nm, I(/sup 2/P/sub 3/2/) and I(/sup 2/P/sub 1/2/) are produced with relative populations 0.54 /plus minus/ 0.05 (..beta.. = -1.0 /plus minus/ 0.2) and 0.46 /plus minus/ 0.05 (..beta.. = 1.7 /plus minus/ 0.2), respectively, while 193-nm HI photodissociation yields an I(/sup 2/P/sub 3/2/) population of greater than or equal to 0.9 (..beta.. approx. /minus/1.0). For 193-nm HBr photodissociation, the Br(/sup 2/P/sub 3/2/) and Br(/sup 2/P/sub 1/2/) populations are 0.86 and 0.14, respectively. Surprisingly, both channels appear to originate primarily from a perpendicular transition, since ..beta.. is /approximately/ /minus/1.0 for each state. This is in contrast to the case of HI, and plausible excitation and dissociation mechanisms are discussed in terms of possible coupling schemes.

  4. Technical note: Boundary layer height determination from lidar for improving air pollution episode modeling: development of new algorithm and evaluation

    Science.gov (United States)

    Yang, Ting; Wang, Zifa; Zhang, Wei; Gbaguidi, Alex; Sugimoto, Nobuo; Wang, Xiquan; Matsui, Ichiro; Sun, Yele

    2017-05-01

    Predicting air pollution events in the low atmosphere over megacities requires a thorough understanding of the tropospheric dynamics and chemical processes, involving, notably, continuous and accurate determination of the boundary layer height (BLH). Through intensive observations experimented over Beijing (China) and an exhaustive evaluation of existing algorithms applied to the BLH determination, persistent critical limitations are noticed, in particular during polluted episodes. Basically, under weak thermal convection with high aerosol loading, none of the retrieval algorithms is able to fully capture the diurnal cycle of the BLH due to insufficient vertical mixing of pollutants in the boundary layer associated with the impact of gravity waves on the tropospheric structure. Consequently, a new approach based on gravity wave theory (the cubic root gradient method: CRGM) is developed to overcome such weakness and accurately reproduce the fluctuations of the BLH under various atmospheric pollution conditions. Comprehensive evaluation of CRGM highlights its high performance in determining BLH from lidar. In comparison with the existing retrieval algorithms, CRGM potentially reduces related computational uncertainties and errors from BLH determination (strong increase of correlation coefficient from 0.44 to 0.91 and significant decreases of the root mean square error from 643 to 142 m). Such a newly developed technique is undoubtedly expected to contribute to improving the accuracy of air quality modeling and forecasting systems.

  5. Preliminary results of an algorithm to determine the total absorption coefficient of water

    Digital Repository Service at National Institute of Oceanography (India)

    Suresh, T.; Talaulikar, M.; Desa, E.J.; Lotlikar, A.

    coefficient of net irradiance, KE were obtained from radiative transfer simulations using Hydrolight with large in-situ measured data from the coastal and estuarine waters of Goa. A refined algorithm of spectral micro as in Ref. [1] is used...

  6. Structural alignment of RNA with complex pseudoknot structure.

    Science.gov (United States)

    Wong, Thomas K F; Lam, T W; Sung, Wing-Kin; Cheung, Brenda W Y; Yiu, S M

    2011-01-01

    The secondary structure of an ncRNA molecule is known to play an important role in its biological functions. Aligning a known ncRNA to a target candidate to determine the sequence and structural similarity helps in identifying de novo ncRNA molecules that are in the same family of the known ncRNA. However, existing algorithms cannot handle complex pseudoknot structures which are found in nature. In this article, we propose algorithms to handle two types of complex pseudoknots: simple non-standard pseudoknots and recursive pseudoknots. Although our methods are not designed for general pseudoknots, it already covers all known ncRNAs in both Rfam and PseudoBase databases. An evaluation of our algorithms shows that it is useful to identify ncRNA molecules in other species which are in the same family of a known ncRNA.

  7. Development of a novel algorithm to determine adherence to chronic pain treatment guidelines using administrative claims

    Science.gov (United States)

    Margolis, Jay M; Princic, Nicole; Smith, David M; Abraham, Lucy; Cappelleri, Joseph C; Shah, Sonali N; Park, Peter W

    2017-01-01

    Objective To develop a claims-based algorithm for identifying patients who are adherent versus nonadherent to published guidelines for chronic pain management. Methods Using medical and pharmacy health care claims from the MarketScan® Commercial and Medicare Supplemental Databases, patients were selected during July 1, 2010, to June 30, 2012, with the following chronic pain conditions: osteoarthritis (OA), gout (GT), painful diabetic peripheral neuropathy (pDPN), post-herpetic neuralgia (PHN), and fibromyalgia (FM). Patients newly diagnosed with 12 months of continuous medical and pharmacy benefits both before and after initial diagnosis (index date) were categorized as adherent, nonadherent, or unsure according to the guidelines-based algorithm using disease-specific pain medication classes grouped as first-line, later-line, or not recommended. Descriptive and multivariate analyses compared patient outcomes with algorithm-derived categorization endpoints. Results A total of 441,465 OA patients, 76,361 GT patients, 10,645 pDPN, 4,010 PHN patients, and 150,321 FM patients were included in the development of the algorithm. Patients found adherent to guidelines included 51.1% for OA, 25% for GT, 59.5% for pDPN, 54.9% for PHN, and 33.5% for FM. The majority (~90%) of patients adherent to the guidelines initiated therapy with prescriptions for first-line pain medications written for a minimum of 30 days. Patients found nonadherent to guidelines included 30.7% for OA, 6.8% for GT, 34.9% for pDPN, 23.1% for PHN, and 34.7% for FM. Conclusion This novel algorithm used real-world pharmacotherapy treatment patterns to evaluate adherence to pain management guidelines in five chronic pain conditions. Findings suggest that one-third to one-half of patients are managed according to guidelines. This method may have valuable applications for health care payers and providers analyzing treatment guideline adherence. PMID:28223842

  8. An operational retrieval algorithm for determining aerosol optical properties in the ultraviolet

    Science.gov (United States)

    Taylor, Thomas E.; L'Ecuyer, Tristan S.; Slusser, James R.; Stephens, Graeme L.; Goering, Christian D.

    2008-02-01

    This paper describes a number of practical considerations concerning the optimization and operational implementation of an algorithm used to characterize the optical properties of aerosols across part of the ultraviolet (UV) spectrum. The algorithm estimates values of aerosol optical depth (AOD) and aerosol single scattering albedo (SSA) at seven wavelengths in the UV, as well as total column ozone (TOC) and wavelength-independent asymmetry factor (g) using direct and diffuse irradiances measured with a UV multifilter rotating shadowband radiometer (UV-MFRSR). A novel method for cloud screening the irradiance data set is introduced, as well as several improvements and optimizations to the retrieval scheme which yield a more realistic physical model for the inversion and increase the efficiency of the algorithm. Introduction of a wavelength-dependent retrieval error budget generated from rigorous forward model analysis as well as broadened covariances on the a priori values of AOD, SSA and g and tightened covariances of TOC allows sufficient retrieval sensitivity and resolution to obtain unique solutions of aerosol optical properties as demonstrated by synthetic retrievals. Analysis of a cloud screened data set (May 2003) from Panther Junction, Texas, demonstrates that the algorithm produces realistic values of the optical properties that compare favorably with pseudo-independent methods for AOD, TOC and calculated Ångstrom exponents. Retrieval errors of all parameters (except TOC) are shown to be negatively correlated to AOD, while the Shannon information content is positively correlated, indicating that retrieval skill improves with increasing atmospheric turbidity. When implemented operationally on more than thirty instruments in the Ultraviolet Monitoring and Research Program's (UVMRP) network, this retrieval algorithm will provide a comprehensive and internally consistent climatology of ground-based aerosol properties in the UV spectral range that can be used

  9. Aligning parallel arrays to reduce communication

    Science.gov (United States)

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

    1994-01-01

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

  10. Development of a novel algorithm to determine adherence to chronic pain treatment guidelines using administrative claims

    Directory of Open Access Journals (Sweden)

    Margolis JM

    2017-02-01

    Full Text Available Jay M Margolis,1 Nicole Princic,2 David M Smith,2 Lucy Abraham,3 Joseph C Cappelleri,4 Sonali N Shah,5 Peter W Park5 1Truven Health Analytics, Bethesda, MD, 2Truven Health Analytics, Cambridge, MA, USA; 3Pfizer Ltd, Tadworth, UK; 4Pfizer Inc, Groton, CT, 5Pfizer Inc, New York, NY, USA Objective: To develop a claims-based algorithm for identifying patients who are adherent versus nonadherent to published guidelines for chronic pain management. Methods: Using medical and pharmacy health care claims from the MarketScan® Commercial and Medicare Supplemental Databases, patients were selected during July 1, 2010, to June 30, 2012, with the following chronic pain conditions: osteoarthritis (OA, gout (GT, painful diabetic peripheral neuropathy (pDPN, post-herpetic neuralgia (PHN, and fibromyalgia (FM. Patients newly diagnosed with 12 months of continuous medical and pharmacy benefits both before and after initial diagnosis (index date were categorized as adherent, nonadherent, or unsure according to the guidelines-based algorithm using disease-specific pain medication classes grouped as first-line, later-line, or not recommended. Descriptive and multivariate analyses compared patient outcomes with algorithm-derived categorization endpoints. Results: A total of 441,465 OA patients, 76,361 GT patients, 10,645 pDPN, 4,010 PHN patients, and 150,321 FM patients were included in the development of the algorithm. Patients found adherent to guidelines included 51.1% for OA, 25% for GT, 59.5% for pDPN, 54.9% for PHN, and 33.5% for FM. The majority (~90% of patients adherent to the guidelines initiated therapy with prescriptions for first-line pain medications written for a minimum of 30 days. Patients found nonadherent to guidelines included 30.7% for OA, 6.8% for GT, 34.9% for pDPN, 23.1% for PHN, and 34.7% for FM. Conclusion: This novel algorithm used real-world pharmacotherapy treatment patterns to evaluate adherence to pain management guidelines in five

  11. DETERMINATION ALGORITHM OF OPTIMAL GEOMETRICAL PARAMETERS FOR COMPONENTS OF FREIGHT CARS ON THE BASIS OF GENERALIZED MATHEMATICAL MODELS

    Directory of Open Access Journals (Sweden)

    O. V. Fomin

    2013-10-01

    Full Text Available Purpose. Presentation of features and example of the use of the offered determination algorithm of optimum geometrical parameters for the components of freight cars on the basis of the generalized mathematical models, which is realized using computer. Methodology. The developed approach to search for optimal geometrical parameters can be described as the determination of optimal decision of the selected set of possible variants. Findings. The presented application example of the offered algorithm proved its operation capacity and efficiency of use. Originality. The determination procedure of optimal geometrical parameters for freight car components on the basis of the generalized mathematical models was formalized in the paper. Practical value. Practical introduction of the research results for universal open cars allows one to reduce container of their design and accordingly to increase the carrying capacity almost by100 kg with the improvement of strength characteristics. Taking into account the mass of their park this will provide a considerable economic effect when producing and operating. The offered approach is oriented to the distribution of the software packages (for example Microsoft Excel, which are used by technical services of the most enterprises, and does not require additional capital investments (acquisitions of the specialized programs and proper technical staff training. This proves the correctness of the research direction. The offered algorithm can be used for the solution of other optimization tasks on the basis of the generalized mathematical models.

  12. Alignment method for solar collector arrays

    Science.gov (United States)

    Driver, Jr., Richard B

    2012-10-23

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

  13. Optimal Nonlinear Filter for INS Alignment

    Institute of Scientific and Technical Information of China (English)

    赵瑞; 顾启泰

    2002-01-01

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

  14. Vibrating wire alignment technique

    CERN Document Server

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

    2013-01-01

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

  15. Study of high speed complex number algorithms. [for determining antenna for field radiation patterns

    Science.gov (United States)

    Heisler, R.

    1981-01-01

    A method of evaluating the radiation integral on the curved surface of a reflecting antenna is presented. A three dimensional Fourier transform approach is used to generate a two dimensional radiation cross-section along a planer cut at any angle phi through the far field pattern. Salient to the method is an algorithm for evaluating a subset of the total three dimensional discrete Fourier transform results. The subset elements are selectively evaluated to yield data along a geometric plane of constant. The algorithm is extremely efficient so that computation of the induced surface currents via the physical optics approximation dominates the computer time required to compute a radiation pattern. Application to paraboloid reflectors with off-focus feeds in presented, but the method is easily extended to offset antenna systems and reflectors of arbitrary shapes. Numerical results were computed for both gain and phase and are compared with other published work.

  16. Towards a robust algorithm to determine topological domains from colocalization data

    Directory of Open Access Journals (Sweden)

    Alexander P. Moscalets

    2015-09-01

    Full Text Available One of the most important tasks in understanding the complex spatial organization of the genome consists in extracting information about this spatial organization, the function and structure of chromatin topological domains from existing experimental data, in particular, from genome colocalization (Hi-C matrices. Here we present an algorithm allowing to reveal the underlying hierarchical domain structure of a polymer conformation from analyzing the modularity of colocalization matrices. We also test this algorithm on several model polymer structures: equilibrium globules, random fractal globules and regular fractal (Peano conformations. We define what we call a spectrum of cluster borders, and show that these spectra behave strikingly di erently for equilibrium and fractal conformations, allowing us to suggest an additional criterion to identify fractal polymer conformations.

  17. Towards a robust algorithm to determine topological domains from colocalization data

    CERN Document Server

    Moscalets, Alexander P; Tamm, Mikhail V

    2016-01-01

    One of the most important tasks in understanding the complex spatial organization of the genome consists in extracting information about this spatial organization, the function and structure of chromatin topological domains from existing experimental data, in particular, from genome colocalization (Hi-C) matrices. Here we present an algorithm allowing to reveal the underlying hierarchical domain structure of a polymer conformation from analyzing the modularity of colocalization matrices. We also test this algorithm on several model polymer structures: equilibrium globules, random fractal globules and regular fractal (Peano) conformations. We define what we call a spectrum of cluster borders, and show that these spectra behave strikingly differently for equilibrium and fractal conformations, allowing us to suggest an additional criterion to identify fractal polymer conformations.

  18. H-- Filtering Algorithms Case Study GPS-Based Satellite Orbit Determination

    Science.gov (United States)

    Kuang, Jinlu; Tan, Soonhie

    In this paper the new Hfiltering algorithms for the design of navigation systems for autonomous LEO satellite is introduced. The nominal orbit (i.e., position and velocity) is computed by integrating the classical orbital differential equations of the LEO satellite by using the 7th-8th order Runge- Kutta algorithms. The perturbations due to the atmospheric drag force, the lunar-solar attraction and the solar radiation pressure are included together with the Earth gravity model (EGM-96). The spherical harmonic coefficients of the EGM-96 are considered up to 72 for the order and degree. By way of the MATLAB GPSoft software, the simulated pseudo ranges between the user LEO satellite and the visible GPS satellites are generated when given the appropriate angle of mask. The effects of the thermal noises, tropospheric refraction, ionospheric refraction, and multipath of the antenna are also compensated numerically in the simulated pseudo ranges. The dynamic Position-Velocity (PV) model is obtained by modeling the velocity as nearly constant being the white noise process. To further accommodate acceleration in the process model, the Position-Velocity-Acceleration (PVA) model is investigated by assuming the acceleration to be the Gaussian- Markov process. The state vector for the PV model becomes 8-dimensional (3-states for positions, 3-states for velocities, 1-state for range (clock) bias error, 1-state for range (clock) drift error). The state vector for the PV model becomes 11-dimensional with the addition of three more acceleration states. Three filtering approaches are used to smooth the orbit solution based upon the GPS pseudo range observables. The numerical simulation shows that the observed orbit root-mean-square errors of 60 meters by using the least squares adjustment method are improved to be less than 5 meters within 16 hours of tracking time by using the Hfiltering algorithms. The results are compared with the ones obtained by using the Extended Kalman

  19. Vertically aligned CNT growth on a microfabricated silicon heater with integrated temperature control—determination of the activation energy from a continuous thermal gradient

    DEFF Research Database (Denmark)

    Engstrøm, Daniel Southcott; Rupesinghe, Nalin L; Teo, Kenneth B K

    2011-01-01

    Silicon microheaters for local growth of a vertically aligned carbon nanotube (VACNT) were fabricated. The microheaters had a four-point-probe structure that measured the silicon conductivity variations in the heated region which is a measure of the temperature. Through FEM simulations the temper...

  20. Parameter Determination of Milling Process Using a Novel Teaching-Learning-Based Optimization Algorithm

    Directory of Open Access Journals (Sweden)

    Zhibo Zhai

    2015-01-01

    Full Text Available Cutting parameter optimization dramatically affects the production time, cost, profit rate, and the quality of the final products, in milling operations. Aiming to select the optimum machining parameters in multitool milling operations such as corner milling, face milling, pocket milling, and slot milling, this paper presents a novel version of TLBO, TLBO with dynamic assignment learning strategy (DATLBO, in which all the learners are divided into three categories based on their results in “Learner Phase”: good learners, moderate learners, and poor ones. Good learners are self-motivated and try to learn by themselves; each moderate learner uses a probabilistic approach to select one of good learners to learn; each poor learner also uses a probabilistic approach to select several moderate learners to learn. The CEC2005 contest benchmark problems are first used to illustrate the effectiveness of the proposed algorithm. Finally, the DATLBO algorithm is applied to a multitool milling process based on maximum profit rate criterion with five practical technological constraints. The unit time, unit cost, and profit rate from the Handbook (HB, Feasible Direction (FD method, Genetic Algorithm (GA method, five other TLBO variants, and DATLBO are compared, illustrating that the proposed approach is more effective than HB, FD, GA, and five other TLBO variants.

  1. Accelerated large-scale multiple sequence alignment

    Directory of Open Access Journals (Sweden)

    Lloyd Scott

    2011-12-01

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

  2. Grassmannian Differential Limited Feedback for Interference Alignment

    CERN Document Server

    Ayach, Omar El

    2011-01-01

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

  3. Recursions for statistical multiple alignment.

    Science.gov (United States)

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

    2003-12-09

    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 O(Pi id=1 Li), 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.

  4. [Determination of carmine in carbonated beverages using 3-D fluorescence spectra coupled with second-order calibration algorithm].

    Science.gov (United States)

    Li, Run; Chen, Guo-qing; Zhu, Chun; Kong, Fan-biao; Hu, Yang-jun

    2014-12-01

    Three-dimensional fluorescence spectra combined with second-order calibration algorithm based on alternate a weighted residual (ANWE) was applied to the direct concentration determination of carmine in carbonated beverages. Firstly, 3-D fluorescence spectra of carmine and sunset yellow mixed solutions with different concentrations were obtained by employing spectrometer, and analyzed by using ANWE, the correlation coefficient between calibration concentration and the actual concentration was 0.9917, and the average recovery was 100.92%±2.71%. The results show that the ANWE algorithm is reliable. Then, the commercial carbonated soft drinks in 8, 9, 12 and 13 times diluted concentration were detected by using ANWE algorithm, the correlation coefficient between relative concentration and the actual concentration were 0.9930, 0.9930, 0.9932 and 0.7932, respectively, and the contents of carmine in beverage were 38.88, 37.71, 37.68 and 39.65 μg · mL(-1), respectively. The average concentration was (38.48±0.96) μg · mL(-1). Finally, the standard addition method was applied to estimate the prediction accuracy between calibration concentration and the actual concentration was 0.9935, and the average recovery was 102.99%±2.15%. The results can provide a new idea for the rapid content determination of food pigments in commercial beverages.

  5. An Algorithm Approach to Determining Smoking Cessation Treatment for Persons Living with HIV/AIDS: Results of a Pilot Trial

    Science.gov (United States)

    Cropsey, Karen L.; Jardin, Bianca; Burkholder, Greer; Clark, C. Brendan; Raper, James L.; Saag, Michael

    2015-01-01

    Background Smoking now represents one of the biggest modifiable risk factors for disease and mortality in PLHIV. To produce significant changes in smoking rates among this population, treatments will need to be both acceptable to the larger segment of PLHIV smokers as well as feasible to implement in busy HIV clinics. The purpose of this study was to evaluate the feasibility and effects of a novel proactive algorithm-based intervention in an HIV/AIDS clinic. Methods PLHIV smokers (N =100) were proactively identified via their electronic medical records and were subsequently randomized at baseline to receive a 12-week pharmacotherapy-based algorithm treatment or treatment as usual. Participants were tracked in-person for 12-weeks. Participants provided information on smoking behaviors and associated constructs of cessation at each follow-up session. Results The findings revealed that many smokers reported utilizing prescribed medications when provided with a supply of cessation medication as determined by an algorithm. Compared to smokers receiving treatment as usual, PLHIV smokers prescribed these medications reported more quit attempts and greater reduction in smoking. Proxy measures of cessation readiness (e.g., motivation, self-efficacy) also favored participants receiving algorithm treatment. Conclusions This algorithm-derived treatment produced positive changes across a number of important clinical markers associated with smoking cessation. Given these promising findings coupled with the brief nature of this treatment, the overall pattern of results suggests strong potential for dissemination into clinical settings as well as significant promise for further advancing clinical health outcomes in this population. PMID:26181705

  6. Inner Detector Track Reconstruction and Alignment at the ATLAS Experiment

    CERN Document Server

    Danninger, Matthias; The ATLAS collaboration

    2017-01-01

    The Inner Detector of the ATLAS experiment at the LHC is responsible for reconstructing the trajectories of charged particles (‘tracks’) with high efficiency and accuracy. It consists of three subdetectors, each using a different technology to provide measurements points. An overview of the use of each of these subdetectors in track reconstruction, as well as the algorithmic approaches taken to the specific tasks of pattern recognition and track fitting, is given. The performance of the Inner Detector tracking will be summarised. Of crucial importance for optimal tracking performance is precise knowledge of the relative positions of the detector elements. ATLAS uses a sophisticated, highly granular software alignment procedure to determine and correct for the positions of the sensors, including time-dependent effects appearing within single data runs. This alignment procedure will be discussed in detail, and its effect on Inner Detector tracking for LHC Run 2 proton-proton collision data highlighted.

  7. Reconstruction of the Electron Density of Molecules with Single-Axis Alignment

    Energy Technology Data Exchange (ETDEWEB)

    Starodub, Dmitri

    2011-08-12

    Diffraction from the individual molecules of a molecular beam, aligned parallel to a single axis by a strong electric field or other means, has been proposed as a means of structure determination of individual molecules. As in fiber diffraction, all the information extractable is contained in a diffraction pattern from incidence of the diffracting beam normal to the molecular alignment axis. We present two methods of structure solution for this case. One is based on the iterative projection algorithms for phase retrieval applied to the coefficients of the cylindrical harmonic expansion of the molecular electron density. Another is the holographic approach utilizing presence of the strongly scattering reference atom for a specific molecule.

  8. Alignment of the Measurement Scale Mark during Immersion Hydrometer Calibration Using an Image Processing System

    Directory of Open Access Journals (Sweden)

    Jose Emilio Vargas-Soto

    2013-10-01

    Full Text Available The present work presents an improved method to align the measurement scale mark in an immersion hydrometer calibration system of CENAM, the National Metrology Institute (NMI of Mexico, The proposed method uses a vision system to align the scale mark of the hydrometer to the surface of the liquid where it is immersed by implementing image processing algorithms. This approach reduces the variability in the apparent mass determination during the hydrostatic weighing in the calibration process, therefore decreasing the relative uncertainty of calibration.

  9. Alignment of the Measurement Scale Mark during Immersion Hydrometer Calibration Using an Image Processing System

    Science.gov (United States)

    Peña-Perez, Luis Manuel; Pedraza-Ortega, Jesus Carlos; Ramos-Arreguin, Juan Manuel; Arriaga, Saul Tovar; Fernandez, Marco Antonio Aceves; Becerra, Luis Omar; Hurtado, Efren Gorrostieta; Vargas-Soto, Jose Emilio

    2013-01-01

    The present work presents an improved method to align the measurement scale mark in an immersion hydrometer calibration system of CENAM, the National Metrology Institute (NMI) of Mexico, The proposed method uses a vision system to align the scale mark of the hydrometer to the surface of the liquid where it is immersed by implementing image processing algorithms. This approach reduces the variability in the apparent mass determination during the hydrostatic weighing in the calibration process, therefore decreasing the relative uncertainty of calibration. PMID:24284770

  10. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed Affan

    2012-01-26

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

  11. Multiple sequence alignment accuracy and phylogenetic inference.

    Science.gov (United States)

    Ogden, T Heath; Rosenberg, Michael S

    2006-04-01

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

  12. Determination of the conformal-field-theory central charge by the Wang-Landau algorithm

    Science.gov (United States)

    Belov, P. A.; Nazarov, A. A.; Sorokin, A. O.

    2017-06-01

    We present a simple method to estimate the central charge of the conformal field theory corresponding to a critical point of a two-dimensional lattice model from Monte Carlo simulations. The main idea is to use the Wang-Landau flat-histogram algorithm, which allows us to obtain the free energy of a lattice model on a torus as a function of torus radii. The central charge is calculated with good precision from a free-energy scaling at the critical point. We apply the method to the Ising, tricritical Ising (Blume-Capel), Potts, and site-diluted Ising models, and we also discuss an estimation of the conformal weights.

  13. Automatic Algorithm for the Determination of the Anderson-wilkins Acuteness Score In Patients With St Elevation Myocardial Infarction

    DEFF Research Database (Denmark)

    Fakhri, Yama; Sejersten-Ripa, Maria; Schoos, Mikkel Malby

    2016-01-01

    percutaneous coronary intervention regardless of patient reported symptom duration. However, due to the complexity of the score, its manual interpretation is time consuming and therefore has not been applied in clinical practice. Automation of this score could facilitate clinical application. Therefore, we...... aimed to develop and validate an automatic algorithm for the AW-score. Methods: The AW-score (obtained from presenting ECG), assesses changes in ST-T-segments, T-waves and Q-waves. Each lead is designated an acuteness phase (1A, 1B, 2A or 2B) and the overall score is calculated. AW-score ranges from 1...... using 50 ECGs. Each ECG lead (except aVR) was manually scored according to AW-score by two independent experts (Exp1 and Exp2) and automatically by our designed algorithm (auto-score). An adjudicated manual score (Adj-score) was determined between Exp1 and Exp2. The inter-rater reliabilities (IRRs...

  14. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez and J. Pivarski

    2011-01-01

    Alignment efforts in the first few months of 2011 have shifted away from providing alignment constants (now a well established procedure) and focussed on some critical remaining issues. The single most important task left was to understand the systematic differences observed between the track-based (TB) and hardware-based (HW) barrel alignments: a systematic difference in r-φ and in z, which grew as a function of z, and which amounted to ~4-5 mm differences going from one end of the barrel to the other. This difference is now understood to be caused by the tracker alignment. The systematic differences disappear when the track-based barrel alignment is performed using the new “twist-free” tracker alignment. This removes the largest remaining source of systematic uncertainty. Since the barrel alignment is based on hardware, it does not suffer from the tracker twist. However, untwisting the tracker causes endcap disks (which are aligned ...

  15. Algorithm Determines Wind Speed and Direction from Venturi-Sensor Data

    Science.gov (United States)

    Zysko, Jan A.; Perotti, Jose M.; Randazzo, John

    2004-01-01

    An algorithm computes the velocity of wind from the readings of an instrument like the one described in another Tech Brief. To recapitulate: The sensor has no moving parts and is a compact, rugged means of measuring wind vectors having magnitudes of as much as 300 mph (134 m/s). The sensor includes a Venturi gap bounded by a curved upper and a curved lower surface that are axisymmetric with respect to a vertical axis and mirror-symmetric with respect to a horizontal midplane. One of the curved surfaces is instrumented with multiple ports for measuring dynamic pressures. The sensor also incorporates auxiliary sensors for measuring temperature, relative humidity, and static atmospheric pressure. The design and operation of the sensor are based on the concepts of (1) using Bernoulli's equation (which expresses the relationship among variations of speed, density, and pressure along a streamline) to calculate the speed of the wind from differences among the pressure readings at the various ports; and (2) calculating the direction of the wind from the angular positions of ports selected according to comparisons among their pressure readings. The present algorithm performs these calculations.

  16. An iterative algorithm for determining depth profiles of collection probability by electron-beam-induced current

    Science.gov (United States)

    Konovalov, Igor; Breitenstein, Otwin

    2001-01-01

    An iterative algorithm for the derivation of depth profiles of the minority carrier collection probability in a semiconductor with or without a coating on the top is presented using energy-resolved electron-beam-induced current measurements in planar geometry. The calculation is based on the depth-dose function of Everhart and Hoff (Everhart T E and Hoff P H 1971 J. Appl. Phys. 42 5837) and on the penetration-range function of Kanaya and Okayama (Kanaya K and Okayama S 1972 J. Phys. D: Appl. Phys. 5 43) or on that of Fitting (Fitting H-J 1974 Phys. Status Solidi/ a 26 525). It can also be performed with any other depth-dose functions. Using this algorithm does not require us to make any assumptions on the shape of the collection profile within the depth of interest. The influence of an absorbing top contact and/or a limited thickness of the semiconductor layer appear in the result, but can also be taken explicitly into account. Examples using silicon and CIS solar cells as well as a GaAs LED are presented.

  17. STELLAR: fast and exact local alignments

    Directory of Open Access Journals (Sweden)

    Weese David

    2011-10-01

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

  18. SWAMP+: multiple subsequence alignment using associative massive parallelism

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-10-18

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

  19. Multiple structure alignment with msTALI

    Directory of Open Access Journals (Sweden)

    Shealy Paul

    2012-05-01

    Full Text Available Abstract Background Multiple structure alignments have received increasing attention in recent years as an alternative to multiple sequence alignments. Although multiple structure alignment algorithms can potentially be applied to a number of problems, they have primarily been used for protein core identification. A method that is capable of solving a variety of problems using structure comparison is still absent. Here we introduce a program msTALI for aligning multiple protein structures. Our algorithm uses several informative features to guide its alignments: torsion angles, backbone Cα atom positions, secondary structure, residue type, surface accessibility, and properties of nearby atoms. The algorithm allows the user to weight the types of information used to generate the alignment, which expands its utility to a wide variety of problems. Results msTALI exhibits competitive results on 824 families from the Homstrad and SABmark databases when compared to Matt and Mustang. We also demonstrate success at building a database of protein cores using 341 randomly selected CATH domains and highlight the contribution of msTALI compared to the CATH classifications. Finally, we present an example applying msTALI to the problem of detecting hinges in a protein undergoing rigid-body motion. Conclusions msTALI is an effective algorithm for multiple structure alignment. In addition to its performance on standard comparison databases, it utilizes clear, informative features, allowing further customization for domain-specific applications. The C++ source code for msTALI is available for Linux on the web at http://ifestos.cse.sc.edu/mstali.

  20. Exact Determination of Optimal Weights for Fastest Distributed Consensus Algorithm in Path Network via SDP

    CERN Document Server

    Jafarizadeh, Saber

    2010-01-01

    Providing an analytical solution for the problem of finding Fastest Distributed Consensus (FDC) is one of the challenging problems in the field of sensor networks. Most of the methods proposed so far deal with the FDC averaging algorithm problem by numerical convex optimization methods and in general no closed-form solution for finding FDC has been offered up to now except in [3] where the conjectured answer for path has been proved. Here in this work we present an analytical solution for the problem of Fastest Distributed Consensus for the Path network using semidefinite programming particularly solving the slackness conditions, where the optimal weights are obtained by inductive comparing of the characteristic polynomials initiated by slackness conditions.

  1. Ontology Alignment at the Instance and Schema Level

    CERN Document Server

    Suchanek, Fabian; Senellart, Pierre

    2011-01-01

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

  2. Gray level co-occurrence and random forest algorithm-based gender determination with maxillary tooth plaster images.

    Science.gov (United States)

    Akkoç, Betül; Arslan, Ahmet; Kök, Hatice

    2016-06-01

    Gender is one of the intrinsic properties of identity, with performance enhancement reducing the cluster when a search is performed. Teeth have durable and resistant structure, and as such are important sources of identification in disasters (accident, fire, etc.). In this study, gender determination is accomplished by maxillary tooth plaster models of 40 people (20 males and 20 females). The images of tooth plaster models are taken with a lighting mechanism set-up. A gray level co-occurrence matrix of the image with segmentation is formed and classified via a Random Forest (RF) algorithm by extracting pertinent features of the matrix. Automatic gender determination has a 90% success rate, with an applicable system to determine gender from maxillary tooth plaster images. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. Aligned natural inflation with modulations

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Kiwoon, E-mail: kchoi@ibs.re.kr [Center for Theoretical Physics of the Universe, Institute for Basic Science (IBS), Daejeon, 34051 (Korea, Republic of); Kim, Hyungjin, E-mail: hjkim06@kaist.ac.kr [Center for Theoretical Physics of the Universe, Institute for Basic Science (IBS), Daejeon, 34051 (Korea, Republic of); Department of Physics, KAIST, Daejeon, 305-701 (Korea, Republic of)

    2016-08-10

    The weak gravity conjecture applied for the aligned natural inflation indicates that generically there can be a modulation of the inflaton potential, with a period determined by sub-Planckian axion scale. We study the oscillations in the primordial power spectrum induced by such modulation, and discuss the resulting observational constraints on the model.

  4. Aligned natural inflation with modulations

    Directory of Open Access Journals (Sweden)

    Kiwoon Choi

    2016-08-01

    Full Text Available The weak gravity conjecture applied for the aligned natural inflation indicates that generically there can be a modulation of the inflaton potential, with a period determined by sub-Planckian axion scale. We study the oscillations in the primordial power spectrum induced by such modulation, and discuss the resulting observational constraints on the model.

  5. An open-source genetic algorithm for determining optimal seed distributions for low-dose-rate prostate brachytherapy.

    Science.gov (United States)

    McGeachy, P; Madamesila, J; Beauchamp, A; Khan, R

    2015-01-01

    An open source optimizer that generates seed distributions for low-dose-rate prostate brachytherapy was designed, tested, and validated. The optimizer was a simple genetic algorithm (SGA) that, given a set of prostate and urethra contours, determines the optimal seed distribution in terms of coverage of the prostate with the prescribed dose while avoiding hotspots within the urethra. The algorithm was validated in a retrospective study on 45 previously contoured low-dose-rate prostate brachytherapy patients. Dosimetric indices were evaluated to ensure solutions adhered to clinical standards. The SGA performance was further benchmarked by comparing solutions obtained from a commercial optimizer (inverse planning simulated annealing [IPSA]) with the same cohort of 45 patients. Clinically acceptable target coverage by the prescribed dose (V100) was obtained for both SGA and IPSA, with a mean ± standard deviation of 98 ± 2% and 99.5 ± 0.5%, respectively. For the prostate D90, SGA and IPSA yielded 177 ± 8 Gy and 186 ± 7 Gy, respectively, which were both clinically acceptable. Both algorithms yielded reasonable dose to the rectum, with V100 open source SGA was validated that provides a research tool for the brachytherapy community. Copyright © 2015 American Brachytherapy Society. Published by Elsevier Inc. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Emanuel Santos

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

  7. Algorithm-Based Fetal Gender Determination Using X and Y Mini-Short Tandem Repeats at Early Gestational Ages

    Directory of Open Access Journals (Sweden)

    Aghanoori

    2016-02-01

    Full Text Available Background Detection of fetal DNA in maternal blood has been examined by many research groups for a few years; thereby, scientists have a shorter way to take to approach prenatal diagnosis of abnormal pregnancies. The Y chromosome sequences have recently become the most common applicable indices for fetal sex determination. Objectives We conducted an algorithmic X and Y mini-Short Tandem Repeats (STRs genotyping method that could solve the problem of false negative (no detection of Y sequences results of previous methods. Patients and Methods Blood samples were obtained from 106 pregnant women and their spouses. Conventional PCR amplified 19 mini-Short Tandem Repeats (STRs and three non-STR markers, which were subsequently genotyped by the means of Polyacrylamide gel electrophoresis (PAGE. Results Sensitivity and specificity of the mini-STR genotyping method for fetal DNA detection were calculated (95.9% and 98%, respectively with a confidence interval of 95%. In addition, sensitivity and informativeness were computed for each of the single mini-STR markers in our conventional PCR method. We also introduced the minimum number of mini-STRs needed to reach maximum validity for fetal gender determination in clinical settings. Conclusions Algorithm-based mini-STR genotyping method significantly increases the reliability (sensitivity and specificity of gender determination using free fetal DNA and could be applied in prenatal clinical testing.

  8. Implementation of Accelerated Beam-Specific Matched-Filter-Based Optical Alignment

    Energy Technology Data Exchange (ETDEWEB)

    Awwal, A S; Rice, K L; Taha, T M

    2009-01-29

    Accurate automated alignment of laser beams in the National Ignition Facility (NIF) is essential for achieving extreme temperature and pressure required for inertial confinement fusion. The alignment achieved by the integrated control systems relies on algorithms processing video images to determine the position of the laser beam images in real-time. Alignment images that exhibit wide variations in beam quality require a matched-filter algorithm for position detection. One challenge in designing a matched-filter based algorithm is to construct a filter template that is resilient to variations in imaging conditions while guaranteeing accurate position determination. A second challenge is to process the image as fast as possible. This paper describes the development of a new analytical template that captures key recurring features present in the beam image to accurately estimate the beam position under good image quality conditions. Depending on the features present in a particular beam, the analytical template allows us to create a highly tailored template containing only those selected features. The second objective is achieved by exploiting the parallelism inherent in the algorithm to accelerate processing using parallel hardware that provides significant performance improvement over conventional processors. In particular, a Xilinx Virtex II Pro FPGA hardware implementation processing 32 templates provided a speed increase of about 253 times over an optimized software implementation running on a 2.0 GHz AMD Opteron core.

  9. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez

    2010-01-01

    The main developments in muon alignment since March 2010 have been the production, approval and deployment of alignment constants for the ICHEP data reprocessing. In the barrel, a new geometry, combining information from both hardware and track-based alignment systems, has been developed for the first time. The hardware alignment provides an initial DT geometry, which is then anchored as a rigid solid, using the link alignment system, to a reference frame common to the tracker. The “GlobalPositionRecords” for both the Tracker and Muon systems are being used for the first time, and the initial tracker-muon relative positioning, based on the link alignment, yields good results within the photogrammetry uncertainties of the Tracker and alignment ring positions. For the first time, the optical and track-based alignments show good agreement between them; the optical alignment being refined by the track-based alignment. The resulting geometry is the most complete to date, aligning all 250 DTs, ...

  10. Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign

    Directory of Open Access Journals (Sweden)

    Sharma Gaurav

    2007-04-01

    Full Text Available Abstract Background Joint alignment and secondary structure prediction of two RNA sequences can significantly improve the accuracy of the structural predictions. Methods addressing this problem, however, are forced to employ constraints that reduce computation by restricting the alignments and/or structures (i.e. folds that are permissible. In this paper, a new methodology is presented for the purpose of establishing alignment constraints based on nucleotide alignment and insertion posterior probabilities. Using a hidden Markov model, posterior probabilities of alignment and insertion are computed for all possible pairings of nucleotide positions from the two sequences. These alignment and insertion posterior probabilities are additively combined to obtain probabilities of co-incidence for nucleotide position pairs. A suitable alignment constraint is obtained by thresholding the co-incidence probabilities. The constraint is integrated with Dynalign, a free energy minimization algorithm for joint alignment and secondary structure prediction. The resulting method is benchmarked against the previous version of Dynalign and against other programs for pairwise RNA structure prediction. Results The proposed technique eliminates manual parameter selection in Dynalign and provides significant computational time savings in comparison to prior constraints in Dynalign while simultaneously providing a small improvement in the structural prediction accuracy. Savings are also realized in memory. In experiments over a 5S RNA dataset with average sequence length of approximately 120 nucleotides, the method reduces computation by a factor of 2. The method performs favorably in comparison to other programs for pairwise RNA structure prediction: yielding better accuracy, on average, and requiring significantly lesser computational resources. Conclusion Probabilistic analysis can be utilized in order to automate the determination of alignment constraints for

  11. Determination of the Cascade Reservoir Operation for Optimal Firm-Energy Using Genetic Algorithms

    Directory of Open Access Journals (Sweden)

    Azmeri

    2013-08-01

    Full Text Available Indonesia today face a new paradigm in water management where aim to apply integrated water resources management has become unavoidable task in purpose of achieving greater level of effectiveness and efficiency. On of most interesting case study is the case of Citarum river, one of the most potential river for water supply in West Java, Indonesia. Alongside the river, Saguling, Cirata and Djuanda Reservoirs had been constructed in series/cascade. Saguling and Cirata reservoirs are particularly operated for hydroelectric power and Djuanda is multipurpose reservoir mainly operated for irrigation and contribute domestic water supply for Jakarta (capital city of Indonesia. Basically all reservoirs are relying on same resources, therefore this condition has considered addressing management and operational problem. Therefore, an approach toward new management and operation system are urgently required in order to achieve the effective and efficient output and to avoid conflicts of water used. This study aims to obtain energy production from Citarum Cascade Reservoir System using Genetic Algorithms optimization with the objective function to maximize firm-energy. Firm-energy is the minimum energy requirements must be available in a certain time period. Then, the result obtained by using the energy produced by GA is compared to the conventional searching technique of Non-Linier Programming (NLP. The GA derived operating curves reveal the higher energy and firm-energy than NLP model

  12. Expectation-maximization algorithm for determining natural selection of Y-linked genes through two-sex branching processes.

    Science.gov (United States)

    González, M; Gutiérrez, C; Martínez, R

    2012-09-01

    A two-dimensional bisexual branching process has recently been presented for the analysis of the generation-to-generation evolution of the number of carriers of a Y-linked gene. In this model, preference of females for males with a specific genetic characteristic is assumed to be determined by an allele of the gene. It has been shown that the behavior of this kind of Y-linked gene is strongly related to the reproduction law of each genotype. In practice, the corresponding offspring distributions are usually unknown, and it is necessary to develop their estimation theory in order to determine the natural selection of the gene. Here we deal with the estimation problem for the offspring distribution of each genotype of a Y-linked gene when the only observable data are each generation's total numbers of males of each genotype and of females. We set out the problem in a non parametric framework and obtain the maximum likelihood estimators of the offspring distributions using an expectation-maximization algorithm. From these estimators, we also derive the estimators for the reproduction mean of each genotype and forecast the distribution of the future population sizes. Finally, we check the accuracy of the algorithm by means of a simulation study.

  13. An improved algorithm for the determination of aerosol optical depth in the ultraviolet spectral range from Brewer spectrophotometer observations

    Science.gov (United States)

    Sellitto, P.; di Sarra, A.; Siani, A. M.

    2006-10-01

    Methods to derive aerosol optical depth in the UV spectral range from ground-based remote-sensing stations equipped with Brewer spectrophotometers have been recently developed. In this study a modified Langley plot method has been implemented to retrieve aerosol optical depth from direct sun Brewer measurements. The method uses measurements over an extended range of atmospheric airmasses obtained with two different neutral density filters, and accounts for short-term variations of total ozone, derived from the same direct sun observations. The improved algorithm has been applied to data collected with a Brewer mark IV, operational in Rome, Italy, and with a Brewer mark III, operational in Lampedusa, Italy, in the Mediterranean. The efficiency of the improved algorithm has been tested comparing the number of determinations of the extraterrestrial constant against those obtained with a standard Langley plot procedure. The improved method produces a larger number of reliable Langley plots, allowing for a better statistical characterization of the extraterrestrial constant and a better study of its temporal variability. The values of aerosol optical depth calculated in Rome and Lampedusa compare well with simultaneous determinations in the 416-440 nm interval derived from MFRSR and CIMEL measurements.

  14. Determining the number of clusters for kernelized fuzzy C-means algorithms for automatic medical image segmentation

    Directory of Open Access Journals (Sweden)

    E.A. Zanaty

    2012-03-01

    Full Text Available In this paper, we determine the suitable validity criterion of kernelized fuzzy C-means and kernelized fuzzy C-means with spatial constraints for automatic segmentation of magnetic resonance imaging (MRI. For that; the original Euclidean distance in the FCM is replaced by a Gaussian radial basis function classifier (GRBF and the corresponding algorithms of FCM methods are derived. The derived algorithms are called as the kernelized fuzzy C-means (KFCM and kernelized fuzzy C-means with spatial constraints (SKFCM. These methods are implemented on eighteen indexes as validation to determine whether indexes are capable to acquire the optimal clusters number. The performance of segmentation is estimated by applying these methods independently on several datasets to prove which method can give good results and with which indexes. Our test spans various indexes covering the classical and the rather more recent indexes that have enjoyed noticeable success in that field. These indexes are evaluated and compared by applying them on various test images, including synthetic images corrupted with noise of varying levels, and simulated volumetric MRI datasets. Comparative analysis is also presented to show whether the validity index indicates the optimal clustering for our datasets.

  15. Determination Of Gas Mixture Components Using Fluctuation Enhanced Sensing And The LS-SVM Regression Algorithm

    Directory of Open Access Journals (Sweden)

    Lentka Łukasz

    2015-09-01

    Full Text Available This paper analyses the effectiveness of determining gas concentrations by using a prototype WO3 resistive gas sensor together with fluctuation enhanced sensing. We have earlier demonstrated that this method can determine the composition of a gas mixture by using only a single sensor. In the present study, we apply Least-Squares Support-Vector-Machine-based (LS-SVM-based nonlinear regression to determine the gas concentration of each constituent in a mixture. We confirmed that the accuracy of the estimated gas concentration could be significantly improved by applying temperature change and ultraviolet irradiation of the WO3 layer. Fluctuation-enhanced sensing allowed us to predict the concentration of both component gases.

  16. Face Alignment Using Boosting and Evolutionary Search

    NARCIS (Netherlands)

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

    2010-01-01

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

  17. Alignment free characterization of 2D gratings

    CERN Document Server

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

    2015-01-01

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

  18. ALGORITHM FOR DETERMINATION OF PREDICTABLE SPECIALISTS’ NUMBER REQUIRED FOR STAFF RECRUITMENT AT ENTERPRISE

    Directory of Open Access Journals (Sweden)

    V. P. Goncharenko

    2010-01-01

    Full Text Available A methodology has been developed which allows to calculate predictable enterprise requirements for skilled staff with the purpose to ensure a normal functioning of its production process and also to determine changes of its staff structure in case of the production development and usage of innovations in production.

  19. Development of simple algorithm for direct and rapid determination of cotton maturity from FTIR spectroscopy

    Science.gov (United States)

    Fourier transform infrared (FTIR) spectra of seed and lint cottons were collected to explore the potential for the discrimination of immature cottons from mature ones and also for the determination of actual cotton maturity. Spectral features of immature and mature cottons revealed large differences...

  20. Predictive algorithms for determination of reflectance data from quantity of pigments within experimental dental resin composites

    OpenAIRE

    Ghinea, Razvan; Pecho, Oscar; Herrera, Luis Javier; Ionescu, Ana Maria; Cardona, Juan de la Cruz; Sanchez, María Purificación; Rade D. Paravina; Perez, María del Mar

    2015-01-01

    Background Being able to estimate (predict) the final spectrum of reflectance of a biomaterial, especially when the final color and appearance are fundamental for their clinical success (as is the case of dental resin composites), could be a very useful tool for the industrial development of these type of materials. The main objective of this study was the development of predictive models which enable the determination of the reflectance spectrum of experimental dental resin composites based ...

  1. Ontology alignment with OLA

    OpenAIRE

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

    2004-01-01

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

  2. A benchmark of multiple sequence alignment programs upon structural RNAs

    DEFF Research Database (Denmark)

    Gardner, P. P.; Wilm, A.; Washietl, S.

    2005-01-01

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

  3. Chunk Alignment for Corpus-Based Machine Translation

    Science.gov (United States)

    Kim, Jae Dong

    2011-01-01

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

  4. Tidal alignment of galaxies

    Energy Technology Data Exchange (ETDEWEB)

    Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš

    2015-08-01

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

  5. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez

    2010-01-01

    Most of the work in muon alignment since December 2009 has focused on the geometry reconstruction from the optical systems and improvements in the internal alignment of the DT chambers. The barrel optical alignment system has progressively evolved from reconstruction of single active planes to super-planes (December 09) to a new, full barrel reconstruction. Initial validation studies comparing this full barrel alignment at 0T with photogrammetry provide promising results. In addition, the method has been applied to CRAFT09 data, and the resulting alignment at 3.8T yields residuals from tracks (extrapolated from the tracker) which look smooth, suggesting a good internal barrel alignment with a small overall offset with respect to the tracker. This is a significant improvement, which should allow the optical system to provide a start-up alignment for 2010. The end-cap optical alignment has made considerable progress in the analysis of transfer line data. The next set of alignment constants for CSCs will there...

  6. The GLAS Algorithm Theoretical Basis Document for Precision Attitude Determination (PAD)

    Science.gov (United States)

    Bae, Sungkoo; Smith, Noah; Schutz, Bob E.

    2013-01-01

    The Geoscience Laser Altimeter System (GLAS) was the sole instrument for NASAs Ice, Cloud and land Elevation Satellite (ICESat) laser altimetry mission. The primary purpose of the ICESat mission was to make ice sheet elevation measurements of the polar regions. Additional goals were to measure the global distribution of clouds and aerosols and to map sea ice, land topography and vegetation. ICESat was the benchmark Earth Observing System (EOS) mission to be used to determine the mass balance of the ice sheets, as well as for providing cloud property information, especially for stratospheric clouds common over polar areas.

  7. Edge determination algorithm of game road for intelligent automobile based on plane array CCD

    Institute of Scientific and Technical Information of China (English)

    CHEN Zhi-kun; WANG Fu-bin; PAN Xiao-di; LIU Jie; HUANG Chang-fa

    2009-01-01

    The contribution factor of automobile movement stability on the structure feature of seek road intelligent automobile chassis was analyzed. The kinematic model of linear two-degree freedom for intelligent automobile was established. The noise influence to the image of game road on the image rebuilding of different acquisition data of game road was analyzed. The threshold for image division was determined by the statistical analysis to grey histogram of game road image. This method indicates its adaption to CCD image of low distinguish ability.

  8. RNA-RNA interaction prediction based on multiple sequence alignments

    CERN Document Server

    Li, Andrew X; Qin, Jing; Reidys, Christian M

    2010-01-01

    Recently, $O(N^6)$ time and $O(N^4)$ space dynamic programming algorithms have become available that compute the partition function of RNA-RNA interaction complexes for pairs of RNA sequences. These algorithms and the biological requirement of more reliable interactions motivate to utilize the additional information contained in multiple sequence alignments and to generalize the above framework to the partition function and base pairing probabilities for multiple sequence alignments.

  9. Do regression-based computer algorithms for determining the ventilatory threshold agree?

    Science.gov (United States)

    Ekkekakis, Panteleimon; Lind, Erik; Hall, Eric E; Petruzzello, Steven J

    2008-07-01

    The determination of the ventilatory threshold has been a persistent problem in research and clinical practice. Several computerized methods have been developed to overcome the subjectivity of visual methods but it remains unclear whether different computerized methods yield similar results. The purpose of this study was to compare nine regression-based computerized methods for the determination of the ventilatory threshold. Two samples of young and healthy volunteers (n = 30 each) participated in incremental treadmill protocols to volitional fatigue. The ventilatory data were averaged in 20-s segments and analysed with a computer program. Significant variance among methods was found in both samples (Sample 1: F = 11.50; Sample 2: F = 11.70, P < 0.001 for both). The estimates of the ventilatory threshold ranged from 2.47 litres.min(-1) (71% VO2max) to 3.13 litres.min(-1) (90% VO2max) in Sample 1 and from 2.37 litres.min(-1) (67% VO2max) to 3.03 litres.min(-1) (83% VO2max) in Sample 2. The substantial differences between methods challenge the practice of relying on any single computerized method. A standardized protocol, likely based on a combination of methods, might be necessary to increase the methodological consistency in both research and clinical practice.

  10. Use of Forward-Scattering Algorithm for Growth Stage Determination of Rice Fields

    Science.gov (United States)

    Yuzugullu, Onur; Erten, Esra; Hajnsek, Irena

    2015-04-01

    Rice is one of the major crops that is highly consumed worldwide. Therefore, there is a requirement for frequent monitoring. The aim of the growth stage monitoring is to optimize crop management practices and reduce the environmental impacts. This study aims to provide a novel approach to determine the growth stage of rice fields by means of polarimetric Synthetic Aperture Radar (PolSAR) data. To estimate the growth stage of rice fields, firstly a hyper space is simulated using a forward scattering model. Then, by assuming that the plant morphology for different polarimetric channels have to be similar, to reduce the size of the simulated hyper space, a set of constraints are applied. Finally, to determine the most possible growth stage the probabilities of the morphological parameters in the minimized hyper spaces are calculated. The proposed method is tested over co-polar TerraSAR-X (TSX) data by exploiting a single acquisition and a priori information. Results of the analysis show that, proposed method is able to estimate growth stage with a ± 5 BBCH accuracy.

  11. ALGORITHM OF DETERMINATION OF POWER AND ENERGY INDEXES OF SCREW INTENSIFIER ON THE BULLDOZER WORKING EQUIPMENT AT TRENCH REFILLINGS

    Directory of Open Access Journals (Sweden)

    KROL R. N.

    2016-03-01

    Full Text Available Raising of problem. A bulldozer work at trench refilings is conducted by cyclic, machine shuttle motions that increases a right-of-way; increasing of time charges, fuel and labour by the side of the continuous refilling method. Besides the indicated defects gets worse also the quality of the trench refilling: the uneven soil output into a trench with large portions results the damages of pipes isolation and emptinesses formation, in consequence  settling and washing of soil. A bulldozer with the screw intensifier (SI, is deprived lacks of an odinary bulldozer  moving along a trench, it moves the loose soil that does not fall on a pipeline, but rolles on it. Thus the circuitous speed of a cutting edge of SI exceeds the speed of the base machine moving that provides the strong soil treatment (before dispersion before output into a trench. Purpose. The algorithm development of the rotational moment determination on the SI driveshaft, the consumable energy, the energy intensity and the working process productivity of the reverse trench refillings depending on physical and mechanical properties of soil, geometrical parameters of SI and bulldozer optimal speed. Conclusion. The developed algorithm allows to define that at the fixed value of the rotational speed the rotational moment and indicated efficiency of SI at the optimum speed increasing of the base machine change on a linear law; the optimum speed change of the base machine practically does not influence on the energy intensity at the considered change of the rotational speed .

  12. AGORA: Assembly Guided by Optical Restriction Alignment

    Directory of Open Access Journals (Sweden)

    Lin Henry C

    2012-08-01

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

  13. Oculus: faster sequence alignment by streaming read compression

    Science.gov (United States)

    2012-01-01

    Background Despite significant advancement in alignment algorithms, the exponential growth of nucleotide sequencing throughput threatens to outpace bioinformatic analysis. Computation may become the bottleneck of genome analysis if growing alignment costs are not mitigated by further improvement in algorithms. Much gain has been gleaned from indexing and compressing alignment databases, but many widely used alignment tools process input reads sequentially and are oblivious to any underlying redundancy in the reads themselves. Results Here we present Oculus, a software package that attaches to standard aligners and exploits read redundancy by performing streaming compression, alignment, and decompression of input sequences. This nearly lossless process (> 99.9%) led to alignment speedups of up to 270% across a variety of data sets, while requiring a modest amount of memory. We expect that streaming read compressors such as Oculus could become a standard addition to existing RNA-Seq and ChIP-Seq alignment pipelines, and potentially other applications in the future as throughput increases. Conclusions Oculus efficiently condenses redundant input reads and wraps existing aligners to provide nearly identical SAM output in a fraction of the aligner runtime. It includes a number of useful features, such as tunable performance and fidelity options, compatibility with FASTA or FASTQ files, and adherence to the SAM format. The platform-independent C++ source code is freely available online, at http://code.google.com/p/oculus-bio. PMID:23148484

  14. Polynomial Time Algorithm for Determining Max-Min Paths in Networks and Solving Zero Value Cyclic Games

    Directory of Open Access Journals (Sweden)

    Dmitrii D. Lozovanu

    2005-10-01

    Full Text Available We study the max-min paths problem, which represents a game version of the shortest and the longest paths problem in a weighted directed graph. In this problem the vertex set V of the weighted directed graph G=(V,E is divided into two disjoint subsets VA and VB which are regarded as positional sets of two players. The players are seeking for a directed path from the given starting position ν 0 to the final position ν f , where the first player intends to maximize the integral cost of the path while the second one has aim to minimize it. Polynomial-time algorithm for determining max-min path in networks is proposed and its application for solving zero value cyclic games is developed. Mathematics Subject Classification 2000: 90B10, 90C35, 90C27.

  15. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez

    2011-01-01

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

  16. FlexSnap: Flexible Non-sequential Protein Structure Alignment

    Directory of Open Access Journals (Sweden)

    Bystroff Chris

    2010-01-01

    Full Text Available Abstract Background Proteins have evolved subject to energetic selection pressure for stability and flexibility. Structural similarity between proteins that have gone through conformational changes can be captured effectively if flexibility is considered. Topologically unrelated proteins that preserve secondary structure packing interactions can be detected if both flexibility and Sequential permutations are considered. We propose the FlexSnap algorithm for flexible non-topological protein structural alignment. Results The effectiveness of FlexSnap is demonstrated by measuring the agreement of its alignments with manually curated non-sequential structural alignments. FlexSnap showed competitive results against state-of-the-art algorithms, like DALI, SARF2, MultiProt, FlexProt, and FATCAT. Moreover on the DynDom dataset, FlexSnap reported longer alignments with smaller rmsd. Conclusions We have introduced FlexSnap, a greedy chaining algorithm that reports both sequential and non-sequential alignments and allows twists (hinges. We assessed the quality of the FlexSnap alignments by measuring its agreements with manually curated non-sequential alignments. On the FlexProt dataset, FlexSnap was competitive to state-of-the-art flexible alignment methods. Moreover, we demonstrated the benefits of introducing hinges by showing significant improvements in the alignments reported by FlexSnap for the structure pairs for which rigid alignment methods reported alignments with either low coverage or large rmsd. Availability An implementation of the FlexSnap algorithm will be made available online at http://www.cs.rpi.edu/~zaki/software/flexsnap.

  17. Physics of Grain Alignment

    CERN Document Server

    Lazarian, A

    2000-01-01

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

  18. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez

    2011-01-01

    A new set of muon alignment constants was approved in August. The relative position between muon chambers is essentially unchanged, indicating good detector stability. The main changes concern the global positioning of the barrel and of the endcap rings to match the new Tracker geometry. Detailed studies of the differences between track-based and optical alignment of DTs have proven to be a valuable tool for constraining Tracker alignment weak modes, and this information is now being used as part of the alignment procedure. In addition to the “split-cosmic” analysis used to investigate the muon momentum resolution at high momentum, a new procedure based on reconstructing the invariant mass of di-muons from boosted Zs is under development. Both procedures show an improvement in the momentum precision of Global Muons with respect to Tracker-only Muons. Recent developments in track-based alignment include a better treatment of the tails of residual distributions and accounting for correla...

  19. SPEAR3 Construction Alignment

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-08-17

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

  20. Predictive algorithms for determination of reflectance data from quantity of pigments within experimental dental resin composites.

    Science.gov (United States)

    Ghinea, Razvan; Pecho, Oscar; Herrera, Luis Javier; Ionescu, Ana Maria; Cardona, Juan de la Cruz; Sanchez, María Purificación; Paravina, Rade D; Perez, María del Mar

    2015-01-01

    Being able to estimate (predict) the final spectrum of reflectance of a biomaterial, especially when the final color and appearance are fundamental for their clinical success (as is the case of dental resin composites), could be a very useful tool for the industrial development of these type of materials. The main objective of this study was the development of predictive models which enable the determination of the reflectance spectrum of experimental dental resin composites based on type and quantity of pigments used in their chemical formulation. 49 types of experimental dental resin composites were formulated as a mixture of organic matrix, inorganic filler, photo activator and other components in minor quantities (accelerator, inhibitor, fluorescent agent and 4 types of pigments). Spectral reflectance of all samples were measured, before and after artificial chromatic aging, using a spectroradiometer. A Multiple Nonlinear Regression Model (MNLR) was used to predict the values of the Reflectance Factors values in the visible range (380 nm-780 nm), before and after aging, from % Pigment (%P1, %P2, %P3 and %P4) within the formulation. The average value of the prediction error of the model was 3.46% (SD: 1.82) across all wavelengths for samples before aging and 3.54% (SD: 1.17) for samples after aging. The differences found between the predicted and measured values of the chromatic coordinates are smaller than the acceptability threshold and, in some cases, are even below the perceptibility threshold. Within the framework of this pilot study, the nonlinear predictive models developed allow the prediction, with a high degree of accuracy, of the reflectance spectrum of the experimental dental resin composites.

  1. Spectrophotometric determination of fluoxetine by molecularly imprinted polypyrrole and optimization by experimental design, artificial neural network and genetic algorithm.

    Science.gov (United States)

    Nezhadali, Azizollah; Motlagh, Maryam Omidvar; Sadeghzadeh, Samira

    2017-09-13

    A selective method based on molecularly imprinted polymer (MIP) solid-phase extraction (SPE) using UV-Vis spectrophotometry as a detection technique was developed for the determination of fluoxetine (FLU) in pharmaceutical and human serum samples. The MIPs were synthesized using pyrrole as a functional monomer in the presence of FLU as a template molecule. The factors that affecting the preparation and extraction ability of MIP such as amount of sorbent, initiator concentration, the amount of monomer to template ratio, uptake shaking rate, uptake time, washing buffer pH, take shaking rate, Taking time and polymerization time were considered for optimization. First a Plackett-Burman design (PBD) consists of 12 randomized runs were applied to determine the influence of each factor. The other optimization processes were performed using central composite design (CCD), artificial neural network (ANN) and genetic algorithm (GA). At optimal condition the calibration curve showed linearity over a concentration range of 10(-7)-10(-8)M with a correlation coefficient (R(2)) of 0.9970. The limit of detection (LOD) for FLU was obtained 6.56×10(-9)M. The repeatability of the method was obtained 1.61%. The synthesized MIP sorbent showed a good selectivity and sensitivity toward FLU. The MIP/SPE method was used for the determination of FLU in pharmaceutical, serum and plasma samples, successfully. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Mango: multiple alignment with N gapped oligos.

    Science.gov (United States)

    Zhang, Zefeng; Lin, Hao; Li, Ming

    2008-06-01

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

  3. RNASTAR: An RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs

    NARCIS (Netherlands)

    Widmann, J.; Stombaugh, J.; Mcdonald, D.; Chocholousova, J.; Gardner, P.; Iyer, M.K.; Liu, Z.Z.; Lozupone, C.A.; Quinn, J.; Smit, S.; Wikman, S.; Zaneveld, J.R.R.; Knight, R.

    2012-01-01

    Automated RNA alignment algorithms often fail to recapture the essential conserved sites that are critical for function. To assist in the refinement of these algorithms, we manually curated a set of 148 alignments with a total of 9600 unique sequences, in which each alignment was backed by at least

  4. Alignment in double capture processes

    Energy Technology Data Exchange (ETDEWEB)

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

    1993-06-05

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

  5. The Analysis of Wind Seismic Noise and Algorithms of its Determination

    Science.gov (United States)

    Kislov, K. V.; Gravirov, V. V.; Labuncov, M.

    2010-12-01

    impacts into obstacles. The influence of a wind direction to seismic noise is not proved. The attempts of searching of this influence came across absence of qualitative data and absence of techniques of determination of a wind operation on oscillations of a ground. It is marked the increase of a noise level with strengthening of a wind only. Any compensation of noise is not made. In the task is illuminated the state of a problem, it is discussed the applicability the existing data and techniques for research and are considered the possible approaches to the solution of a problem and requirement to experimental data. The examples of sharing of the seismic noise data, atmospheric pressure, force and direction of a wind are shown. The methodology of researches consists of two directions: it is offered to represent a wind as a vector (direction, force of a wind) and to compare it to appropriate vector of the noise, chosen from a the seismic data on direction; other method - to decompose the wind on ranges (on a direction and on a force) and separately to investigate seismic noise appropriate to each wind range.

  6. Conformational fluctuations affect protein alignment in dilute liquid crystal media

    DEFF Research Database (Denmark)

    Louhivuori, M.; Otten, R.; Lindorff-Larsen, Kresten

    2006-01-01

    The discovery of dilute liquid crystalline media to align biological macromolecules has opened many new possibilities to study protein and nucleic acid structures by NMR spectroscopy. We inspect the basic alignment phenomenon for an ensemble of protein conformations to deduce relative contributions...... molecular surfaces. Furthermore, we consider the implications of a dynamic bias to structure determination using data from the weak alignment method....

  7. Hardware Accelerated Sequence Alignment with Traceback

    Directory of Open Access Journals (Sweden)

    Scott Lloyd

    2009-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2005-01-01

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

  9. Alignment of the ATLAS Inner Detector Tracking System

    CERN Document Server

    Gorfine, Grant

    2009-01-01

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

  10. Band alignment of atomic layer deposited MgO/Zn{sub 0.8}Al{sub 0.2}O heterointerface determined by charge corrected X-ray photoelectron spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Baojun, E-mail: yanbj@ihep.ac.cn [State Key Laboratory of Particle Detection and Electronics, Institute of High Energy Physics of Chinese Academy of Sciences, Beijing P. O. Box 100049 (China); Liu, Shulin [State Key Laboratory of Particle Detection and Electronics, Institute of High Energy Physics of Chinese Academy of Sciences, Beijing P. O. Box 100049 (China); Yang, Yuzhen [State Key Laboratory of Particle Detection and Electronics, Institute of High Energy Physics of Chinese Academy of Sciences, Beijing P. O. Box 100049 (China); Department of Physics, Nanjing University, Nanjing P. O. Box 210093 (China); Heng, Yuekun [State Key Laboratory of Particle Detection and Electronics, Institute of High Energy Physics of Chinese Academy of Sciences, Beijing P. O. Box 100049 (China)

    2016-05-15

    Highlights: • Band alignment of MgO/Zn{sub 0.8}Al{sub 0.2}O heterojunction were investigated systematically using charge corrected X-ray photoelectron spectroscopy. • Differential charging phenomenon is observed in determination VBOs of insulator/semiconductor heterojunction. • Valence and conduction band offsets have been determined to be 0.72 ± 0.11 eV and 3.26 ± 0.11 eV, respectively, with a type-II band line-up. - Abstract: Pure magnesium (MgO) and zinc oxide doped with aluminum oxide (Zn{sub 0.8}Al{sub 0.2}O) were prepared via atomic layer deposition. We have studied the structure and band gap of bulk Zn{sub 0.8}Al{sub 0.2}O material by X-ray diffractometer (XRD) and Tauc method, and the band offsets and alignment of atomic layer deposited MgO/Zn{sub 0.8}Al{sub 0.2}O heterointerface were investigated systematically using X-ray photoelectron spectroscopy (XPS) in this study. Different methodologies, such as neutralizing electron gun, the use of C 1s peak recalibration and zero charging method, were applied to recover the actual position of the core levels in insulator materials which were easily influenced by differential charging phenomena. Schematic band alignment diagram, valence band offset (ΔE{sub V}) and conduction band offset (ΔE{sub C}) for the interface of the MgO/Zn{sub 0.8}Al{sub 0.2}O heterostructure have been constructed. An accurate value of ΔE{sub V} = 0.72 ± 0.11 eV was obtained from various combinations of core levels of heterojunction with varied MgO thickness. Given the experimental band gaps of 7.83 eV for MgO and 5.29 eV for Zn{sub 0.8}Al{sub 0.2}O, a type-II heterojunction with a ΔE{sub C} of 3.26 ± 0.11 eV was found. Band offsets and alignment studies of these heterojunctions are important for gaining deep consideration to the design of various optoelectronic devices based on such heterointerface.

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

    Science.gov (United States)

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

    2012-01-01

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

  12. Evaluation of the use of five laboratory determined ozone absorption cross sections in brewer and dobson retrieval algorithms

    Directory of Open Access Journals (Sweden)

    A. Redondas

    2013-09-01

    Full Text Available The primary ground-based instruments used to report total column ozone (TOC are Brewer and Dobson Spectrophotometers, in separate networks. These instruments make measurements of the UV irradiances, and through a well-defined process a TOC value is produced. Inherent in the algorithm is the use of a laboratory determined cross-section data set. We used five ozone cross section data sets: three Bass and Paur, Daumont, Malicet and Brion (DMB and a new Institute of Environmental Physics (IUP, University of Bremen, set. The three Bass and Paur (1985 sets are: quadratic temperature coefficients from IGACO web page (IGQ4, the Brewer network operational calibration set (BOp, and the set used by Bernhard et al. (2005, in the reanalysis of the Dobson absorption coefficient values (B05. The ozone absorption coefficients for Brewer and Dobson are then calculated using the normal Brewer operative method which is essentially the same as used on Dobson. Considering the standard TOC algorithm for the Brewer instruments and comparing to the Brewer standard operational calibration data set, using the slit functions for the individual instruments: we find the UIP data set changes the calculated TOC by −0.5%, the DBM data set changes the calculate TOC by −3.2%, and the IGQ4 data set at −45 °C changes the calculated TOC by +1.3%. Considering the standard algorithm for the Dobson instruments, and comparing to results using the official 1992 ozone absorption coefficients values and the single set of slit functions defined for all Dobson instruments, the calculated TOC changes by +1%, with little variation depending on which data set is used We applied the changes to the European Dobson and Brewer reference instruments during the Izaña 2012 Absolute Calibration Campaign. The application of a common Langley calibration and the IUP cross section the differences between Brewer and Dobson vanish whereas using Bass and Paur and DBM produce differences of 1.5% and 2

  13. Galaxy alignments: An overview

    CERN Document Server

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

    2015-01-01

    The alignments between galaxies, their underlying matter structures, and the cosmic web constitute vital ingredients for a comprehensive understanding of gravity, the nature of matter, and structure formation in the Universe. We provide an overview on the state of the art in the study of these alignment processes and their observational signatures, aimed at a non-specialist audience. The development of the field over the past one hundred years is briefly reviewed. We also discuss the impact of galaxy alignments on measurements of weak gravitational lensing, and discuss avenues for making theoretical and observational progress over the coming decade.

  14. Discriminative Shape Alignment

    DEFF Research Database (Denmark)

    Loog, M.; de Bruijne, M.

    2009-01-01

    The alignment of shape data to a common mean before its subsequent processing is an ubiquitous step within the area shape analysis. Current approaches to shape analysis or, as more specifically considered in this work, shape classification perform the alignment in a fully unsupervised way......, not taking into account that eventually the shapes are to be assigned to two or more different classes. This work introduces a discriminative variation to well-known Procrustes alignment and demonstrates its benefit over this classical method in shape classification tasks. The focus is on two......-dimensional shapes from a two-class recognition problem....

  15. [Near-infrared spectra combining with CARS and SPA algorithms to screen the variables and samples for quantitatively determining the soluble solids content in strawberry].

    Science.gov (United States)

    Li, Jiang-bo; Guo, Zhi-ming; Huang, Wen-qian; Zhang, Bao-hua; Zhao, Chun-jiang

    2015-02-01

    In using spectroscopy to quantitatively or qualitatively analyze the quality of fruit, how to obtain a simple and effective correction model is very critical for the application and maintenance of the developed model. Strawberry as the research object, this research mainly focused on selecting the key variables and characteristic samples for quantitatively determining the soluble solids content. Competitive adaptive reweighted sampling (CARS) algorithm was firstly proposed to select the spectra variables. Then, Samples of correction set were selected by successive projections algorithm (SPA), and 98 characteristic samples were obtained. Next, based on the selected variables and characteristic samples, the second variable selection was performed by using SPA method. 25 key variables were obtained. In order to verify the performance of the proposed CARS algorithm, variable selection algorithms including Monte Carlo-uninformative variable elimination (MC-UVE) and SPA were used as the comparison algorithms. Results showed that CARS algorithm could eliminate uninformative variables and remove the collinearity information at the same time. Similarly, in order to assess the performance of the proposed SPA algorithm for selecting the characteristic samples, SPA algorithm was compared with classical Kennard-Stone algorithm Results showed that SPA algorithm could be used for selection of the characteristic samples in the calibration set. Finally, PLS and MLR model for quantitatively predicting the SSC (soluble solids content) in the strawberry were proposed based on the variables/samples subset (25/98), respectively. Results show that models built by using the 0.59% and 65.33% information of original variables and samples could obtain better performance than using the ones obtained by using all information of the original variables and samples. MLR model was the best with R(pre)2 = 0.9097, RMSEP=0.3484 and RPD = 3.3278.

  16. 基于大失准角时变参数罗经初始对准算法%Variable parameter gyrocompass alignment algorithm based on large error angle model

    Institute of Scientific and Technical Information of China (English)

    翁浚; 严恭敏; 秦永元; 张金红

    2012-01-01

    To solve the initial self-alignment problem of strapdown inertial navigation system(SINS) under large error angle condition, a new gyrocompass alignment scheme is put forward by analyzing SINS large error angle model and based on the principle of compass effect in platform inertial navigation system(PINS). The scheme can be divided into three steps: horizontal alignment with azimuth angle uncertainty; time-vary parameter gyrocompass alignment for large error angle; fixed parameter gyrocompass alignment. Converge time can be shorten by adjusting gyrocompass parameter in real time in this scheme. A more accurate error transfer mode in strapdown inertial navigation system(SINS) is depicted by large azimuth error angle model instead of small error angle model. At last, a simulation is made using this scheme which shows that the gyro bias is stabilized at 0.01 (°)/h, and azimuth precision can reach 1° in 60 s and 3' at end of alignment.%为了解决大失准角条件下的捷联惯导初始自对准问题,通过分析捷联惯导系统大失准角误差模型,利用平台惯导系统罗经对准原理,提出了一种新的捷联惯导系统罗经对准方案.该方案的具体实现划分为三个阶段:方位角未知情况下的水平对准;大失准角时变参数罗经方位对准;定参数罗经对准.该方案通过实时调节罗经参数缩短了对准时间;利用大方位失准角模型代替小失准角模型,在算法收敛阶段更加准确地描述了捷联惯导系统的误差传递方式.仿真试验表明,使用陀螺随机漂移稳定性为0.01(°)/h的捷联惯导系统,该对准方案能在60 s内方位精度到达1°,并能在对准结束时达到3′的方位对准精度.

  17. DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies.

    Directory of Open Access Journals (Sweden)

    Shaun Mahony

    2007-03-01

    Full Text Available Transcription factor (TF proteins recognize a small number of DNA sequences with high specificity and control the expression of neighbouring genes. The evolution of TF binding preference has been the subject of a number of recent studies, in which generalized binding profiles have been introduced and used to improve the prediction of new target sites. Generalized profiles are generated by aligning and merging the individual profiles of related TFs. However, the distance metrics and alignment algorithms used to compare the binding profiles have not yet been fully explored or optimized. As a result, binding profiles depend on TF structural information and sometimes may ignore important distinctions between subfamilies. Prediction of the identity or the structural class of a protein that binds to a given DNA pattern will enhance the analysis of microarray and ChIP-chip data where frequently multiple putative targets of usually unknown TFs are predicted. Various comparison metrics and alignment algorithms are evaluated (a total of 105 combinations. We find that local alignments are generally better than global alignments at detecting eukaryotic DNA motif similarities, especially when combined with the sum of squared distances or Pearson's correlation coefficient comparison metrics. In addition, multiple-alignment strategies for binding profiles and tree-building methods are tested for their efficiency in constructing generalized binding models. A new method for automatic determination of the optimal number of clusters is developed and applied in the construction of a new set of familial binding profiles which improves upon TF classification accuracy. A software tool, STAMP, is developed to host all tested methods and make them publicly available. This work provides a high quality reference set of familial binding profiles and the first comprehensive platform for analysis of DNA profiles. Detecting similarities between DNA motifs is a key step in the

  18. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez

    Since September, the muon alignment system shifted from a mode of hardware installation and commissioning to operation and data taking. All three optical subsystems (Barrel, Endcap and Link alignment) have recorded data before, during and after CRAFT, at different magnetic fields and during ramps of the magnet. This first data taking experience has several interesting goals: •    study detector deformations and movements under the influence of the huge magnetic forces; •    study the stability of detector structures and of the alignment system over long periods, •    study geometry reproducibility at equal fields (specially at 0T and 3.8T); •    reconstruct B=0T geometry and compare to nominal/survey geometries; •    reconstruct B=3.8T geometry and provide DT and CSC alignment records for CMSSW. However, the main goal is to recons...

  19. Parallel progressive multiple sequence alignment on reconfigurable meshes

    Directory of Open Access Journals (Sweden)

    Nguyen Ken D

    2011-12-01

    Full Text Available Abstract Background One of the most fundamental and challenging tasks in bio-informatics is to identify related sequences and their hidden biological significance. The most popular and proven best practice method to accomplish this task is aligning multiple sequences together. However, multiple sequence alignment is a computing extensive task. In addition, the advancement in DNA/RNA and Protein sequencing techniques has created a vast amount of sequences to be analyzed that exceeding the capability of traditional computing models. Therefore, an effective parallel multiple sequence alignment model capable of resolving these issues is in a great demand. Results We design O(1 run-time solutions for both local and global dynamic programming pair-wise alignment algorithms on reconfigurable mesh computing model. To align m sequences with max length n, we combining the parallel pair-wise dynamic programming solutions with newly designed parallel components. We successfully reduce the progressive multiple sequence alignment algorithm's run-time complexity from O(m × n4 to O(m using O(m × n3 processing units for scoring schemes that use three distinct values for match/mismatch/gap-extension. The general solution to multiple sequence alignment algorithm takes O(m × n4 processing units and completes in O(m time. Conclusions To our knowledge, this is the first time the progressive multiple sequence alignment algorithm is completely parallelized with O(m run-time. We also provide a new parallel algorithm for the Longest Common Subsequence (LCS with O(1 run-time using O(n3 processing units. This is a big improvement over the current best constant-time algorithm that uses O(n4 processing units.

  20. An auroral westward flow channel (AWFC and its relationship to field-aligned current, ring current, and plasmapause location determined using multiple spacecraft observations

    Directory of Open Access Journals (Sweden)

    M. L. Parkinson

    2007-02-01

    Full Text Available An auroral westward flow channel (AWFC is a latitudinally narrow channel of unstable F-region plasma with intense westward drift in the dusk-to-midnight sector ionosphere. AWFCs tend to overlap the equatorward edge of the auroral oval, and their life cycle is often synchronised to that of substorms: they commence close to substorm expansion phase onset, intensify during the expansion phase, and then decay during the recovery phase. Here we define for the first time the relationship between an AWFC, large-scale field-aligned current (FAC, the ring current, and plasmapause location. The Tasman International Geospace Environment Radar (TIGER, a Southern Hemisphere HF SuperDARN radar, observed a jet-like AWFC during ~08:35 to 13:28 UT on 7 April 2001. The initiation of the AWFC was preceded by a band of equatorward expanding ionospheric scatter (BEES which conveyed an intense poleward electric field through the inner plasma sheet. Unlike previous AWFCs, this event was not associated with a distinct substorm surge; rather it occurred during an interval of persistent, moderate magnetic activity characterised by AL~−200 nT. The four Cluster spacecraft had perigees within the dusk sector plasmasphere, and their trajectories were magnetically conjugate to the radar observations. The Waves of High frequency and Sounder for Probing Electron density by Relaxation (WHISPER instruments on board Cluster were used to identify the plasmapause location. The Imager for Magnetopause-to-Aurora Global Exploration (IMAGE EUV experiment also provided global-scale observations of the plasmapause. The Cluster fluxgate magnetometers (FGM provided successive measurements specifying the relative location of the ring current and filamentary plasma sheet current. An analysis of Iridium spacecraft magnetometer measurements provided estimates of large-scale ionospheric FAC in relation to the AWFC evolution. Peak flows in the AWFC were located close to the peak of a Region 2

  1. HAMSA: Highly Accelerated Multiple Sequence Aligner

    Directory of Open Access Journals (Sweden)

    Naglaa M. Reda

    2016-06-01

    Full Text Available For biologists, the existence of an efficient tool for multiple sequence alignment is essential. This work presents a new parallel aligner called HAMSA. HAMSA is a bioinformatics application designed for highly accelerated alignment of multiple sequences of proteins and DNA/RNA on a multi-core cluster system. The design of HAMSA is based on a combination of our new optimized algorithms proposed recently of vectorization, partitioning, and scheduling. It mainly operates on a distance vector instead of a distance matrix. It accomplishes similarity computations and generates the guide tree in a highly accelerated and accurate manner. HAMSA outperforms MSAProbs with 21.9- fold speedup, and ClustalW-MPI of 11-fold speedup. It can be considered as an essential tool for structure prediction, protein classification, motive finding and drug design studies.

  2. Incremental Alignment Manifold Learning

    Institute of Scientific and Technical Information of China (English)

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

    2011-01-01

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

  3. The Analysis of Alpha Beta Pruning and MTD(f) Algorithm to Determine the Best Algorithm to be Implemented at Connect Four Prototype

    Science.gov (United States)

    Tommy, Lukas; Hardjianto, Mardi; Agani, Nazori

    2017-04-01

    Connect Four is a two-player game which the players take turns dropping discs into a grid to connect 4 of one’s own discs next to each other vertically, horizontally, or diagonally. At Connect Four, Computer requires artificial intelligence (AI) in order to play properly like human. There are many AI algorithms that can be implemented to Connect Four, but the suitable algorithms are unknown. The suitable algorithm means optimal in choosing move and its execution time is not slow at search depth which is deep enough. In this research, analysis and comparison between standard alpha beta (AB) Pruning and MTD(f) will be carried out at the prototype of Connect Four in terms of optimality (win percentage) and speed (execution time and the number of leaf nodes). Experiments are carried out by running computer versus computer mode with 12 different conditions, i.e. varied search depth (5 through 10) and who moves first. The percentage achieved by MTD(f) based on experiments is win 45,83%, lose 37,5% and draw 16,67%. In the experiments with search depth 8, MTD(f) execution time is 35, 19% faster and evaluate 56,27% fewer leaf nodes than AB Pruning. The results of this research are MTD(f) is as optimal as AB Pruning at Connect Four prototype, but MTD(f) on average is faster and evaluates fewer leaf nodes than AB Pruning. The execution time of MTD(f) is not slow and much faster than AB Pruning at search depth which is deep enough.

  4. Evaluation of elastix-based propagated align algorithm for VOI- and voxel-based analysis of longitudinal (18)F-FDG PET/CT data from patients with non-small cell lung cancer (NSCLC).

    Science.gov (United States)

    Kerner, Gerald Sma; Fischer, Alexander; Koole, Michel Jb; Pruim, Jan; Groen, Harry Jm

    2015-01-01

    Deformable image registration allows volume of interest (VOI)- and voxel-based analysis of longitudinal changes in fluorodeoxyglucose (FDG) tumor uptake in patients with non-small cell lung cancer (NSCLC). This study evaluates the performance of the elastix toolbox deformable image registration algorithm for VOI and voxel-wise assessment of longitudinal variations in FDG tumor uptake in NSCLC patients. Evaluation of the elastix toolbox was performed using (18)F-FDG PET/CT at baseline and after 2 cycles of therapy (follow-up) data in advanced NSCLC patients. The elastix toolbox, an integrated part of the IMALYTICS workstation, was used to apply a CT-based non-linear image registration of follow-up PET/CT data using the baseline PET/CT data as reference. Lesion statistics were compared to assess the impact on therapy response assessment. Next, CT-based deformable image registration was performed anew on the deformed follow-up PET/CT data using the original follow-up PET/CT data as reference, yielding a realigned follow-up PET dataset. Performance was evaluated by determining the correlation coefficient between original and realigned follow-up PET datasets. The intra- and extra-thoracic tumors were automatically delineated on the original PET using a 41% of maximum standardized uptake value (SUVmax) adaptive threshold. Equivalence between reference and realigned images was tested (determining 95% range of the difference) and estimating the percentage of voxel values that fell within that range. Thirty-nine patients with 191 tumor lesions were included. In 37/39 and 12/39 patients, respectively, thoracic and non-thoracic lesions were evaluable for response assessment. Using the EORTC/SUVmax-based criteria, 5/37 patients had a discordant response of thoracic, and 2/12 a discordant response of non-thoracic lesions between the reference and the realigned image. FDG uptake values of corresponding tumor voxels in the original and realigned reference PET correlated well (R

  5. Determining Optimal Link Capacity Expansions in Road Networks Using Cuckoo Search Algorithm with Lévy Flights

    Directory of Open Access Journals (Sweden)

    Ozgur Baskan

    2013-01-01

    Full Text Available During the last two decades, Continuous Network Design Problem (CNDP has received much more attention because of increasing trend of traffic congestion in road networks. In the CNDP, the problem is to find optimal link capacity expansions by minimizing the sum of total travel time and investment cost of capacity expansions in a road network. Considering both increasing traffic congestion and limited budgets of local authorities, the CNDP deserves to receive more attention in order to use available budget economically and to mitigate traffic congestion. The CNDP can generally be formulated as bilevel programming model in which the upper level deals with finding optimal link capacity expansions, whereas at the lower level, User Equilibrium (UE link flows are determined by Wardrop’s first principle. In this paper, cuckoo search (CS algorithm with Lévy flights is introduced for finding optimal link capacity expansions because of its recent successful applications in solving such complex problems. CS is applied to the 16-link and Sioux Falls networks and compared with available methods in the literature. Results show the potential of CS for finding optimal or near optimal link capacity expansions in a given road network.

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

    CERN Document Server

    Saeed, Fahad

    2009-01-01

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

  7. Software alignment of the BESⅢ main drift chamber using the Kalman Filter method

    Institute of Scientific and Technical Information of China (English)

    WANG Ji-Ke; MAO Ze-Pu; BIAN Jian-Ming; CAO Guo-Fu; CAO Xue-Xiang; CHEN Shen-Jian; DENG Zi-Yan; FU Cheng-Dong; GAO Yuan-Ning; HE Kang-Lin; HE Miao; HUA Chun-Fei; HUANG Bin; HUANG Xing-Tao; JI Xiao-Bin; LI Fei; LI Hai-Bo; LI Wei-Dong; LIANG Yu-Tie; LIU Chun-Xiu; LIU Huai-Min; LIU Suo; LIU Ying-Jie; MA Qiu-Mei; MA Xiang; MAO Ya-Jun; MO Xiao-Hu; PAN Ming-Hua; PANG Cai-Ying; PING Rong-Gang; QIN Ya-Hong; QIU Jin-Fa; SUN Sheng-Sen; SUN Yong-Zhao; WANG Liang-Liang; WEN Shuo-Pin; WU Ling-Hui; XIE Yu-Guang; XU Min; YAN Liang; YOU Zheng-Yun; YUAN Chang-Zheng; YUAN Ye; ZHANG Bing-Yun; ZHANG Chang-Chun; ZHANG Jian-Yong; ZHANG Xue-Yao; ZHANG Yao; ZHENG Yang-Heng; ZHU Ke-Jun; ZHU Yong-Sheng; ZHU Zhi-Li; ZOU Jia-Heng

    2009-01-01

    Software alignment is quite important for a tracking detector to reach its ultimate position accuracy and momentum resolution. We developed a new alignment algorithm for the BESⅢ Main Drift Chamber using the Kalman Filter method. Two different types of data which are helix tracks and straight tracks are used to test this algorithm, and the results show that the design and implementation is successful.

  8. SVM with discriminative dynamic time alignment

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    In the past several years, support vector machines (SVM) have achieved a huge success in many field, especially in pattern recognition. But the standard SVM cannot deal with length-variable vectors, which is one severe obstacle for its applications to some important areas, such as speech recognition and part-of-speech tagging. The paper proposed a novel SVM with discriminative dynamic time alignment (DDTA-SVM) to solve this problem. When training DDTA-SVM classifier, according to the category information of the training Samples, different time alignment strategies were adopted to manipulate them in the kernel functions, which contributed to great improvement for training speed and generalization capability of the classifier. Since the alignment operator was embedded in kernel functions, the training algorithms of standard SVM were still compatible in DDTA-SVM. In order to increase the reliability of the classification, a new classification algorithm was suggested. The preliminary experimental results on Chinese confusable syllables speech classification task show that DDTA-SVM obtains faster convergence speed and better classification performance than dynamic time alignment kernel SVM (DTAK-SVM).Moreover, DDTA-SVM also gives higher classification precision compared to the conventional HMM. This proves that the proposed method is effective, especially for confusable lengthvariable pattern classification tasks.

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

    Science.gov (United States)

    Squires, David

    2012-01-01

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

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

    Science.gov (United States)

    Squires, David

    2012-01-01

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

  11. A fast and accurate initial alignment method for strapdown inertial navigation system on stationary base

    Institute of Scientific and Technical Information of China (English)

    Xinlong WANG; Gongxun SHEN

    2005-01-01

    In this work,a fast and accurate stationary alignment method for strapdown inertial navigation system (SINS) is proposed.It has been demonstrated that the stationary alignment of SINS can be improved by employing the multiposition technique,but the alignment time of the azimuth error is relatively longer.Over here,the two-position alignment principle is presented.On the basis of this SINS error model,a fast estimation algorithm of the azimuth error for the initial alignment of SINS on stationary base is derived fully from the horizontal velocity outputs and the output rates,and the novel azimuth error estimation algorithm is used for the two-position alignment.Consequently,the speed and accuracy of the SINS's initial alignment is enhanced greatly.The computer simulation results illustrate the efficiency of this alignment method.

  12. Multiple sequence alignment with user-defined anchor points

    Directory of Open Access Journals (Sweden)

    Pöhler Dirk

    2006-04-01

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

  13. Parameter Identification Method for SINS Initial Alignment under Inertial Frame

    Directory of Open Access Journals (Sweden)

    Haijian Xue

    2016-01-01

    Full Text Available The performance of a strapdown inertial navigation system (SINS largely depends on the accuracy and rapidness of the initial alignment. The conventional alignment method with parameter identification has been already applied widely, but it needs to calculate the gyroscope drifts through two-position method; then the time of initial alignment is greatly prolonged. For this issue, a novel self-alignment algorithm by parameter identification method under inertial frame for SINS is proposed in this paper. Firstly, this coarse alignment method using the gravity in the inertial frame as a reference is discussed to overcome the limit of dynamic disturbance on a rocking base and fulfill the requirement for the fine alignment. Secondly, the fine alignment method by parameter identification under inertial frame is formulated. The theoretical analysis results show that the fine alignment model is fully self-aligned with no external reference information and the gyrodrifts can be estimated in real time. The simulation results demonstrate that the proposed method can achieve rapid and highly accurate initial alignment for SINS.

  14. Secure Fingerprint Alignment and Matching Protocols

    OpenAIRE

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

    2017-01-01

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

  15. MaxAlign: maximizing usable data in an alignment

    DEFF Research Database (Denmark)

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

    2007-01-01

    BACKGROUND: The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic and other analyses, for instance, gapped columns are often discarded entirely from the alignment. RESULTS: MaxAlign is a program that optimizes...... the alignment prior to such analyses. Specifically, it maximizes the number of nucleotide (or amino acid) symbols that are present in gap-free columns - the alignment area - by selecting the optimal subset of sequences to exclude from the alignment. MaxAlign can be used prior to phylogenetic and bioinformatical...... analyses as well as in other situations where this form of alignment improvement is useful. In this work we test MaxAlign's performance in these tasks and compare the accuracy of phylogenetic estimates including and excluding gapped columns from the analysis, with and without processing with MaxAlign...

  16. FAAST: Flow-space Assisted Alignment Search Tool

    Directory of Open Access Journals (Sweden)

    Persson Bengt

    2011-07-01

    Full Text Available Abstract Background High throughput pyrosequencing (454 sequencing is the major sequencing platform for producing long read high throughput data. While most other sequencing techniques produce reading errors mainly comparable with substitutions, pyrosequencing produce errors mainly comparable with gaps. These errors are less efficiently detected by most conventional alignment programs and may produce inaccurate alignments. Results We suggest a novel algorithm for calculating the optimal local alignment which utilises flowpeak information in order to improve alignment accuracy. Flowpeak information can be retained from a 454 sequencing run through interpretation of the binary SFF-file format. This novel algorithm has been implemented in a program named FAAST (Flow-space Assisted Alignment Search Tool. Conclusions We present and discuss the results of simulations that show that FAAST, through the use of the novel algorithm, can gain several percentage points of accuracy compared to Smith-Waterman-Gotoh alignments, depending on the 454 data quality. Furthermore, through an efficient multi-thread aware implementation, FAAST is able to perform these high quality alignments at high speed. The tool is available at http://www.ifm.liu.se/bioinfo/

  17. M2Align: parallel multiple sequence alignment with a multi-objective metaheuristic.

    Science.gov (United States)

    Zambrano-Vega, Cristian; Nebro, Antonio J; García-Nieto, José; Aldana Montes, José F

    2017-05-24

    Multiple Sequence Alignment (MSA) is an NP-complete optimization problem found in computational biology, where the time complexity of finding an optimal alignment raises exponentially along with the number of sequences and their lengths. Additionally, to assess the quality of a MSA, a number of objectives can be taken into account, such as maximizing the sum-of-pairs, maximizing the totally conserved columns, minimizing the number of gaps, or maximizing structural information based scores such as STRIKE. An approach to deal with MSA problems is to use multi-objective metaheuristics, which are non-exact stochastic optimization methods that can produce high quality solutions to complex problems having two or more objectives to be optimized at the same time. Our motivation is to provide a multi-objective metaheuristic for MSA that can run in parallel taking advantage of multi-core based computers. The software tool we propose, called M2Align (Multi-objective Multiple Sequence Alignment), is a parallel and more efficient version of the three-objective optimizer for sequence alignments MO-SAStrE, able of reducing the algorithm computing time by exploiting the computing capabilities of common multicore CPU clusters. Our performance evaluation over datasets of the benchmark BAliBASE (v3.0) shows that significant time reductions can be achieved by using up to 20 cores. Even in sequential executions, M2Align is faster than MO-SAStrE, thanks to the encoding method used for the alignments. M2Align is an open source project hosted in GitHub, where the source code and sample datasets can be freely obtained: https://github.com/KhaosResearch/M2Align. antonio@lcc.uma.es. Supplementary data are available at Bioinformatics online.

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

    Directory of Open Access Journals (Sweden)

    Pang Bin

    2012-02-01

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

  19. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    Gervasio Gomez

    2012-01-01

      The new alignment for the DT chambers has been successfully used in physics analysis starting with the 52X Global Tag. The remaining main areas of development over the next few months will be preparing a new track-based CSC alignment and producing realistic APEs (alignment position errors) and MC misalignment scenarios to match the latest muon alignment constants. Work on these items has been delayed from the intended timeline, mostly due to a large involvement of the muon alignment man-power in physics analyses over the first half of this year. As CMS keeps probing higher and higher energies, special attention must be paid to the reconstruction of very-high-energy muons. Recent muon POG reports from mid-June show a φ-dependence in curvature bias in Monte Carlo samples. This bias is observed already at the tracker level, where it is constant with muon pT, while it grows with pT as muon chamber information is added to the tracks. Similar studies show a much smaller effect in data, at le...

  20. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez

    2010-01-01

    For the last three months, the Muon Alignment group has focussed on providing a new, improved set of alignment constants for the end-of-year data reprocessing. These constants were delivered on time and approved by the CMS physics validation team on November 17. The new alignment incorporates several improvements over the previous one from March for nearly all sub-systems. Motivated by the loss of information from a hardware failure in May (an entire MAB was lost), the optical barrel alignment has moved from a modular, super-plane reconstruction, to a full, single loop calculation of the entire geometry for all DTs in stations 1, 2 and 3. This makes better use of the system redundancy, mitigating the effect of the information loss. Station 4 is factorised and added afterwards to make the system smaller (and therefore faster to run), and also because the MAB calibration at the MB4 zone is less precise. This new alignment procedure was tested at 0 T against photogrammetry resulting in precisions of the order...

  1. Ergodic Secret Alignment

    CERN Document Server

    Bassily, Raef

    2010-01-01

    In this paper, we introduce two new achievable schemes for the fading multiple access wiretap channel (MAC-WT). In the model that we consider, we assume that perfect knowledge of the state of all channels is available at all the nodes in a causal fashion. Our schemes use this knowledge together with the time varying nature of the channel model to align the interference from different users at the eavesdropper perfectly in a one-dimensional space while creating a higher dimensionality space for the interfering signals at the legitimate receiver hence allowing for better chance of recovery. While we achieve this alignment through signal scaling at the transmitters in our first scheme (scaling based alignment (SBA)), we let nature provide this alignment through the ergodicity of the channel coefficients in the second scheme (ergodic secret alignment (ESA)). For each scheme, we obtain the resulting achievable secrecy rate region. We show that the secrecy rates achieved by both schemes scale with SNR as 1/2log(SNR...

  2. FMIT alignment cart

    Energy Technology Data Exchange (ETDEWEB)

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

    1981-01-01

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

  3. Background suppression for a top quark mass measurement in the lepton+jets t anti t decay channel and alignment of the ATLAS silicon detectors with cosmic rays

    Energy Technology Data Exchange (ETDEWEB)

    Goettfert, Tobias

    2010-01-21

    The investigation of top quark properties will be amongst the first measurements of observables of the Standard Model of particle physics at the Large Hadron Collider. This thesis deals with the suppression of background sources contributing to the event sample used for the determination of the top quark mass. Several techniques to reduce the contamination of the selected sample with events from W+jets production and combinatorial background from wrong jet associations are evaluated. The usage of the jet merging scales of a k{sub T} jet algorithm as event shapes is laid out and a multivariate technique (Fisher discriminant) is applied to discriminate signal from physics background. Several kinematic variables are reviewed upon their capability to suppress wrong jet associations. The second part presents the achievements on the alignment of the silicon part of the Inner Detector of the ATLAS experiment. A well-aligned tracking detector will be crucial for measurements that involve particle trajectories, e.g. for reliably identifying b-quark jets. Around 700,000 tracks from cosmic ray muons are used to infer the alignment of all silicon modules of ATLAS using the track-based local {chi}{sup 2} alignment algorithm. Various additions to the method that deal with the peculiarities of alignment with cosmic rays are developed and presented. The achieved alignment precision is evaluated and compared to previous results. (orig.)

  4. Are you bleeding? Validation of a machine-learning algorithm for determination of blood volume status: application to remote triage

    National Research Council Canada - National Science Library

    Caroline A. Rickards; Nisarg Vyas; Kathy L. Ryan; Kevin R. Ward; David Andre; Gennifer M. Hurst; Chelsea R. Barrera; Victor A. Convertino

    2014-01-01

    .... The purpose of this study was to test the hypothesis that low-level physiological signals can be used to develop a machine-learning algorithm for tracking changes in central blood volume that will...

  5. High-resolution structure determination of the CylR2 homodimer using paramagnetic relaxation enhancement and structure-based prediction of molecular alignment

    Energy Technology Data Exchange (ETDEWEB)

    Rumpel, Sigrun; Becker, Stefan; Zweckstetter, Markus [Max Planck Institute for Biophysical Chemistry, Department for NMR-based Structural Biology (Germany)], E-mail: mzwecks@gwdg.de

    2008-01-15

    Structure determination of homooligomeric proteins by NMR spectroscopy is difficult due to the lack of chemical shift perturbation data, which is very effective in restricting the binding interface in heterooligomeric systems, and the difficulty of obtaining a sufficient number of intermonomer distance restraints. Here we solved the high-resolution solution structure of the 15.4 kDa homodimer CylR2, the regulator of cytolysin production from Enterococcus faecalis, which deviates by 1.1 A from the previously determined X-ray structure. We studied the influence of different experimental information such as long-range distances derived from paramagnetic relaxation enhancement, residual dipolar couplings, symmetry restraints and intermonomer Nuclear Overhauser Effect restraints on the accuracy of the derived structure. In addition, we show that it is useful to combine experimental information with methods of ab initio docking when the available experimental data are not sufficient to obtain convergence to the correct homodimeric structure. In particular, intermonomer distances may not be required when residual dipolar couplings are compared to values predicted on the basis of the charge distribution and the shape of ab initio docking solutions.

  6. Strategic Alignment of Business Intelligence

    OpenAIRE

    Cederberg, Niclas

    2010-01-01

    This thesis is about the concept of strategic alignment of business intelligence. It is based on a theoretical foundation that is used to define and explain business intelligence, data warehousing and strategic alignment. By combining a number of different methods for strategic alignment a framework for alignment of business intelligence is suggested. This framework addresses all different aspects of business intelligence identified as relevant for strategic alignment of business intelligence...

  7. PILOT optical alignment

    Science.gov (United States)

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

    2016-07-01

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

  8. Orientation and Alignment Echoes

    CERN Document Server

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

    2015-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-01-15

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

  10. Automatic Determination of the Need for Intravenous Contrast in Musculoskeletal MRI Examinations Using IBM Watson's Natural Language Processing Algorithm.

    Science.gov (United States)

    Trivedi, Hari; Mesterhazy, Joseph; Laguna, Benjamin; Vu, Thienkhai; Sohn, Jae Ho

    2017-09-18

    Magnetic resonance imaging (MRI) protocoling can be time- and resource-intensive, and protocols can often be suboptimal dependent upon the expertise or preferences of the protocoling radiologist. Providing a best-practice recommendation for an MRI protocol has the potential to improve efficiency and decrease the likelihood of a suboptimal or erroneous study. The goal of this study was to develop and validate a machine learning-based natural language classifier that can automatically assign the use of intravenous contrast for musculoskeletal MRI protocols based upon the free-text clinical indication of the study, thereby improving efficiency of the protocoling radiologist and potentially decreasing errors. We utilized a deep learning-based natural language classification system from IBM Watson, a question-answering supercomputer that gained fame after challenging the best human players on Jeopardy! in 2011. We compared this solution to a series of traditional machine learning-based natural language processing techniques that utilize a term-document frequency matrix. Each classifier was trained with 1240 MRI protocols plus their respective clinical indications and validated with a test set of 280. Ground truth of contrast assignment was obtained from the clinical record. For evaluation of inter-reader agreement, a blinded second reader radiologist analyzed all cases and determined contrast assignment based on only the free-text clinical indication. In the test set, Watson demonstrated overall accuracy of 83.2% when compared to the original protocol. This was similar to the overall accuracy of 80.2% achieved by an ensemble of eight traditional machine learning algorithms based on a term-document matrix. When compared to the second reader's contrast assignment, Watson achieved 88.6% agreement. When evaluating only the subset of cases where the original protocol and second reader were concordant (n = 251), agreement climbed further to 90.0%. The classifier was

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

    Science.gov (United States)

    Chavez, Melissa A.

    2011-01-01

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

  12. Robust local intervertebral disc alignment for spinal MRI

    Science.gov (United States)

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

    2006-03-01

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

  13. A unified model of grain alignment: Radiative Alignment of Interstellar Grains with magnetic inclusions

    CERN Document Server

    Hoang, Thiem

    2016-01-01

    The radiative torque (RAT) alignment of interstellar grains with ordinary paramagnetic susceptibilities has been supported by a number of earlier studies. The alignment of such grains depends on the so-called RAT parameter $q^{\\max}$ that is determined by the grain shape. For interstellar grains with a broad range of $q^{\\max}$, a significant fraction of grains is expected to get aligned with low angular momentum at the so-called low-J attractor points, which entail degrees of alignment between 20 or 30 percent, irrespectively of the strength of RATs. The latter value may not be sufficient for explaining the observed interstellar alignment in the diffuse medium. In this paper, we elaborate our model of radiative alignment for grains with enhanced magnetic susceptibility due to magnetic inclusions, such that both Magnetic torque and RAdiative Torque (MRAT) play a role in grain alignment. Such grains can get aligned with high angular momentum at the so-called high-J attractor points, which achieve a high degree...

  14. Understanding the critical challenges of self-aligned octuple patterning

    Science.gov (United States)

    Yu, Ji; Xiao, Wei; Kang, Weiling; Chen, Yijian

    2014-03-01

    In this paper, we present a thorough investigation of self-aligned octuple patterning (SAOP) process characteristics, cost structure, integration challenges, and layout decomposition. The statistical characteristics of SAOP CD variations such as multi-modality are analyzed and contributions from various features to CDU and MTT (mean-to-target) budgets are estimated. The gap space is found to have the worst CDU+MTT performance and is used to determine the required overlay accuracy to ensure a satisfactory edge-placement yield of a cut process. Moreover, we propose a 5-mask positive-tone SAOP (pSAOP) process for memory FEOL patterning and a 3-mask negative-tone SAOP (nSAOP) process for logic BEOL patterning. The potential challenges of 2-D SAOP layout decomposition for BEOL applications are identified. Possible decomposition approaches are explored and the functionality of several developed algorithm is verified using 2-D layout examples from Open Cell Library.

  15. Aligning Responsible Business Practices

    DEFF Research Database (Denmark)

    Weller, Angeli E.

    2017-01-01

    This article offers an in-depth case study of a global high tech manufacturer that aligned its ethics and compliance, corporate social responsibility, and sustainability practices. Few large companies organize their responsible business practices this way, despite conceptual relevance and calls...... and managers interested in understanding how responsible business practices may be collectively organized....

  16. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez and Y. Pakhotin

    2012-01-01

      A new track-based alignment for the DT chambers is ready for deployment: an offline tag has already been produced which will become part of the 52X Global Tag. This alignment was validated within the muon alignment group both at low and high momentum using a W/Z skim sample. It shows an improved mass resolution for pairs of stand-alone muons, improved curvature resolution at high momentum, and improved DT segment extrapolation residuals. The validation workflow for high-momentum muons used to depend solely on the “split cosmics” method, looking at the curvature difference between muon tracks reconstructed in the upper or lower half of CMS. The validation has now been extended to include energetic muons decaying from heavily boosted Zs: the di-muon invariant mass for global and stand-alone muons is reconstructed, and the invariant mass resolution is compared for different alignments. The main areas of development over the next few months will be preparing a new track-based C...

  17. Aligning Theory with Practice

    Science.gov (United States)

    Kurz, Terri L.; Batarelo, Ivana

    2009-01-01

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

  18. Alignment of concerns

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  19. Aligning Mental Representations

    DEFF Research Database (Denmark)

    Kano Glückstad, Fumiko

    2013-01-01

    on the application of the BMG to publicly available datasets, the Leuven natural concept database [3] representing semantic structures of domain knowledge possessed by individual subjects [3]. Results indicate that the BMG is potentially a model applicable to simulating the alignment of domain knowledge from...

  20. Multiple sequence alignment accuracy and evolutionary distance estimation.

    Science.gov (United States)

    Rosenberg, Michael S

    2005-11-23

    Sequence alignment is a common tool in bioinformatics and comparative genomics. It is generally assumed that multiple sequence alignment yields better results than pair wise sequence alignment, but this assumption has rarely been tested, and never with the control provided by simulation analysis. This study used sequence simulation to examine the gain in accuracy of adding a third sequence to a pair wise alignment, particularly concentrating on how the phylogenetic position of the additional sequence relative to the first pair changes the accuracy of the initial pair's alignment as well as their estimated evolutionary distance. The maximal gain in alignment accuracy was found not when the third sequence is directly intermediate between the initial two sequences, but rather when it perfectly subdivides the branch leading from the root of the tree to one of the original sequences (making it half as close to one sequence as the other). Evolutionary distance estimation in the multiple alignment framework, however, is largely unrelated to alignment accuracy and rather is dependent on the position of the third sequence; the closer the branch leading to the third sequence is to the root of the tree, the larger the estimated distance between the first two sequences. The bias in distance estimation appears to be a direct result of the standard greedy progressive algorithm used by many multiple alignment methods. These results have implications for choosing new taxa and genomes to sequence when resources are limited.

  1. Design of practical alignment device in KSTAR Thomson diagnostic

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-11-15

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

  2. Evaluation of elastix-based propagated align algorithm for VOI- and voxel-based analysis of longitudinal F-18-FDG PET/CT data from patients with non-small cell lung cancer (NSCLC)

    OpenAIRE

    Kerner, Gerald S. M. A.; Fischer, Alexander; Koole, Michel J. B.; Pruim, Jan; Groen, Harry J M

    2015-01-01

    Background: Deformable image registration allows volume of interest (VOI)- and voxel-based analysis of longitudinal changes in fluorodeoxyglucose (FDG) tumor uptake in patients with non-small cell lung cancer (NSCLC). This study evaluates the performance of the elastix toolbox deformable image registration algorithm for VOI and voxel-wise assessment of longitudinal variations in FDG tumor uptake in NSCLC patients. Methods: Evaluation of the elastix toolbox was performed using F-18-FDG PET/CT ...

  3. Evaluation of elastix-based propagated align algorithm for VOI- and voxel-based analysis of longitudinal 18F-FDG PET/CT data from patients with non-small cell lung cancer (NSCLC)

    OpenAIRE

    Kerner, Gerald SMA; Fischer, Alexander; Koole, Michel JB; Pruim, Jan; Groen, Harry JM

    2015-01-01

    Background Deformable image registration allows volume of interest (VOI)- and voxel-based analysis of longitudinal changes in fluorodeoxyglucose (FDG) tumor uptake in patients with non-small cell lung cancer (NSCLC). This study evaluates the performance of the elastix toolbox deformable image registration algorithm for VOI and voxel-wise assessment of longitudinal variations in FDG tumor uptake in NSCLC patients. Methods Evaluation of the elastix toolbox was performed using 18F-FDG PET/CT at ...

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

    CERN Document Server

    Suchanek, Fabian M; Senellart, Pierre

    2011-01-01

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

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

    CERN Document Server

    Arribas-Gil, Ana

    2011-01-01

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

  6. Application of stochastic particle swarm optimization algorithm to determine the graded refractive index distribution in participating media

    Science.gov (United States)

    Wei, Lin-Yang; Qi, Hong; Ren, Ya-Tao; Ruan, Li-Ming

    2016-11-01

    Inverse estimation of the refractive index distribution in one-dimensional participating media with graded refractive index (GRI) is investigated. The forward radiative transfer problem is solved by the Chebyshev collocation spectral method. The stochastic particle swarm optimization (SPSO) algorithm is employed to retrieve three kinds of GRI distribution, i.e. the linear, sinusoidal and quadratic GRI distribution. The retrieval accuracy of GRI distribution with different wall emissivity, optical thickness, absorption coefficients and scattering coefficients are discussed thoroughly. To improve the retrieval accuracy of quadratic GRI distribution, a double-layer model is proposed to supply more measurement information. The influence of measurement errors upon the precision of estimated results is also investigated. Considering the GRI distribution is unknown beforehand in practice, a quadratic function is employed to retrieve the linear GRI by SPSO algorithm. All the results show that the SPSO algorithm is applicable to retrieve different GRI distributions in participating media accurately even with noisy data.

  7. Lateral pupil alignment tolerance in peripheral refractometry.

    Science.gov (United States)

    Fedtke, Cathleen; Ehrmann, Klaus; Ho, Arthur; Holden, Brien A

    2011-05-01

    To investigate the tolerance to lateral pupil misalignment in peripheral refraction compared with central refraction. A Shin-Nippon NVision-K5001 open-view auto-refractor was used to measure central and peripheral refraction (30° temporal and 30° nasal visual field) of the right eyes of 10 emmetropic and 10 myopic participants. At each of the three fixation angles, five readings were recorded for each of the following alignment positions relative to pupil center: centrally aligned, 1 and 2 mm temporally aligned, and 1 and 2 mm nasally aligned. For central fixation, increasing dealignment from pupil center produced a quadratic decrease (r ≥ 0.98, p < 0.04) in the refractive power vectors M and J180 which, when interpolated, reached clinical significance (i.e., ≥ 0.25 diopter for M and ≥ 0.125 diopter for J180 and J45) for an alignment error of 0.79 mm or greater. M and J180 as measured in the 30° temporal and 30° nasal visual field led to a significant linear correlation (r ≥ 0.94, p < 0.02) as pupil dealignment gradually changed from temporal to nasal. As determined from regression analysis, a pupil alignment error of 0.20 mm or greater would introduce errors in M and J180 that are clinically significant. Tolerance to lateral pupil alignment error decreases strongly in the periphery compared with the greater tolerance in central refraction. Thus, precise alignment of the entrance pupil with the instrument axis is critical for accurate and reliable peripheral refraction.

  8. SOAP2: an improved ultrafast tool for short read alignment

    DEFF Research Database (Denmark)

    Li, Ruiqiang; Yu, Chang; Li, Yingrui

    2009-01-01

    SUMMARY: SOAP2 is a significantly improved version of the short oligonucleotide alignment program that both reduces computer memory usage and increases alignment speed at an unprecedented rate. We used a Burrows Wheeler Transformation (BWT) compression index to substitute the seed strategy...... for indexing the reference sequence in the main memory. We tested it on the whole human genome and found that this new algorithm reduced memory usage from 14.7 to 5.4 GB and improved alignment speed by 20-30 times. SOAP2 is compatible with both single- and paired-end reads. Additionally, this tool now supports...

  9. Speeding up Batch Alignment of Large Ontologies Using MapReduce.

    Science.gov (United States)

    Thayasivam, Uthayasanker; Doshi, Prashant

    2013-09-01

    Real-world ontologies tend to be very large with several containing thousands of entities. Increasingly, ontologies are hosted in repositories, which often compute the alignment between the ontologies. As new ontologies are submitted or ontologies are updated, their alignment with others must be quickly computed. Therefore, aligning several pairs of ontologies quickly becomes a challenge for these repositories. We project this problem as one of batch alignment and show how it may be approached using the distributed computing paradigm of MapReduce. Our approach allows any alignment algorithm to be utilized on a MapReduce architecture. Experiments using four representative alignment algorithms demonstrate flexible and significant speedup of batch alignment of large ontology pairs using MapReduce.

  10. New algorithm to determine true colocalization in combination with image restoration and time-lapse confocal microscopy to MAP kinases in mitochondria.

    Directory of Open Access Journals (Sweden)

    Jorge Ignacio Villalta

    Full Text Available The subcellular localization and physiological functions of biomolecules are closely related and thus it is crucial to precisely determine the distribution of different molecules inside the intracellular structures. This is frequently accomplished by fluorescence microscopy with well-characterized markers and posterior evaluation of the signal colocalization. Rigorous study of colocalization requires statistical analysis of the data, albeit yet no single technique has been established as a standard method. Indeed, the few methods currently available are only accurate in images with particular characteristics. Here, we introduce a new algorithm to automatically obtain the true colocalization between images that is suitable for a wide variety of biological situations. To proceed, the algorithm contemplates the individual contribution of each pixel's fluorescence intensity in a pair of images to the overall Pearsońs correlation and Manders' overlap coefficients. The accuracy and reliability of the algorithm was validated on both simulated and real images that reflected the characteristics of a range of biological samples. We used this algorithm in combination with image restoration by deconvolution and time-lapse confocal microscopy to address the localization of MEK1 in the mitochondria of different cell lines. Appraising the previously described behavior of Akt1 corroborated the reliability of the combined use of these techniques. Together, the present work provides a novel statistical approach to accurately and reliably determine the colocalization in a variety of biological images.

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

    Science.gov (United States)

    Zhang, Zefeng; Lin, Hao; Li, Ming

    2007-01-01

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

  12. Alignement automatise de fibres optiques amorces monomodes

    Science.gov (United States)

    St-Amant, Yves

    Cette these jette les bases necessaires au developpement d'algorithmes a base de modele pour l'automatisation de l'alignement de fibres amorces monomodes. A partir de la methode de l'integrale de recouvrement et de deux solutions approximatives existantes, un modele analytique d'efficacite de couplage optique permettant d'estimer la puissance transmise entre un composant et une fibre amorce monomode est d'abord formule. Avec celui-ci, sept proprietes pouvant etre utiles au developpement d'algorithmes a base de modele sont ensuite identifiees et validees. Enfin, a l'aide de ces proprietes, une strategie d'alignement a base de modele est developpee et validee experimentalement. Les resultats obtenus demontrent clairement la repetitivite, la robustesse, la precision et la rapidite de la strategie proposee. Ils demontrent aussi qu'il est possible de realiser un alignement complet sans l'utilisation de systemes auxiliaires tels des systemes de vision, des cameras infrarouges, des capteurs de contact ou des systemes de fixation hautement precis.

  13. A hierarchical algorithm for molecular similarity (H-FORMS).

    Science.gov (United States)

    Ramirez-Manzanares, Alonso; Peña, Joaquin; Azpiroz, Jon M; Merino, Gabriel

    2015-07-15

    A new hierarchical method to determine molecular similarity is introduced. The goal of this method is to detect if a pair of molecules has the same structure by estimating a rigid transformation that aligns the molecules and a correspondence function that matches their atoms. The algorithm firstly detect similarity based on the global spatial structure. If this analysis is not sufficient, the algorithm computes novel local structural rotation-invariant descriptors for the atom neighborhood and uses this information to match atoms. Two strategies (deterministic and stochastic) on the matching based alignment computation are tested. As a result, the atom-matching based on local similarity indexes decreases the number of testing trials and significantly reduces the dimensionality of the Hungarian assignation problem. The experiments on well-known datasets show that our proposal outperforms state-of-the-art methods in terms of the required computational time and accuracy. © 2015 Wiley Periodicals, Inc.

  14. Multiscale Point Correspondence Using Feature Distribution and Frequency Domain Alignment

    Directory of Open Access Journals (Sweden)

    Zeng-Shun Zhao

    2012-01-01

    Full Text Available In this paper, a hybrid scheme is proposed to find the reliable point-correspondences between two images, which combines the distribution of invariant spatial feature description and frequency domain alignment based on two-stage coarse to fine refinement strategy. Firstly, the source and the target images are both down-sampled by the image pyramid algorithm in a hierarchical multi-scale way. The Fourier-Mellin transform is applied to obtain the transformation parameters at the coarse level between the image pairs; then, the parameters can serve as the initial coarse guess, to guide the following feature matching step at the original scale, where the correspondences are restricted in a search window determined by the deformation between the reference image and the current image; Finally, a novel matching strategy is developed to reject the false matches by validating geometrical relationships between candidate matching points. By doing so, the alignment parameters are refined, which is more accurate and more flexible than a robust fitting technique. This in return can provide a more accurate result for feature correspondence. Experiments on real and synthetic image-pairs show that our approach provides satisfactory feature matching performance.

  15. Inflation by alignment

    Energy Technology Data Exchange (ETDEWEB)

    Burgess, C.P. [PH -TH Division, CERN,CH-1211, Genève 23 (Switzerland); Department of Physics & Astronomy, McMaster University,1280 Main Street West, Hamilton ON (Canada); Perimeter Institute for Theoretical Physics,31 Caroline Street North, Waterloo ON (Canada); Roest, Diederik [Van Swinderen Institute for Particle Physics and Gravity, University of Groningen,Nijenborgh 4, 9747 AG Groningen (Netherlands)

    2015-06-08

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

  16. Aligning component upgrades

    Directory of Open Access Journals (Sweden)

    Roberto Di Cosmo

    2011-08-01

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

  17. Inflation by Alignment

    CERN Document Server

    Burgess, Cliff

    2015-01-01

    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 > Mp, 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.

  18. Aligning component upgrades

    CERN Document Server

    Di Cosmo, Roberto; Michel, Claude; 10.4204/EPTCS.65.1

    2011-01-01

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

  19. Plant Leaf Recognition through Local Discriminative Tangent Space Alignment

    Directory of Open Access Journals (Sweden)

    Chuanlei Zhang

    2016-01-01

    Full Text Available Manifold learning based dimensionality reduction algorithms have been payed much attention in plant leaf recognition as the algorithms can select a subset of effective and efficient discriminative features in the leaf images. In this paper, a dimensionality reduction method based on local discriminative tangent space alignment (LDTSA is introduced for plant leaf recognition based on leaf images. The proposed method can embrace part optimization and whole alignment and encapsulate the geometric and discriminative information into a local patch. The experiments on two plant leaf databases, ICL and Swedish plant leaf datasets, demonstrate the effectiveness and feasibility of the proposed method.

  20. Generation and Detection of Alignments in Gabor Patterns

    Directory of Open Access Journals (Sweden)

    Samy Blusseau

    2016-11-01

    Full Text Available This paper presents a method to be used in psychophysical experiments to compare directly visual perception to an a contrario algorithm, on a straight patterns detection task. The method is composed of two parts. The first part consists in building a stimulus, namely an array of oriented elements, in which an alignment is present with variable salience. The second part focuses on a detection algorithm, based on the a contrario theory, which is designed to predict which alignment will be considered as the most salient in a given stimulus.

  1. Alignment of concerns

    DEFF Research Database (Denmark)

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

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

  2. Novel Access Control and Interference Alignment Based MIMO Link Scheduling Algorithm%基于接入控制与干扰对齐的MIMO链路调度算法

    Institute of Scientific and Technical Information of China (English)

    熊最; 王可人; 金虎; 徐云

    2016-01-01

    干扰对齐(Interference Alignment,IA)因其能提升MIMO(Multiple Input Multiple Output)系统性能受到了广泛关注.现有链路调度将接入控制与最小干扰泄露准则(Minimum Interference Leakage,MinL)的IA相结合以保证系统稳定性,但MinL准则下LA获取的期望信号增益较弱.为了弥补这一不足,提出将基于MaxSINR准则的IA算法,提出了一种基于IA-MaxSINR的半分布式调度算法SDSIA-MaxSINR.理论分析和仿真实验表明,MaxSINR-IA算法的计算复杂度比MinL-IA算法高,但在高INR需求下,DSIA-MaxSINR算法所获取的吞吐量明显高于DSIA-MinL算法.

  3. Nuclear reactor alignment plate configuration

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-01-28

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

  4. Track based alignment of the CMS silicon tracker and its implication on physics performance

    Energy Technology Data Exchange (ETDEWEB)

    Draeger, Jula

    2011-08-15

    In order to fully exploit the discovery potential of the CMS detector for new physics beyond the Standard Model at the high luminosity and centre-of-mass energy provided by the Large Hadron Collider, a careful calibration of the detector and profound understanding of its impact on physics performance are necessary to provide realistic uncertainties for the measurements of physics processes. This thesis describes the track-based alignment of the inner tracking system of CMS with the Millepede II algorithm. Using the combined information of tracks from cosmic rays and collisions taken in 2010, a remarkable local alignment precision has been reached that meets the design specification for most regions of the detector and takes into account instabilities of the detector geometry over time. In addition, the impact of the alignment of b tagging or the Z boson resonance are investigated. The latter is studied to investigate the impact of correlated detector distortions which hardly influence the overall solution of the minimisation problem but introduce biases in the track parameters and thus the derived physics quantities. The determination and constraint of these weak modes present the future challenge of the alignment task at CMS. (orig.)

  5. Profile-Based LC-MS data alignment--a Bayesian approach.

    Science.gov (United States)

    Tsai, Tsung-Heng; Tadesse, Mahlet G; Wang, Yue; Ressom, Habtom W

    2013-01-01

    A Bayesian alignment model (BAM) is proposed for alignment of liquid chromatography-mass spectrometry (LC-MS) data. BAM belongs to the category of profile-based approaches, which are composed of two major components: a prototype function and a set of mapping functions. Appropriate estimation of these functions is crucial for good alignment results. BAM uses Markov chain Monte Carlo (MCMC) methods to draw inference on the model parameters and improves on existing MCMC-based alignment methods through 1) the implementation of an efficient MCMC sampler and 2) an adaptive selection of knots. A block Metropolis-Hastings algorithm that mitigates the problem of the MCMC sampler getting stuck at local modes of the posterior distribution is used for the update of the mapping function coefficients. In addition, a stochastic search variable selection (SSVS) methodology is used to determine the number and positions of knots. We applied BAM to a simulated data set, an LC-MS proteomic data set, and two LC-MS metabolomic data sets, and compared its performance with the Bayesian hierarchical curve registration (BHCR) model, the dynamic time-warping (DTW) model, and the continuous profile model (CPM). The advantage of applying appropriate profile-based retention time correction prior to performing a feature-based approach is also demonstrated through the metabolomic data sets.

  6. Aligning, analyzing, and visualizing sequences for antibody engineering: Automated recognition of immunoglobulin variable region features.

    Science.gov (United States)

    Jarasch, Alexander; Skerra, Arne

    2017-01-01

    The analysis and comparison of large numbers of immunoglobulin (Ig) sequences that arise during an antibody selection campaign can be time-consuming and tedious. Typically, the identification and annotation of framework as well as complementarity-determining regions (CDRs) is based on multiple sequence alignments using standardized numbering schemes, which allow identification of equivalent residues among different family members but often necessitate expert knowledge and manual intervention. Moreover, due to the enormous length variability of some CDRs the benefit of conventional Ig numbering schemes is limited and the calculation of correct sequence alignments can become challenging. Whereas, in principle, a well established set of rules permits the assignment of CDRs from the amino acid sequence alone, no currently available sequence alignment editor provides an algorithm to annotate new Ig sequences accordingly. Here we present a unique pattern matching method implemented into our recently developed ANTICALIgN editor that automatically identifies all hypervariable and framework regions in experimentally elucidated antibody sequences using so-called "regular expressions." By combination of this widely supported software syntax with the unique capabilities of real-time aligning, editing and analyzing extended sets of amino acid and/or nucleotide sequences simultaneously on a local workstation, ANTICALIgN provides a powerful utility for antibody engineering. Proteins 2016; 85:65-71. © 2016 Wiley Periodicals, Inc.

  7. Seeking the perfect alignment

    CERN Multimedia

    2002-01-01

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

  8. RECAT - Redundant Channel Alignment Technique

    Science.gov (United States)

    2016-06-07

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

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

    OpenAIRE

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

    2012-01-01

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

  10. Sigma: multiple alignment of weakly-conserved non-coding DNA sequence

    Directory of Open Access Journals (Sweden)

    Siddharthan Rahul

    2006-03-01

    Full Text Available Abstract Background Existing tools for multiple-sequence alignment focus on aligning protein sequence or protein-coding DNA sequence, and are often based on extensions to Needleman-Wunsch-like pairwise alignment methods. We introduce a new tool, Sigma, with a new algorithm and scoring scheme designed specifically for non-coding DNA sequence. This problem acquires importance with the increasing number of published sequences of closely-related species. In particular, studies of gene regulation seek to take advantage of comparative genomics, and recent algorithms for finding regulatory sites in phylogenetically-related intergenic sequence require alignment as a preprocessing step. Much can also be learned about evolution from intergenic DNA, which tends to evolve faster than coding DNA. Sigma uses a strategy of seeking the best possible gapless local alignments (a strategy earlier used by DiAlign, at each step making the best possible alignment consistent with existing alignments, and scores the significance of the alignment based on the lengths of the aligned fragments and a background model which may be supplied or estimated from an auxiliary file of intergenic DNA. Results Comparative tests of sigma with five earlier algorithms on synthetic data generated to mimic real data show excellent performance, with Sigma balancing high "sensitivity" (more bases aligned with effective filtering of "incorrect" alignments. With real data, while "correctness" can't be directly quantified for the alignment, running the PhyloGibbs motif finder on pre-aligned sequence suggests that Sigma's alignments are superior. Conclusion By taking into account the peculiarities of non-coding DNA, Sigma fills a gap in the toolbox of bioinformatics.

  11. New supervised alignment method as a preprocessing tool for chromatographic data in metabolomic studies.

    Science.gov (United States)

    Struck, Wiktoria; Wiczling, Paweł; Waszczuk-Jankowska, Małgorzata; Kaliszan, Roman; Markuszewski, Michał Jan

    2012-09-21

    The purpose of this work was to develop a new aligning algorithm called supervised alignment and to compare its performance with the correlation optimized warping. The supervised alignment is based on a "supervised" selection of a few common peaks presented on each chromatogram. The selected peaks are aligned based on a difference in the retention time of the selected analytes in the sample and the reference chromatogram. The retention times of the fragments between known peaks are subsequently linearly interpolated. The performance of the proposed algorithm has been tested on a series of simulated and experimental chromatograms. The simulated chromatograms comprised analytes with a systematic or random retention time shifts. The experimental chromatographic (RP-HPLC) data have been obtained during the analysis of nucleosides from 208 urine samples and consists of both the systematic and random displacements. All the data sets have been aligned using the correlation optimized warping and the supervised alignment. The time required to complete the alignment, the overall complexity of both algorithms, and its performance measured by the average correlation coefficients are compared to assess performance of tested methods. In the case of systematic shifts, both methods lead to the successful alignment. However, for random shifts, the correlation optimized warping in comparison to the supervised alignment requires more time (few hours versus few minutes) and the quality of the alignment described as correlation coefficient of the newly aligned matrix is worse 0.8593 versus 0.9629. For the experimental dataset supervised alignment successfully aligns 208 samples using 10 prior identified peaks. The knowledge about retention times of few analytes' in the data sets is necessary to perform the supervised alignment for both systematic and random shifts. The supervised alignment method is faster, more effective and simpler preprocessing method than the correlation optimized

  12. Method for alignment of microwires

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-01-24

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

  13. Matt: local flexibility aids protein multiple structure alignment.

    Directory of Open Access Journals (Sweden)

    Matthew Menke

    2008-01-01

    Full Text Available Even when there is agreement on what measure a protein multiple structure alignment should be optimizing, finding the optimal alignment is computationally prohibitive. One approach used by many previous methods is aligned fragment pair chaining, where short structural fragments from all the proteins are aligned against each other optimally, and the final alignment chains these together in geometrically consistent ways. Ye and Godzik have recently suggested that adding geometric flexibility may help better model protein structures in a variety of contexts. We introduce the program Matt (Multiple Alignment with Translations and Twists, an aligned fragment pair chaining algorithm that, in intermediate steps, allows local flexibility between fragments: small translations and rotations are temporarily allowed to bring sets of aligned fragments closer, even if they are physically impossible under rigid body transformations. After a dynamic programming assembly guided by these "bent" alignments, geometric consistency is restored in the final step before the alignment is output. Matt is tested against other recent multiple protein structure alignment programs on the popular Homstrad and SABmark benchmark datasets. Matt's global performance is competitive with the other programs on Homstrad, but outperforms the other programs on SABmark, a benchmark of multiple structure alignments of proteins with more distant homology. On both datasets, Matt demonstrates an ability to better align the ends of alpha-helices and beta-strands, an important characteristic of any structure alignment program intended to help construct a structural template library for threading approaches to the inverse protein-folding problem. The related question of whether Matt alignments can be used to distinguish distantly homologous structure pairs from pairs of proteins that are not homologous is also considered. For this purpose, a p-value score based on the length of the common core

  14. Connectivity independent protein-structure alignment: a hierarchical approach

    Directory of Open Access Journals (Sweden)

    Schmidt-Goenner Tobias

    2006-11-01

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

  15. Nonlinear Alignment and Its Local Linear Iterative Solution

    Directory of Open Access Journals (Sweden)

    Sumin Zhang

    2016-01-01

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

  16. Data Mining of Determinants of Intrauterine Growth Retardation Revisited Using Novel Algorithms Generating Semantic Maps and Prototypical Discriminating Variable Profiles.

    Directory of Open Access Journals (Sweden)

    Massimo Buscema

    Full Text Available Intra-uterine growth retardation is often of unknown origin, and is of great interest as a "Fetal Origin of Adult Disease" has been now well recognized. We built a benchmark based upon a previously analysed data set related to Intrauterine Growth Retardation with 46 subjects described by 14 variables, related with the insulin-like growth factor system and pro-inflammatory cytokines, namely interleukin-6 and tumor necrosis factor-α.We used new algorithms for optimal information sorting based on the combination of two neural network algorithms: Auto-contractive Map and Activation and Competition System. Auto-Contractive Map spatializes the relationships among variables or records by constructing a suitable embedding space where 'closeness' among variables or records reflects accurately their associations. The Activation and Competition System algorithm instead works as a dynamic non linear associative memory on the weight matrices of other algorithms, and is able to produce a prototypical variable profile of a given target.Classical statistical analysis, proved to be unable to distinguish intrauterine growth retardation from appropriate-for-gestational age (AGA subjects due to the high non-linearity of underlying functions. Auto-contractive map succeeded in clustering and differentiating completely the conditions under study, while Activation and Competition System allowed to develop the profile of variables which discriminated the two conditions under study better than any other previous form of attempt. In particular, Activation and Competition System showed that ppropriateness for gestational age was explained by IGF-2 relative gene expression, and by IGFBP-2 and TNF-α placental contents. IUGR instead was explained by IGF-I, IGFBP-1, IGFBP-2 and IL-6 gene expression in placenta.This further analysis provided further insight into the placental key-players of fetal growth within the insulin-like growth factor and cytokine systems. Our previous

  17. An Algorithm to Determine the Optimum Tilt Angle of a Solar Panel from Global Horizontal Solar Radiation

    OpenAIRE

    Emanuele Calabrò

    2013-01-01

    This paper proposes an algorithm to calculate the optimum tilt angle of solar panels by means of global horizontal solar radiation data, provided from Earth-based meteorological stations. This mathematical modeling is based on the maximization of the theoretical expression of the global solar irradiation impinging on an inclined surface, with respect to the slope and orientation of the panel and to the solar hour angle. A set of transcendent equations resulted, whose solutions give the optimu...

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

    Science.gov (United States)

    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.

  19. FASMA: A Service to Format and Analyze Sequences in Multiple Alignments

    Institute of Scientific and Technical Information of China (English)

    Susan Costantini; Giovanni Colonna; Angelo M. Facchiano

    2007-01-01

    Multiple sequence alignments are successfully applied in many studies for under- standing the structural and functional relations among single nucleic acids and pro- tein 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 /.

  20. Dynamic Programming Used to Align Protein Structures with a Spectrum Is Robust

    Directory of Open Access Journals (Sweden)

    Allen Holder

    2013-11-01

    Full Text Available Several efficient algorithms to conduct pairwise comparisons among large databases of protein structures have emerged in the recent literature. The central theme is the design of a measure between the Cα atoms of two protein chains, from which dynamic programming is used to compute an alignment. The efficiency and efficacy of these algorithms allows large-scale computational studies that would have been previously impractical. The computational study herein shows that the structural alignment algorithm eigen-decomposition alignment with the spectrum (EIGAs is robust against both parametric and structural variation.