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.

BitPAl: a bit-parallel, general integer-scoring sequence alignment algorithm.

Science.gov (United States)

Loving, Joshua; Hernandez, Yozen; Benson, Gary

2014-11-15

Mapping of high-throughput sequencing data and other bulk sequence comparison applications have motivated a search for high-efficiency sequence alignment algorithms. The bit-parallel approach represents individual cells in an alignment scoring matrix as bits in computer words and emulates the calculation of scores by a series of logic operations composed of AND, OR, XOR, complement, shift and addition. Bit-parallelism has been successfully applied to the longest common subsequence (LCS) and edit-distance problems, producing fast algorithms in practice. We have developed BitPAl, a bit-parallel algorithm for general, integer-scoring global alignment. Integer-scoring schemes assign integer weights for match, mismatch and insertion/deletion. The BitPAl method uses structural properties in the relationship between adjacent scores in the scoring matrix to construct classes of efficient algorithms, each designed for a particular set of weights. In timed tests, we show that BitPAl runs 7-25 times faster than a standard iterative algorithm. Source code is freely available for download at http://lobstah.bu.edu/BitPAl/BitPAl.html. BitPAl is implemented in C and runs on all major operating systems. jloving@bu.edu or yhernand@bu.edu or gbenson@bu.edu Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Iterative local Chi2 alignment algorithm for the ATLAS Pixel detector

CERN Document Server

Göttfert, Tobias

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

Fitting-free algorithm for efficient quantification of collagen fiber alignment in SHG imaging applications.

Science.gov (United States)

Hall, Gunnsteinn; Liang, Wenxuan; Li, Xingde

2017-10-01

Collagen fiber alignment derived from second harmonic generation (SHG) microscopy images can be important for disease diagnostics. Image processing algorithms are needed to robustly quantify the alignment in images with high sensitivity and reliability. Fourier transform (FT) magnitude, 2D power spectrum, and image autocorrelation have previously been used to extract fiber information from images by assuming a certain mathematical model (e.g. Gaussian distribution of the fiber-related parameters) and fitting. The fitting process is slow and fails to converge when the data is not Gaussian. Herein we present an efficient constant-time deterministic algorithm which characterizes the symmetricity of the FT magnitude image in terms of a single parameter, named the fiber alignment anisotropy R ranging from 0 (randomized fibers) to 1 (perfect alignment). This represents an important improvement of the technology and may bring us one step closer to utilizing the technology for various applications in real time. In addition, we present a digital image phantom-based framework for characterizing and validating the algorithm, as well as assessing the robustness of the algorithm against different perturbations.

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.

An extensive assessment of network alignment algorithms for comparison of brain connectomes.

Science.gov (United States)

Milano, Marianna; Guzzi, Pietro Hiram; Tymofieva, Olga; Xu, Duan; Hess, Christofer; Veltri, Pierangelo; Cannataro, Mario

2017-06-06

Recently the study of the complex system of connections in neural systems, i.e. the connectome, has gained a central role in neurosciences. The modeling and analysis of connectomes are therefore a growing area. Here we focus on the representation of connectomes by using graph theory formalisms. Macroscopic human brain connectomes are usually derived from neuroimages; the analyzed brains are co-registered in the image domain and brought to a common anatomical space. An atlas is then applied in order to define anatomically meaningful regions that will serve as the nodes of the network - this process is referred to as parcellation. The atlas-based parcellations present some known limitations in cases of early brain development and abnormal anatomy. Consequently, it has been recently proposed to perform atlas-free random brain parcellation into nodes and align brains in the network space instead of the anatomical image space, as a way to deal with the unknown correspondences of the parcels. Such process requires modeling of the brain using graph theory and the subsequent comparison of the structure of graphs. The latter step may be modeled as a network alignment (NA) problem. In this work, we first define the problem formally, then we test six existing state of the art of network aligners on diffusion MRI-derived brain networks. We compare the performances of algorithms by assessing six topological measures. We also evaluated the robustness of algorithms to alterations of the dataset. The results confirm that NA algorithms may be applied in cases of atlas-free parcellation for a fully network-driven comparison of connectomes. The analysis shows MAGNA++ is the best global alignment algorithm. The paper presented a new analysis methodology that uses network alignment for validating atlas-free parcellation brain connectomes. The methodology has been experimented on several brain datasets.

Concept of AHRS Algorithm Designed for Platform Independent Imu Attitude Alignment

Science.gov (United States)

Tomaszewski, Dariusz; Rapiński, Jacek; Pelc-Mieczkowska, Renata

2017-12-01

Nowadays, along with the advancement of technology one can notice the rapid development of various types of navigation systems. So far the most popular satellite navigation, is now supported by positioning results calculated with use of other measurement system. The method and manner of integration will depend directly on the destination of system being developed. To increase the frequency of readings and improve the operation of outdoor navigation systems, one will support satellite navigation systems (GPS, GLONASS ect.) with inertial navigation. Such method of navigation consists of several steps. The first stage is the determination of initial orientation of inertial measurement unit, called INS alignment. During this process, on the basis of acceleration and the angular velocity readings, values of Euler angles (pitch, roll, yaw) are calculated allowing for unambiguous orientation of the sensor coordinate system relative to external coordinate system. The following study presents the concept of AHRS (Attitude and heading reference system) algorithm, allowing to define the Euler angles.The study were conducted with the use of readings from low-cost MEMS cell phone sensors. Subsequently the results of the study were analyzed to determine the accuracy of featured algorithm. On the basis of performed experiments the legitimacy of developed algorithm was stated.

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.

A Rapid Convergent Low Complexity Interference Alignment Algorithm for Wireless Sensor Networks

Directory of Open Access Journals (Sweden)

Lihui Jiang

2015-07-01

Full Text Available Interference alignment (IA is a novel technique that can effectively eliminate the interference and approach the sum capacity of wireless sensor networks (WSNs when the signal-to-noise ratio (SNR is high, by casting the desired signal and interference into different signal subspaces. The traditional alternating minimization interference leakage (AMIL algorithm for IA shows good performance in high SNR regimes, however, the complexity of the AMIL algorithm increases dramatically as the number of users and antennas increases, posing limits to its applications in the practical systems. In this paper, a novel IA algorithm, called directional quartic optimal (DQO algorithm, is proposed to minimize the interference leakage with rapid convergence and low complexity. The properties of the AMIL algorithm are investigated, and it is discovered that the difference between the two consecutive iteration results of the AMIL algorithm will approximately point to the convergence solution when the precoding and decoding matrices obtained from the intermediate iterations are sufficiently close to their convergence values. Based on this important property, the proposed DQO algorithm employs the line search procedure so that it can converge to the destination directly. In addition, the optimal step size can be determined analytically by optimizing a quartic function. Numerical results show that the proposed DQO algorithm can suppress the interference leakage more rapidly than the traditional AMIL algorithm, and can achieve the same level of sum rate as that of AMIL algorithm with far less iterations and execution time.

A Rapid Convergent Low Complexity Interference Alignment Algorithm for Wireless Sensor Networks.

Science.gov (United States)

Jiang, Lihui; Wu, Zhilu; Ren, Guanghui; Wang, Gangyi; Zhao, Nan

2015-07-29

Interference alignment (IA) is a novel technique that can effectively eliminate the interference and approach the sum capacity of wireless sensor networks (WSNs) when the signal-to-noise ratio (SNR) is high, by casting the desired signal and interference into different signal subspaces. The traditional alternating minimization interference leakage (AMIL) algorithm for IA shows good performance in high SNR regimes, however, the complexity of the AMIL algorithm increases dramatically as the number of users and antennas increases, posing limits to its applications in the practical systems. In this paper, a novel IA algorithm, called directional quartic optimal (DQO) algorithm, is proposed to minimize the interference leakage with rapid convergence and low complexity. The properties of the AMIL algorithm are investigated, and it is discovered that the difference between the two consecutive iteration results of the AMIL algorithm will approximately point to the convergence solution when the precoding and decoding matrices obtained from the intermediate iterations are sufficiently close to their convergence values. Based on this important property, the proposed DQO algorithm employs the line search procedure so that it can converge to the destination directly. In addition, the optimal step size can be determined analytically by optimizing a quartic function. Numerical results show that the proposed DQO algorithm can suppress the interference leakage more rapidly than the traditional AMIL algorithm, and can achieve the same level of sum rate as that of AMIL algorithm with far less iterations and execution time.

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...

Optimizing multiple sequence alignments using a genetic algorithm based on three objectives: structural information, non-gaps percentage and totally conserved columns.

Science.gov (United States)

Ortuño, Francisco M; Valenzuela, Olga; Rojas, Fernando; Pomares, Hector; Florido, Javier P; Urquiza, Jose M; Rojas, Ignacio

2013-09-01

Multiple sequence alignments (MSAs) are widely used approaches in bioinformatics to carry out other tasks such as structure predictions, biological function analyses or phylogenetic modeling. However, current tools usually provide partially optimal alignments, as each one is focused on specific biological features. Thus, the same set of sequences can produce different alignments, above all when sequences are less similar. Consequently, researchers and biologists do not agree about which is the most suitable way to evaluate MSAs. Recent evaluations tend to use more complex scores including further biological features. Among them, 3D structures are increasingly being used to evaluate alignments. Because structures are more conserved in proteins than sequences, scores with structural information are better suited to evaluate more distant relationships between sequences. The proposed multiobjective algorithm, based on the non-dominated sorting genetic algorithm, aims to jointly optimize three objectives: STRIKE score, non-gaps percentage and totally conserved columns. It was significantly assessed on the BAliBASE benchmark according to the Kruskal-Wallis test (P algorithm also outperforms other aligners, such as ClustalW, Multiple Sequence Alignment Genetic Algorithm (MSA-GA), PRRP, DIALIGN, Hidden Markov Model Training (HMMT), Pattern-Induced Multi-sequence Alignment (PIMA), MULTIALIGN, Sequence Alignment Genetic Algorithm (SAGA), PILEUP, Rubber Band Technique Genetic Algorithm (RBT-GA) and Vertical Decomposition Genetic Algorithm (VDGA), according to the Wilcoxon signed-rank test (P 0.05) with the advantage of being able to use less structures. Structural information is included within the objective function to evaluate more accurately the obtained alignments. The source code is available at http://www.ugr.es/~fortuno/MOSAStrE/MO-SAStrE.zip.

Fast global sequence alignment technique

KAUST Repository

Bonny, Mohamed Talal; Salama, Khaled N.

2011-01-01

fast alignment algorithm, called 'Alignment By Scanning' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the 'GAP' (which is heuristic) and the 'Needleman

SPA: a probabilistic algorithm for spliced alignment.

Directory of Open Access Journals (Sweden)

2006-04-01

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

ABS: Sequence alignment by scanning

KAUST Repository

Bonny, Mohamed Talal; Salama, Khaled N.

2011-01-01

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

ABS: Sequence alignment by scanning

KAUST Repository

Bonny, Mohamed Talal

2011-08-01

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

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.

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.

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.

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.)

Software alignment of the LHCb Outer Tracker chambers

International Nuclear Information System (INIS)

Deissenroth, Marc

2010-01-01

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 μm) for the translational degrees of freedom and of O(10 -2 - 10 -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 ∝ 90 μm. 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.)

Antares beam-alignment-system performance

International Nuclear Information System (INIS)

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

1983-01-01

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

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

Alignment of Short Reads: A Crucial Step for Application of Next-Generation Sequencing Data in Precision Medicine

Directory of Open Access Journals (Sweden)

Hao Ye

2015-11-01

Full Text Available Precision medicine or personalized medicine has been proposed as a modernized and promising medical strategy. Genetic variants of patients are the key information for implementation of precision medicine. Next-generation sequencing (NGS is an emerging technology for deciphering genetic variants. Alignment of raw reads to a reference genome is one of the key steps in NGS data analysis. Many algorithms have been developed for alignment of short read sequences since 2008. Users have to make a decision on which alignment algorithm to use in their studies. Selection of the right alignment algorithm determines not only the alignment algorithm but also the set of suitable parameters to be used by the algorithm. Understanding these algorithms helps in selecting the appropriate alignment algorithm for different applications in precision medicine. Here, we review current available algorithms and their major strategies such as seed-and-extend and q-gram filter. We also discuss the challenges in current alignment algorithms, including alignment in multiple repeated regions, long reads alignment and alignment facilitated with known genetic variants.

Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner

DEFF Research Database (Denmark)

Lu, David V; Brown, Randall H; Arumugam, Manimozhiyan

2009-01-01

MOTIVATION: The most accurate way to determine the intron-exon structures in a genome is to align spliced cDNA sequences to the genome. Thus, cDNA-to-genome alignment programs are a key component of most annotation pipelines. The scoring system used to choose the best alignment is a primary...... determinant of alignment accuracy, while heuristics that prevent consideration of certain alignments are a primary determinant of runtime and memory usage. Both accuracy and speed are important considerations in choosing an alignment algorithm, but scoring systems have received much less attention than...

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.

Application of a clustering-based peak alignment algorithm to analyze various DNA fingerprinting data.

Science.gov (United States)

Ishii, Satoshi; Kadota, Koji; Senoo, Keishi

2009-09-01

DNA fingerprinting analysis such as amplified ribosomal DNA restriction analysis (ARDRA), repetitive extragenic palindromic PCR (rep-PCR), ribosomal intergenic spacer analysis (RISA), and denaturing gradient gel electrophoresis (DGGE) are frequently used in various fields of microbiology. The major difficulty in DNA fingerprinting data analysis is the alignment of multiple peak sets. We report here an R program for a clustering-based peak alignment algorithm, and its application to analyze various DNA fingerprinting data, such as ARDRA, rep-PCR, RISA, and DGGE data. The results obtained by our clustering algorithm and by BioNumerics software showed high similarity. Since several R packages have been established to statistically analyze various biological data, the distance matrix obtained by our R program can be used for subsequent statistical analyses, some of which were not previously performed but are useful in DNA fingerprinting studies.

Evaluation of GMI and PMI diffeomorphic‐based demons algorithms for aligning PET and CT Images

Science.gov (United States)

Yang, Juan; Zhang, You; Yin, Yong

2015-01-01

Fusion of anatomic information in computed tomography (CT) and functional information in F18‐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 F18‐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 F18‐FDG PET/CT scanner for each patient. The modified Hausdorff distance (dMH) was used to evaluate the registration accuracy of the two algorithms. Of all patients, the mean values and standard deviations (SDs) of dMH 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 F18‐FDG PET/CT scanner was used for image acquisition. The PMI

Pairwise Sequence Alignment Library

Energy Technology Data Exchange (ETDEWEB)

2015-05-20

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

THE ATLAS INNER DETECTOR TRACK BASED ALIGNMENT

CERN Document Server

Marti i Garcia, Salvador; The ATLAS collaboration

2018-01-01

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

A Secure Alignment Algorithm for Mapping Short Reads to Human Genome.

Science.gov (United States)

Zhao, Yongan; Wang, Xiaofeng; Tang, Haixu

2018-05-09

The elastic and inexpensive computing resources such as clouds have been recognized as a useful solution to analyzing massive human genomic data (e.g., acquired by using next-generation sequencers) in biomedical researches. However, outsourcing human genome computation to public or commercial clouds was hindered due to privacy concerns: even a small number of human genome sequences contain sufficient information for identifying the donor of the genomic data. This issue cannot be directly addressed by existing security and cryptographic techniques (such as homomorphic encryption), because they are too heavyweight to carry out practical genome computation tasks on massive data. In this article, we present a secure algorithm to accomplish the read mapping, one of the most basic tasks in human genomic data analysis based on a hybrid cloud computing model. Comparing with the existing approaches, our algorithm delegates most computation to the public cloud, while only performing encryption and decryption on the private cloud, and thus makes the maximum use of the computing resource of the public cloud. Furthermore, our algorithm reports similar results as the nonsecure read mapping algorithms, including the alignment between reads and the reference genome, which can be directly used in the downstream analysis such as the inference of genomic variations. We implemented the algorithm in C++ and Python on a hybrid cloud system, in which the public cloud uses an Apache Spark system.

RNA Structural Alignments, Part I

DEFF Research Database (Denmark)

Havgaard, Jakob Hull; Gorodkin, Jan

2014-01-01

Simultaneous alignment and secondary structure prediction of RNA sequences is often referred to as "RNA structural alignment." A class of the methods for structural alignment is based on the principles proposed by Sankoff more than 25 years ago. The Sankoff algorithm simultaneously folds and aligns...... is so high that it took more than a decade before the first implementation of a Sankoff style algorithm was published. However, with the faster computers available today and the improved heuristics used in the implementations the Sankoff-based methods have become practical. This chapter describes...... the methods based on the Sankoff algorithm. All the practical implementations of the algorithm use heuristics to make them run in reasonable time and memory. These heuristics are also described in this chapter....

Computational complexity of algorithms for sequence comparison, short-read assembly and genome alignment.

Science.gov (United States)

Baichoo, Shakuntala; Ouzounis, Christos A

A multitude of algorithms for sequence comparison, short-read assembly and whole-genome alignment have been developed in the general context of molecular biology, to support technology development for high-throughput sequencing, numerous applications in genome biology and fundamental research on comparative genomics. The computational complexity of these algorithms has been previously reported in original research papers, yet this often neglected property has not been reviewed previously in a systematic manner and for a wider audience. We provide a review of space and time complexity of key sequence analysis algorithms and highlight their properties in a comprehensive manner, in order to identify potential opportunities for further research in algorithm or data structure optimization. The complexity aspect is poised to become pivotal as we will be facing challenges related to the continuous increase of genomic data on unprecedented scales and complexity in the foreseeable future, when robust biological simulation at the cell level and above becomes a reality. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

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...

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 ...

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

Directory of Open Access Journals (Sweden)

Gianluca Valentino

2014-02-01

Full Text Available 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.

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.

Optimization of sequence alignment for simple sequence repeat regions

Directory of Open Access Journals (Sweden)

Ogbonnaya Francis C

2011-07-01

Full Text Available Abstract Background Microsatellites, or simple sequence repeats (SSRs, are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs. SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships. Findings To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type. When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm. Conclusions The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic

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.

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.

Efficient GPS Position Determination Algorithms

National Research Council Canada - National Science Library

Nguyen, Thao Q

2007-01-01

... differential GPS algorithm for a network of users. The stand-alone user GPS algorithm is a direct, closed-form, and efficient new position determination algorithm that exploits the closed-form solution of the GPS trilateration equations and works...

BinAligner: a heuristic method to align biological networks.

Science.gov (United States)

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

2013-01-01

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

Ancestral sequence alignment under optimal conditions

Directory of Open Access Journals (Sweden)

Brown Daniel G

2005-11-01

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

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

NARCIS (Netherlands)

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

2009-01-01

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

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.

Experimental image alignment system

Science.gov (United States)

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

1980-01-01

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

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

Directory of Open Access Journals (Sweden)

Giovanni Ciriello

Full Text Available Local network alignment is an important component of the analysis of protein-protein interaction networks that may lead to the identification of evolutionary related complexes. We present AlignNemo, a new algorithm that, given the networks of two organisms, uncovers subnetworks of proteins that relate in biological function and topology of interactions. The discovered conserved subnetworks have a general topology and need not to correspond to specific interaction patterns, so that they more closely fit the models of functional complexes proposed in the literature. The algorithm is able to handle sparse interaction data with an expansion process that at each step explores the local topology of the networks beyond the proteins directly interacting with the current solution. To assess the performance of AlignNemo, we ran a series of benchmarks using statistical measures as well as biological knowledge. Based on reference datasets of protein complexes, AlignNemo shows better performance than other methods in terms of both precision and recall. We show our solutions to be biologically sound using the concept of semantic similarity applied to Gene Ontology vocabularies. The binaries of AlignNemo and supplementary details about the algorithms and the experiments are available at: sourceforge.net/p/alignnemo.

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.

Aligning Biomolecular Networks Using Modular Graph Kernels

Science.gov (United States)

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

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

An Adaptive Hybrid Multiprocessor technique for bioinformatics sequence alignment

KAUST Repository

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

2012-01-01

Sequence alignment algorithms such as the Smith-Waterman algorithm are among the most important applications in the development of bioinformatics. Sequence alignment algorithms must process large amounts of data which may take a long time. Here, we

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.

Use artificial neural network to align biological ontologies.

Science.gov (United States)

Huang, Jingshan; Dang, Jiangbo; Huhns, Michael N; Zheng, W Jim

2008-09-16

Being formal, declarative knowledge representation models, ontologies help to address the problem of imprecise terminologies in biological and biomedical research. However, ontologies constructed under the auspices of the Open Biomedical Ontologies (OBO) group have exhibited a great deal of variety, because different parties can design ontologies according to their own conceptual views of the world. It is therefore becoming critical to align ontologies from different parties. During automated/semi-automated alignment across biological ontologies, different semantic aspects, i.e., concept name, concept properties, and concept relationships, contribute in different degrees to alignment results. Therefore, a vector of weights must be assigned to these semantic aspects. It is not trivial to determine what those weights should be, and current methodologies depend a lot on human heuristics. In this paper, we take an artificial neural network approach to learn and adjust these weights, and thereby support a new ontology alignment algorithm, customized for biological ontologies, with the purpose of avoiding some disadvantages in both rule-based and learning-based aligning algorithms. This approach has been evaluated by aligning two real-world biological ontologies, whose features include huge file size, very few instances, concept names in numerical strings, and others. The promising experiment results verify our proposed hypothesis, i.e., three weights for semantic aspects learned from a subset of concepts are representative of all concepts in the same ontology. Therefore, our method represents a large leap forward towards automating biological ontology alignment.

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.

Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters.

Science.gov (United States)

Lan, Haidong; Chan, Yuandong; Xu, Kai; Schmidt, Bertil; Peng, Shaoliang; Liu, Weiguo

2016-07-19

Computing alignments between two or more sequences are common operations frequently performed in computational molecular biology. The continuing growth of biological sequence databases establishes the need for their efficient parallel implementation on modern accelerators. This paper presents new approaches to high performance biological sequence database scanning with the Smith-Waterman algorithm and the first stage of progressive multiple sequence alignment based on the ClustalW heuristic on a Xeon Phi-based compute cluster. Our approach uses a three-level parallelization scheme to take full advantage of the compute power available on this type of architecture; i.e. cluster-level data parallelism, thread-level coarse-grained parallelism, and vector-level fine-grained parallelism. Furthermore, we re-organize the sequence datasets and use Xeon Phi shuffle operations to improve I/O efficiency. Evaluations show that our method achieves a peak overall performance up to 220 GCUPS for scanning real protein sequence databanks on a single node consisting of two Intel E5-2620 CPUs and two Intel Xeon Phi 7110P cards. It also exhibits good scalability in terms of sequence length and size, and number of compute nodes for both database scanning and multiple sequence alignment. Furthermore, the achieved performance is highly competitive in comparison to optimized Xeon Phi and GPU implementations. Our implementation is available at https://github.com/turbo0628/LSDBS-mpi .

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

Node fingerprinting: an efficient heuristic for aligning biological networks.

Science.gov (United States)

Radu, Alex; Charleston, Michael

2014-10-01

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

A cross-species alignment tool (CAT)

DEFF Research Database (Denmark)

Li, Heng; Guan, Liang; Liu, Tao

2007-01-01

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

RNA structure alignment by a unit-vector approach.

Science.gov (United States)

Capriotti, Emidio; Marti-Renom, Marc A

2008-08-15

The recent discovery of tiny RNA molecules such as microRNAs and small interfering RNA are transforming the view of RNA as a simple information transfer molecule. Similar to proteins, the native three-dimensional structure of RNA determines its biological activity. Therefore, classifying the current structural space is paramount for functionally annotating RNA molecules. The increasing numbers of RNA structures deposited in the PDB requires more accurate, automatic and benchmarked methods for RNA structure comparison. In this article, we introduce a new algorithm for RNA structure alignment based on a unit-vector approach. The algorithm has been implemented in the SARA program, which results in RNA structure pairwise alignments and their statistical significance. The SARA program has been implemented to be of general applicability even when no secondary structure can be calculated from the RNA structures. A benchmark against the ARTS program using a set of 1275 non-redundant pairwise structure alignments results in inverted approximately 6% extra alignments with at least 50% structurally superposed nucleotides and base pairs. A first attempt to perform RNA automatic functional annotation based on structure alignments indicates that SARA can correctly assign the deepest SCOR classification to >60% of the query structures. The SARA program is freely available through a World Wide Web server http://sgu.bioinfo.cipf.es/services/SARA/. Supplementary data are available at Bioinformatics online.

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.

Ontology Alignment Repair through Modularization and Confidence-Based Heuristics.

Science.gov (United States)

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

2015-01-01

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

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...

Simulation of beamline alignment operations

International Nuclear Information System (INIS)

Annese, C; Miller, M G.

1999-01-01

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

Determination of the three-dimensional structure for weakly aligned biomolecules by NMR spectroscopy

International Nuclear Information System (INIS)

Shahkhatuni, Astghik A; Shahkhatuni, Aleksan G

2002-01-01

The key achievements and the potential of NMR spectroscopy for weakly aligned biomolecules are considered. Due to weak alignment, it becomes possible to determine a number of NMR parameters dependent on the orientation of biomolecules, which are averaged to zero in usual isotropic media. The addition of new orientational constraints to standard procedures of 3D structure determination markedly increases the achievable accuracy. The possibility of structure determination for biomolecules using only orientation-dependent parameters without invoking other NMR data is discussed. The methods of orientation, experimental techniques, and calculation methods are systematised. The main results obtained and the prospects of using NMR spectroscopy of weakly aligned systems to study different classes of biomolecules and to solve various problems of molecular biology are analysed. Examples of biomolecules whose structures have been determined using orientation-dependent parameters are given. The bibliography includes 508 references.

Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner.

Science.gov (United States)

Lu, David V; Brown, Randall H; Arumugam, Manimozhiyan; Brent, Michael R

2009-07-01

The most accurate way to determine the intron-exon structures in a genome is to align spliced cDNA sequences to the genome. Thus, cDNA-to-genome alignment programs are a key component of most annotation pipelines. The scoring system used to choose the best alignment is a primary determinant of alignment accuracy, while heuristics that prevent consideration of certain alignments are a primary determinant of runtime and memory usage. Both accuracy and speed are important considerations in choosing an alignment algorithm, but scoring systems have received much less attention than heuristics. We present Pairagon, a pair hidden Markov model based cDNA-to-genome alignment program, as the most accurate aligner for sequences with high- and low-identity levels. We conducted a series of experiments testing alignment accuracy with varying sequence identity. We first created 'perfect' simulated cDNA sequences by splicing the sequences of exons in the reference genome sequences of fly and human. The complete reference genome sequences were then mutated to various degrees using a realistic mutation simulator and the perfect cDNAs were aligned to them using Pairagon and 12 other aligners. To validate these results with natural sequences, we performed cross-species alignment using orthologous transcripts from human, mouse and rat. We found that aligner accuracy is heavily dependent on sequence identity. For sequences with 100% identity, Pairagon achieved accuracy levels of >99.6%, with one quarter of the errors of any other aligner. Furthermore, for human/mouse alignments, which are only 85% identical, Pairagon achieved 87% accuracy, higher than any other aligner. Pairagon source and executables are freely available at http://mblab.wustl.edu/software/pairagon/

Differential evolution-simulated annealing for multiple sequence alignment

Science.gov (United States)

Addawe, R. C.; Addawe, J. M.; Sueño, M. R. K.; Magadia, J. C.

2017-10-01

Multiple sequence alignments (MSA) are used in the analysis of molecular evolution and sequence structure relationships. In this paper, a hybrid algorithm, Differential Evolution - Simulated Annealing (DESA) is applied in optimizing multiple sequence alignments (MSAs) based on structural information, non-gaps percentage and totally conserved columns. DESA is a robust algorithm characterized by self-organization, mutation, crossover, and SA-like selection scheme of the strategy parameters. Here, the MSA problem is treated as a multi-objective optimization problem of the hybrid evolutionary algorithm, DESA. Thus, we name the algorithm as DESA-MSA. Simulated sequences and alignments were generated to evaluate the accuracy and efficiency of DESA-MSA using different indel sizes, sequence lengths, deletion rates and insertion rates. The proposed hybrid algorithm obtained acceptable solutions particularly for the MSA problem evaluated based on the three objectives.

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

International Nuclear Information System (INIS)

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

2009-01-01

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.

CMS silicon tracker alignment strategy with the Millepede II algorithm

International Nuclear Information System (INIS)

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

2008-01-01

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

Introducing difference recurrence relations for faster semi-global alignment of long sequences.

Science.gov (United States)

Suzuki, Hajime; Kasahara, Masahiro

2018-02-19

The read length of single-molecule DNA sequencers is reaching 1 Mb. Popular alignment software tools widely used for analyzing such long reads often take advantage of single-instruction multiple-data (SIMD) operations to accelerate calculation of dynamic programming (DP) matrices in the Smith-Waterman-Gotoh (SWG) algorithm with a fixed alignment start position at the origin. Nonetheless, 16-bit or 32-bit integers are necessary for storing the values in a DP matrix when sequences to be aligned are long; this situation hampers the use of the full SIMD width of modern processors. We proposed a faster semi-global alignment algorithm, "difference recurrence relations," that runs more rapidly than the state-of-the-art algorithm by a factor of 2.1. Instead of calculating and storing all the values in a DP matrix directly, our algorithm computes and stores mainly the differences between the values of adjacent cells in the matrix. Although the SWG algorithm and our algorithm can output exactly the same result, our algorithm mainly involves 8-bit integer operations, enabling us to exploit the full width of SIMD operations (e.g., 32) on modern processors. We also developed a library, libgaba, so that developers can easily integrate our algorithm into alignment programs. Our novel algorithm and optimized library implementation will facilitate accelerating nucleotide long-read analysis algorithms that use pairwise alignment stages. The library is implemented in the C programming language and available at https://github.com/ocxtal/libgaba .

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

Science.gov (United States)

Kokiopoulou, Effrosyni; Kressner, Daniel; Frossard, Pascal

2011-06-01

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

SPHINX--an algorithm for taxonomic binning of metagenomic sequences.

Science.gov (United States)

Mohammed, Monzoorul Haque; Ghosh, Tarini Shankar; Singh, Nitin Kumar; Mande, Sharmila S

2011-01-01

Compared with composition-based binning algorithms, the binning accuracy and specificity of alignment-based binning algorithms is significantly higher. However, being alignment-based, the latter class of algorithms require enormous amount of time and computing resources for binning huge metagenomic datasets. The motivation was to develop a binning approach that can analyze metagenomic datasets as rapidly as composition-based approaches, but nevertheless has the accuracy and specificity of alignment-based algorithms. This article describes a hybrid binning approach (SPHINX) that achieves high binning efficiency by utilizing the principles of both 'composition'- and 'alignment'-based binning algorithms. Validation results with simulated sequence datasets indicate that SPHINX is able to analyze metagenomic sequences as rapidly as composition-based algorithms. Furthermore, the binning efficiency (in terms of accuracy and specificity of assignments) of SPHINX is observed to be comparable with results obtained using alignment-based algorithms. A web server for the SPHINX algorithm is available at http://metagenomics.atc.tcs.com/SPHINX/.

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...

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.

Software alignment of the LHCb inner tracker sensors

Energy Technology Data Exchange (ETDEWEB)

Maciuc, Florin

2009-04-20

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

Software alignment of the LHCb inner tracker sensors

International Nuclear Information System (INIS)

Maciuc, Florin

2009-01-01

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

Software alignment of the LHCb inner tracker sensors

Energy Technology Data Exchange (ETDEWEB)

Maciuc, Florin

2009-04-20

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

FEAST: sensitive local alignment with multiple rates of evolution.

Science.gov (United States)

Hudek, Alexander K; Brown, Daniel G

2011-01-01

We present a pairwise local aligner, FEAST, which uses two new techniques: a sensitive extension algorithm for identifying homologous subsequences, and a descriptive probabilistic alignment model. We also present a new procedure for training alignment parameters and apply it to the human and mouse genomes, producing a better parameter set for these sequences. Our extension algorithm identifies homologous subsequences by considering all evolutionary histories. It has higher maximum sensitivity than Viterbi extensions, and better balances specificity. We model alignments with several submodels, each with unique statistical properties, describing strongly similar and weakly similar regions of homologous DNA. Training parameters using two submodels produces superior alignments, even when we align with only the parameters from the weaker submodel. Our extension algorithm combined with our new parameter set achieves sensitivity 0.59 on synthetic tests. In contrast, LASTZ with default settings achieves sensitivity 0.35 with the same false positive rate. Using the weak submodel as parameters for LASTZ increases its sensitivity to 0.59 with high error. FEAST is available at http://monod.uwaterloo.ca/feast/.

Quasiparticle Level Alignment for Photocatalytic Interfaces.

Science.gov (United States)

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

2014-05-13

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

Inverting Image Data For Optical Testing And Alignment

Science.gov (United States)

Shao, Michael; Redding, David; Yu, Jeffrey W.; Dumont, Philip J.

1993-01-01

Data from images produced by slightly incorrectly figured concave primary mirror in telescope processed into estimate of spherical aberration of mirror, by use of algorithm finding nonlinear least-squares best fit between actual images and synthetic images produced by multiparameter mathematical model of telescope optical system. Estimated spherical aberration, in turn, converted into estimate of deviation of reflector surface from nominal precise shape. Algorithm devised as part of effort to determine error in surface figure of primary mirror of Hubble space telescope, so corrective lens designed. Modified versions of algorithm also used to find optical errors in other components of telescope or of other optical systems, for purposes of testing, alignment, and/or correction.

CMS Tracker Alignment Performance Results Start-Up 2017

CERN Document Server

CMS Collaboration

2017-01-01

During the LHC shutdown in Winter 2016/17, the CMS pixel detector, the inner component of the CMS Tracker, was replaced by the Phase-1 upgrade detector. Among others improvements, the new pixel detector consists of four instead of three layers in the central barrel region (BPIX) and three instead of two disks in the endcap regions (FPIX). In this report, performance plots of the first pixel-detector alignment results are presented, which were obtained with cosmic-ray data taken prior to the start of the 2017 LHC pp operation. Alignment constants have been derived using the data collected initially at 0T and later at 3.8T magnetic field to the level of single module positions in the pixel detector, while keeping the alignment parameters of the strip detector fixed at the values determined in the end of 2016. The complete understanding of the alignment and biases was derived by using two algorithms, Millepede-II and HipPy. The results confirm each other.

Cellular and Nuclear Alignment Analysis for Determining Epithelial Cell Chirality

Science.gov (United States)

Raymond, Michael J.; Ray, Poulomi; Kaur, Gurleen; Singh, Ajay V.; Wan, Leo Q.

2015-01-01

Left-right (LR) asymmetry is a biologically conserved property in living organisms that can be observed in the asymmetrical arrangement of organs and tissues and in tissue morphogenesis, such as the directional looping of the gastrointestinal tract and heart. The expression of LR asymmetry in embryonic tissues can be appreciated in biased cell alignment. Previously an in vitro chirality assay was reported by patterning multiple cells on microscale defined geometries and quantified the cell phenotype–dependent LR asymmetry, or cell chirality. However, morphology and chirality of individual cells on micropatterned surfaces has not been well characterized. Here, a Python-based algorithm was developed to identify and quantify immunofluorescence stained individual epithelial cells on multicellular patterns. This approach not only produces results similar to the image intensity gradient-based method reported previously, but also can capture properties of single cells such as area and aspect ratio. We also found that cell nuclei exhibited biased alignment. Around 35% cells were misaligned and were typically smaller and less elongated. This new imaging analysis approach is an effective tool for measuring single cell chirality inside multicellular structures and can potentially help unveil biophysical mechanisms underlying cellular chiral bias both in vitro and in vivo. PMID:26294010

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

Directory of Open Access Journals (Sweden)

Searle Stephen MJ

2003-10-01

Full Text Available Abstract Background The alignment of two or more protein sequences provides a powerful guide in the prediction of the protein structure and in identifying key functional residues, however, the utility of any prediction is completely dependent on the accuracy of the alignment. In this paper we describe a suite of reference alignments derived from the comparison of protein three-dimensional structures together with evaluation measures and software that allow automatically generated alignments to be benchmarked. We test the OXBench benchmark suite on alignments generated by the AMPS multiple alignment method, then apply the suite to compare eight different multiple alignment algorithms. The benchmark shows the current state-of-the art for alignment accuracy and provides a baseline against which new alignment algorithms may be judged. Results The simple hierarchical multiple alignment algorithm, AMPS, performed as well as or better than more modern methods such as CLUSTALW once the PAM250 pair-score matrix was replaced by a BLOSUM series matrix. AMPS gave an accuracy in Structurally Conserved Regions (SCRs of 89.9% over a set of 672 alignments. The T-COFFEE method on a data set of families with http://www.compbio.dundee.ac.uk. Conclusions The OXBench suite of reference alignments, evaluation software and results database provide a convenient method to assess progress in sequence alignment techniques. Evaluation measures that were dependent on comparison to a reference alignment were found to give good discrimination between methods. The STAMP Sc Score which is independent of a reference alignment also gave good discrimination. Application of OXBench in this paper shows that with the exception of T-COFFEE, the majority of the improvement in alignment accuracy seen since 1985 stems from improved pair-score matrices rather than algorithmic refinements. The maximum theoretical alignment accuracy obtained by pooling results over all methods was 94

Numerical optimization of alignment reproducibility for customizable surgical guides.

Science.gov (United States)

Kroes, Thomas; Valstar, Edward; Eisemann, Elmar

2015-10-01

Computer-assisted orthopedic surgery aims at minimizing invasiveness, postoperative pain, and morbidity with computer-assisted preoperative planning and intra-operative guidance techniques, of which camera-based navigation and patient-specific templates (PST) are the most common. PSTs are one-time templates that guide the surgeon initially in cutting slits or drilling holes. This method can be extended to reusable and customizable surgical guides (CSG), which can be adapted to the patients' bone. Determining the right set of CSG input parameters by hand is a challenging task, given the vast amount of input parameter combinations and the complex physical interaction between the PST/CSG and the bone. This paper introduces a novel algorithm to solve the problem of choosing the right set of input parameters. Our approach predicts how well a CSG instance is able to reproduce the planned alignment based on a physical simulation and uses a genetic optimization algorithm to determine optimal configurations. We validate our technique with a prototype of a pin-based CSG and nine rapid prototyped distal femora. The proposed optimization technique has been compared to manual optimization by experts, as well as participants with domain experience. Using the optimization technique, the alignment errors remained within practical boundaries of 1.2 mm translation and [Formula: see text] rotation error. In all cases, the proposed method outperformed manual optimization. Manually optimizing CSG parameters turns out to be a counterintuitive task. Even after training, subjects with and without anatomical background fail in choosing appropriate CSG configurations. Our optimization algorithm ensures that the CSG is configured correctly, and we could demonstrate that the intended alignment of the CSG is accurately reproduced on all tested bone geometries.

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.

MUON DETECTORS: ALIGNMENT

CERN Multimedia

G. Gomez

2012-01-01

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

MUON DETECTORS: ALIGNMENT

CERN Multimedia

M. Dallavalle

2013-01-01

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

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.

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.

DNA motif alignment by evolving a population of Markov chains.

Science.gov (United States)

Bi, Chengpeng

2009-01-30

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

Genetic algorithms for protein threading.

Science.gov (United States)

Yadgari, J; Amir, A; Unger, R

1998-01-01

Despite many years of efforts, a direct prediction of protein structure from sequence is still not possible. As a result, in the last few years researchers have started to address the "inverse folding problem": Identifying and aligning a sequence to the fold with which it is most compatible, a process known as "threading". In two meetings in which protein folding predictions were objectively evaluated, it became clear that threading as a concept promises a real breakthrough, but that much improvement is still needed in the technique itself. Threading is a NP-hard problem, and thus no general polynomial solution can be expected. Still a practical approach with demonstrated ability to find optimal solutions in many cases, and acceptable solutions in other cases, is needed. We applied the technique of Genetic Algorithms in order to significantly improve the ability of threading algorithms to find the optimal alignment of a sequence to a structure, i.e. the alignment with the minimum free energy. A major progress reported here is the design of a representation of the threading alignment as a string of fixed length. With this representation validation of alignments and genetic operators are effectively implemented. Appropriate data structure and parameters have been selected. It is shown that Genetic Algorithm threading is effective and is able to find the optimal alignment in a few test cases. Furthermore, the described algorithm is shown to perform well even without pre-definition of core elements. Existing threading methods are dependent on such constraints to make their calculations feasible. But the concept of core elements is inherently arbitrary and should be avoided if possible. While a rigorous proof is hard to submit yet an, we present indications that indeed Genetic Algorithm threading is capable of finding consistently good solutions of full alignments in search spaces of size up to 10(70).

Multiple network alignment on quantum computers

Science.gov (United States)

Daskin, Anmer; Grama, Ananth; Kais, Sabre

2014-12-01

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

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.

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.

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.

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.

Mirror position determination for the alignment of Cherenkov Telescopes

Energy Technology Data Exchange (ETDEWEB)

Adam, J. [TU Dortmund, Experimental Physics 5 Otto-Hahn-Str. 4, 44221 Dortmund (Germany); Ahnen, M.L. [ETH Zurich, Institute for Particle Physics Otto-Stern-Weg 5, 8093 Zurich (Switzerland); Baack, D. [TU Dortmund, Experimental Physics 5 Otto-Hahn-Str. 4, 44221 Dortmund (Germany); Balbo, M. [University of Geneva, ISDC Data Center for Astrophysics Chemin Ecogia 16, 1290 Versoix (Switzerland); Bergmann, M. [Universität Würzburg, Institute for Theoretical Physics and Astrophysics Emil-Fischer-Str. 31, 97074 Würzburg (Germany); Biland, A. [ETH Zurich, Institute for Particle Physics Otto-Stern-Weg 5, 8093 Zurich (Switzerland); Blank, M. [Universität Würzburg, Institute for Theoretical Physics and Astrophysics Emil-Fischer-Str. 31, 97074 Würzburg (Germany); Bretz, T. [ETH Zurich, Institute for Particle Physics Otto-Stern-Weg 5, 8093 Zurich (Switzerland); RWTH Aachen (Germany); Bruegge, K.A.; Buss, J. [TU Dortmund, Experimental Physics 5 Otto-Hahn-Str. 4, 44221 Dortmund (Germany); Dmytriiev, A. [University of Geneva, ISDC Data Center for Astrophysics Chemin Ecogia 16, 1290 Versoix (Switzerland); Domke, M. [TU Dortmund, Experimental Physics 5 Otto-Hahn-Str. 4, 44221 Dortmund (Germany); Dorner, D. [Universität Würzburg, Institute for Theoretical Physics and Astrophysics Emil-Fischer-Str. 31, 97074 Würzburg (Germany); FAU Erlangen (Germany); Einecke, S. [TU Dortmund, Experimental Physics 5 Otto-Hahn-Str. 4, 44221 Dortmund (Germany); Hempfling, C. [Universität Würzburg, Institute for Theoretical Physics and Astrophysics Emil-Fischer-Str. 31, 97074 Würzburg (Germany); and others

2017-07-11

Imaging Atmospheric Cherenkov Telescopes (IACTs) need imaging optics with large apertures to map the faint Cherenkov light emitted in extensive air showers onto their image sensors. Segmented reflectors fulfill these needs using mass produced and light weight mirror facets. However, as the overall image is the sum of the individual mirror facet images, alignment is important. Here we present a method to determine the mirror facet positions on a segmented reflector in a very direct way. Our method reconstructs the mirror facet positions from photographs and a laser distance meter measurement which goes from the center of the image sensor plane to the center of each mirror facet. We use our method to both align the mirror facet positions and to feed the measured positions into our IACT simulation. We demonstrate our implementation on the 4 m First Geiger-mode Avalanche Cherenkov Telescope (FACT).

Agent Based Model in SAS Environment for Rail Transit System Alignment Determination

Directory of Open Access Journals (Sweden)

I Made Indradjaja Brunner

2018-04-01

Full Text Available Transit system had been proposed for the urban area of Honolulu. One consideration to be determined is the alignment of the transit system. Decision to set the transit alignment will have influences on which areas will be served, who will be benefiting, as well as who will be impacted. Inputs for the decision usually conducted through public meetings, where community members are shown numbers of maps with pre-set routes. That approach could lead to a rather subjective decision by the community members. This paper attempts to discuss the utilization of grid map in determining the best alignment for rail transit system in Honolulu, Hawaii. It tries to use a more objective approach using various data derived from thematic maps. Overlaid maps are aggregated into a uniform 0.1-square mile vector based grid map system in GIS environment. The large dataset in the GIS environment is analyzed and manipulated using SAS software. The SAS procedure is applied to select the location of the alignment using a rational and deterministic approach. Grid cells that are superior compared to the others are selected based on several predefined criteria. Location of the dominant cells indicates possible transit alignment. The SAS procedure is designed to allow a transient vector called the GUIDE (Grid Unit with Intelligent Directional Expertise agent to analyze several cells at its vicinity and to move towards a cell with the highest value. Each time the agent landed on a cell, it left a mark. The chain of those marks shows location for the transit alignment. This study shows that the combination of ArcGIS and SAS allows a robust analysis of spatial data and manipulation of its datasets, which can be used to run a simulation mimicking the Agent-Based Modelling. This study also opens up further study possibilities by increasing number of factors analyzed by the agent, as well as creating a composite value of multi-factors.

Stochastic split determinant algorithms

International Nuclear Information System (INIS)

Horvatha, Ivan

2000-01-01

I propose a large class of stochastic Markov processes associated with probability distributions analogous to that of lattice gauge theory with dynamical fermions. The construction incorporates the idea of approximate spectral split of the determinant through local loop action, and the idea of treating the infrared part of the split through explicit diagonalizations. I suggest that exact algorithms of practical relevance might be based on Markov processes so constructed

The CMS Muon System Alignment

CERN Document Server

Martinez Ruiz-Del-Arbol, P

2009-01-01

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

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

Science.gov (United States)

Hara, Kazuo; Shimbo, Masashi; Matsumoto, Yuji

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

Band Alignment Determination of Two-Dimensional Heterojunctions and Their Electronic Applications

KAUST Repository

Chiu, Ming-Hui

2018-05-09

Two-dimensional (2D) layered materials such as MoS2 have been recognized as high on-off ratio semiconductors which are promising candidates for electronic and optoelectronic devices. In addition to the use of individual 2D materials, the accelerated field of 2D heterostructures enables even greater functionalities. Device designs differ, and they are strongly controlled by the electronic band alignment. For example, photovoltaic cells require type II heterostructures for light harvesting, and light-emitting diodes benefit from multiple quantum wells with the type I band alignment for high emission efficiency. The vertical tunneling field-effect transistor for next-generation electronics depends on nearly broken-gap band alignment for boosting its performance. To tailor these 2D layered materials toward possible future applications, the understanding of 2D heterostructure band alignment becomes critically important. In the first part of this thesis, we discuss the band alignment of 2D heterostructures. To do so, we firstly study the interlayer coupling between two dissimilar 2D materials. We conclude that a post-anneal process could enhance the interlayer coupling of as-transferred 2D heterostructures, and heterostructural stacking imposes similar symmetry changes as homostructural stacking. Later, we precisely determine the quasi particle bandgap and band alignment of the MoS2/WSe2 heterostructure by using scan tunneling microscopy/spectroscopy (STM/S) and micron-beam X-ray photoelectron spectroscopy (μ-XPS) techniques. Lastly, we prove that the band alignment of 2D heterojunctions can be accurately predicted by Anderson’s model, which has previously failed to predict conventional bulk heterostructures. In the second part of this thesis, we develop a new Chemical Vapor Deposition (CVD) method capable of precisely controlling the growth area of p- and n-type transition metal dichalcogenides (TMDCs) and further form lateral or vertical 2D heterostructures. This

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. Copyright © 2012 IPEM. Published by Elsevier Ltd. All rights reserved.

Cascaded face alignment via intimacy definition feature

Science.gov (United States)

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

2017-09-01

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

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

OpenAIRE

Pe?a-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,...

libgapmis: extending short-read alignments.

Science.gov (United States)

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

2013-01-01

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

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.

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.

Heuristics for multiobjective multiple sequence alignment.

Science.gov (United States)

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

2016-07-15

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

Image stack alignment in full-field X-ray absorption spectroscopy using SIFT_PyOCL.

Science.gov (United States)

Paleo, Pierre; Pouyet, Emeline; Kieffer, Jérôme

2014-03-01

Full-field X-ray absorption spectroscopy experiments allow the acquisition of millions of spectra within minutes. However, the construction of the hyperspectral image requires an image alignment procedure with sub-pixel precision. While the image correlation algorithm has originally been used for image re-alignment using translations, the Scale Invariant Feature Transform (SIFT) algorithm (which is by design robust versus rotation, illumination change, translation and scaling) presents an additional advantage: the alignment can be limited to a region of interest of any arbitrary shape. In this context, a Python module, named SIFT_PyOCL, has been developed. It implements a parallel version of the SIFT algorithm in OpenCL, providing high-speed image registration and alignment both on processors and graphics cards. The performance of the algorithm allows online processing of large datasets.

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....

Automatic Angular alignment of LHC Collimators

CERN Document Server

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

2017-01-01

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

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

2013-10-24

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.

Simulator for beam-based LHC collimator alignment

Science.gov (United States)

Valentino, Gianluca; Aßmann, Ralph; Redaelli, Stefano; Sammut, Nicholas

2014-02-01

In the CERN Large Hadron Collider, collimators need to be set up to form a multistage hierarchy to ensure efficient multiturn cleaning of halo particles. Automatic algorithms were introduced during the first run to reduce the beam time required for beam-based setup, improve the alignment accuracy, and reduce the risk of human errors. Simulating the alignment procedure would allow for off-line tests of alignment policies and algorithms. A simulator was developed based on a diffusion beam model to generate the characteristic beam loss signal spike and decay produced when a collimator jaw touches the beam, which is observed in a beam loss monitor (BLM). Empirical models derived from the available measurement data are used to simulate the steady-state beam loss and crosstalk between multiple BLMs. The simulator design is presented, together with simulation results and comparison to measurement data.

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.

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 ...... native multicore state of the art on challenging workloads by an increasing margin as more cores and sockets are utilised....

CAMPways: constrained alignment framework for the comparative analysis of a pair of metabolic pathways.

Science.gov (United States)

Abaka, Gamze; Bıyıkoğlu, Türker; Erten, Cesim

2013-07-01

Given a pair of metabolic pathways, an alignment of the pathways corresponds to a mapping between similar substructures of the pair. Successful alignments may provide useful applications in phylogenetic tree reconstruction, drug design and overall may enhance our understanding of cellular metabolism. We consider the problem of providing one-to-many alignments of reactions in a pair of metabolic pathways. We first provide a constrained alignment framework applicable to the problem. We show that the constrained alignment problem even in a primitive setting is computationally intractable, which justifies efforts for designing efficient heuristics. We present our Constrained Alignment of Metabolic Pathways (CAMPways) algorithm designed for this purpose. Through extensive experiments involving a large pathway database, we demonstrate that when compared with a state-of-the-art alternative, the CAMPways algorithm provides better alignment results on metabolic networks as far as measures based on same-pathway inclusion and biochemical significance are concerned. The execution speed of our algorithm constitutes yet another important improvement over alternative algorithms. Open source codes, executable binary, useful scripts, all the experimental data and the results are freely available as part of the Supplementary Material at http://code.google.com/p/campways/. Supplementary data are available at Bioinformatics online.

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.

Automated and Adaptable Quantification of Cellular Alignment from Microscopic Images for Tissue Engineering Applications

Science.gov (United States)

Xu, Feng; Beyazoglu, Turker; Hefner, Evan; Gurkan, Umut Atakan

2011-01-01

Cellular alignment plays a critical role in functional, physical, and biological characteristics of many tissue types, such as muscle, tendon, nerve, and cornea. Current efforts toward regeneration of these tissues include replicating the cellular microenvironment by developing biomaterials that facilitate cellular alignment. To assess the functional effectiveness of the engineered microenvironments, one essential criterion is quantification of cellular alignment. Therefore, there is a need for rapid, accurate, and adaptable methodologies to quantify cellular alignment for tissue engineering applications. To address this need, we developed an automated method, binarization-based extraction of alignment score (BEAS), to determine cell orientation distribution in a wide variety of microscopic images. This method combines a sequenced application of median and band-pass filters, locally adaptive thresholding approaches and image processing techniques. Cellular alignment score is obtained by applying a robust scoring algorithm to the orientation distribution. We validated the BEAS method by comparing the results with the existing approaches reported in literature (i.e., manual, radial fast Fourier transform-radial sum, and gradient based approaches). Validation results indicated that the BEAS method resulted in statistically comparable alignment scores with the manual method (coefficient of determination R2=0.92). Therefore, the BEAS method introduced in this study could enable accurate, convenient, and adaptable evaluation of engineered tissue constructs and biomaterials in terms of cellular alignment and organization. PMID:21370940

The Application of the Weighted k-Partite Graph Problem to the Multiple Alignment for Metabolic Pathways.

Science.gov (United States)

Chen, Wenbin; Hendrix, William; Samatova, Nagiza F

2017-12-01

The problem of aligning multiple metabolic pathways is one of very challenging problems in computational biology. A metabolic pathway consists of three types of entities: reactions, compounds, and enzymes. Based on similarities between enzymes, Tohsato et al. gave an algorithm for aligning multiple metabolic pathways. However, the algorithm given by Tohsato et al. neglects the similarities among reactions, compounds, enzymes, and pathway topology. How to design algorithms for the alignment problem of multiple metabolic pathways based on the similarity of reactions, compounds, and enzymes? It is a difficult computational problem. In this article, we propose an algorithm for the problem of aligning multiple metabolic pathways based on the similarities among reactions, compounds, enzymes, and pathway topology. First, we compute a weight between each pair of like entities in different input pathways based on the entities' similarity score and topological structure using Ay et al.'s methods. We then construct a weighted k-partite graph for the reactions, compounds, and enzymes. We extract a mapping between these entities by solving the maximum-weighted k-partite matching problem by applying a novel heuristic algorithm. By analyzing the alignment results of multiple pathways in different organisms, we show that the alignments found by our algorithm correctly identify common subnetworks among multiple pathways.

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.

Constructing Aligned Assessments Using Automated Test Construction

Science.gov (United States)

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

2013-01-01

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

Alignment of whole genomes.

Science.gov (United States)

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

1999-01-01

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

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

OpenAIRE

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

2017-01-01

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

Cryo-EM image alignment based on nonuniform fast Fourier transform

International Nuclear Information System (INIS)

Yang Zhengfan; Penczek, Pawel A.

2008-01-01

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

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

Science.gov (United States)

Yang, Zhengfan; Penczek, Pawel A

2008-08-01

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

Statistical distributions of optimal global alignment scores of random protein sequences

Directory of Open Access Journals (Sweden)

Tang Jiaowei

2005-10-01

Full Text Available Abstract Background The inference of homology from statistically significant sequence similarity is a central issue in sequence alignments. So far the statistical distribution function underlying the optimal global alignments has not been completely determined. Results In this study, random and real but unrelated sequences prepared in six different ways were selected as reference datasets to obtain their respective statistical distributions of global alignment scores. All alignments were carried out with the Needleman-Wunsch algorithm and optimal scores were fitted to the Gumbel, normal and gamma distributions respectively. The three-parameter gamma distribution performs the best as the theoretical distribution function of global alignment scores, as it agrees perfectly well with the distribution of alignment scores. The normal distribution also agrees well with the score distribution frequencies when the shape parameter of the gamma distribution is sufficiently large, for this is the scenario when the normal distribution can be viewed as an approximation of the gamma distribution. Conclusion We have shown that the optimal global alignment scores of random protein sequences fit the three-parameter gamma distribution function. This would be useful for the inference of homology between sequences whose relationship is unknown, through the evaluation of gamma distribution significance between sequences.

A fast fiducial marker tracking model for fully automatic alignment in electron tomography

KAUST Repository

Han, Renmin; Zhang, Fa; Gao, Xin

2017-01-01

Automatic alignment, especially fiducial marker-based alignment, has become increasingly important due to the high demand of subtomogram averaging and the rapid development of large-field electron microscopy. Among the alignment steps, fiducial marker tracking is a crucial one that determines the quality of the final alignment. Yet, it is still a challenging problem to track the fiducial markers accurately and effectively in a fully automatic manner.In this paper, we propose a robust and efficient scheme for fiducial marker tracking. Firstly, we theoretically prove the upper bound of the transformation deviation of aligning the positions of fiducial markers on two micrographs by affine transformation. Secondly, we design an automatic algorithm based on the Gaussian mixture model to accelerate the procedure of fiducial marker tracking. Thirdly, we propose a divide-and-conquer strategy against lens distortions to ensure the reliability of our scheme. To our knowledge, this is the first attempt that theoretically relates the projection model with the tracking model. The real-world experimental results further support our theoretical bound and demonstrate the effectiveness of our algorithm. This work facilitates the fully automatic tracking for datasets with a massive number of fiducial markers.The C/C ++ source code that implements the fast fiducial marker tracking is available at https://github.com/icthrm/gmm-marker-tracking. Markerauto 1.6 version or later (also integrated in the AuTom platform at http://ear.ict.ac.cn/) offers a complete implementation for fast alignment, in which fast fiducial marker tracking is available by the

A fast fiducial marker tracking model for fully automatic alignment in electron tomography

KAUST Repository

Han, Renmin

2017-10-20

Automatic alignment, especially fiducial marker-based alignment, has become increasingly important due to the high demand of subtomogram averaging and the rapid development of large-field electron microscopy. Among the alignment steps, fiducial marker tracking is a crucial one that determines the quality of the final alignment. Yet, it is still a challenging problem to track the fiducial markers accurately and effectively in a fully automatic manner.In this paper, we propose a robust and efficient scheme for fiducial marker tracking. Firstly, we theoretically prove the upper bound of the transformation deviation of aligning the positions of fiducial markers on two micrographs by affine transformation. Secondly, we design an automatic algorithm based on the Gaussian mixture model to accelerate the procedure of fiducial marker tracking. Thirdly, we propose a divide-and-conquer strategy against lens distortions to ensure the reliability of our scheme. To our knowledge, this is the first attempt that theoretically relates the projection model with the tracking model. The real-world experimental results further support our theoretical bound and demonstrate the effectiveness of our algorithm. This work facilitates the fully automatic tracking for datasets with a massive number of fiducial markers.The C/C ++ source code that implements the fast fiducial marker tracking is available at https://github.com/icthrm/gmm-marker-tracking. Markerauto 1.6 version or later (also integrated in the AuTom platform at http://ear.ict.ac.cn/) offers a complete implementation for fast alignment, in which fast fiducial marker tracking is available by the

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.

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.

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

De novo determination of internuclear vector orientations from residual dipolar couplings measured in three independent alignment media

International Nuclear Information System (INIS)

Ruan Ke; Briggman, Kathryn B.; Tolman, Joel R.

2008-01-01

The straightforward interpretation of solution state residual dipolar couplings (RDCs) in terms of internuclear vector orientations generally requires prior knowledge of the alignment tensor, which in turn is normally estimated using a structural model. We have developed a protocol which allows the requirement for prior structural knowledge to be dispensed with as long as RDC measurements can be made in three independent alignment media. This approach, called Rigid Structure from Dipolar Couplings (RSDC), allows vector orientations and alignment tensors to be determined de novo from just three independent sets of RDCs. It is shown that complications arising from the existence of multiple solutions can be overcome by careful consideration of alignment tensor magnitudes in addition to the agreement between measured and calculated RDCs. Extensive simulations as well applications to the proteins ubiquitin and Staphylococcal protein GB1 demonstrate that this method can provide robust determinations of alignment tensors and amide N-H bond orientations often with better than 10 o accuracy, even in the presence of modest levels of internal dynamics

Enhanced Dynamic Algorithm of Genome Sequence Alignments

OpenAIRE

Arabi E. keshk

2014-01-01

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 se...

Modified compensation algorithm of lever-arm effect and flexural deformation for polar shipborne transfer alignment based on improved adaptive Kalman filter

International Nuclear Information System (INIS)

Wang, Tongda; Cheng, Jianhua; Guan, Dongxue; Kang, Yingyao; Zhang, Wei

2017-01-01

Due to the lever-arm effect and flexural deformation in the practical application of transfer alignment (TA), the TA performance is decreased. The existing polar TA algorithm only compensates a fixed lever-arm without considering the dynamic lever-arm caused by flexural deformation; traditional non-polar TA algorithms also have some limitations. Thus, the performance of existing compensation algorithms is unsatisfactory. In this paper, a modified compensation algorithm of the lever-arm effect and flexural deformation is proposed to promote the accuracy and speed of the polar TA. On the basis of a dynamic lever-arm model and a noise compensation method for flexural deformation, polar TA equations are derived in grid frames. Based on the velocity-plus-attitude matching method, the filter models of polar TA are designed. An adaptive Kalman filter (AKF) is improved to promote the robustness and accuracy of the system, and then applied to the estimation of the misalignment angles. Simulation and experiment results have demonstrated that the modified compensation algorithm based on the improved AKF for polar TA can effectively compensate the lever-arm effect and flexural deformation, and then improve the accuracy and speed of TA in the polar region. (paper)

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...

SVM-dependent pairwise HMM: an application to protein pairwise alignments.

Science.gov (United States)

Orlando, Gabriele; Raimondi, Daniele; Khan, Taushif; Lenaerts, Tom; Vranken, Wim F

2017-12-15

Methods able to provide reliable protein alignments are crucial for many bioinformatics applications. In the last years many different algorithms have been developed and various kinds of information, from sequence conservation to secondary structure, have been used to improve the alignment performances. This is especially relevant for proteins with highly divergent sequences. However, recent works suggest that different features may have different importance in diverse protein classes and it would be an advantage to have more customizable approaches, capable to deal with different alignment definitions. Here we present Rigapollo, a highly flexible pairwise alignment method based on a pairwise HMM-SVM that can use any type of information to build alignments. Rigapollo lets the user decide the optimal features to align their protein class of interest. It outperforms current state of the art methods on two well-known benchmark datasets when aligning highly divergent sequences. A Python implementation of the algorithm is available at http://ibsquare.be/rigapollo. wim.vranken@vub.be. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

LHCb: Alignment of the LHCb Detector with Kalman Filter Fitted Tracks

CERN Multimedia

Amoraal, J; Hulsbergen, W; Needham, M; Nicolas, L; Pozzi, S; Raven, G; Vecchi, S

2009-01-01

We report on an implementation of a global chisquare algorithm for the simultaneous alignment of all tracking systems in the LHCb detector. Our algorithm uses hit residuals from the standard LHCb track fit which is based on a Kalman filter. The algorithm is implemented in the LHCb reconstruction framework and exploits the fact that all sensitive detector elements have the same geometry interface. A vertex constraint is implemented by fitting tracks to a common point and propagating the change in track parameters to the hit residuals. To remove unconstrained or poorly constrained degrees of freedom (so-called weak modes) the average movements of (subsets of) alignable detector elements can be fixed with Lagrange constraints. Alternatively, weak modes can be removed with a cutoff in the eigenvalue spectrum of the second derivative of the chisquare. As for all LHCb reconstruction and analysis software the configuration of the algorithm is done in python and gives detailed control over the selection of alignable ...

Automated Ontology Alignment with Fuselets for Community of Interest (COI) Integration

National Research Council Canada - National Science Library

Starz, James; Roberts, Joe

2008-01-01

Discusses the ontology alignment problem by presenting a tool called Ontrapro-the Ontology Translation Protocol, which allows users to apply a myriad of ontology alignment algorithms in an iterative fashion...

STAR/SVT alignment within a finite magnetic field

International Nuclear Information System (INIS)

Barannikova, O.Yu.; Belaga, V.V.; Ososkov, G.A.; Panebrattsev, Yu.A.; Bellweid, R.K.; Pruneau, C.A.; Wilson, W.K.

1999-01-01

We report on the development of SVT (Silicon Vertex Tracker) software for the purpose of the SVT and TPC (Time Projection Chamber) relative alignment as well as the internal alignment of the SVT components. The alignment procedure described complements the internal SVT alignment procedure discussed in Star Note 356. It involves track reconstruction in both the Star TPC and SVT for the calibration of the SVT geometry in the presence of a finite magnetic field. This new software has been integrated under the package SAL already running under STAR. Both the implementation and the performance of the alignment algorithm are described. We find that the current software implementation in SAL should enable a very satisfactory internal SVT alignment as well as an excellent SVT to TPC relative alignment

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.

An Adaptive Hybrid Multiprocessor technique for bioinformatics sequence alignment

KAUST Repository

Bonny, Talal

2012-07-28

Sequence alignment algorithms such as the Smith-Waterman algorithm are among the most important applications in the development of bioinformatics. Sequence alignment algorithms must process large amounts of data which may take a long time. Here, we introduce our Adaptive Hybrid Multiprocessor technique to accelerate the implementation of the Smith-Waterman algorithm. Our technique utilizes both the graphics processing unit (GPU) and the central processing unit (CPU). It adapts to the implementation according to the number of CPUs given as input by efficiently distributing the workload between the processing units. Using existing resources (GPU and CPU) in an efficient way is a novel approach. The peak performance achieved for the platforms GPU + CPU, GPU + 2CPUs, and GPU + 3CPUs is 10.4 GCUPS, 13.7 GCUPS, and 18.6 GCUPS, respectively (with the query length of 511 amino acid). © 2010 IEEE.

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.

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).

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.

Rapid Transfer Alignment of MEMS SINS Based on Adaptive Incremental Kalman Filter.

Science.gov (United States)

Chu, Hairong; Sun, Tingting; Zhang, Baiqiang; Zhang, Hongwei; Chen, Yang

2017-01-14

In airborne MEMS SINS transfer alignment, the error of MEMS IMU is highly environment-dependent and the parameters of the system model are also uncertain, which may lead to large error and bad convergence of the Kalman filter. In order to solve this problem, an improved adaptive incremental Kalman filter (AIKF) algorithm is proposed. First, the model of SINS transfer alignment is defined based on the "Velocity and Attitude" matching method. Then the detailed algorithm progress of AIKF and its recurrence formulas are presented. The performance and calculation amount of AKF and AIKF are also compared. Finally, a simulation test is designed to verify the accuracy and the rapidity of the AIKF algorithm by comparing it with KF and AKF. The results show that the AIKF algorithm has better estimation accuracy and shorter convergence time, especially for the bias of the gyroscope and the accelerometer, which can meet the accuracy and rapidity requirement of transfer alignment.

Rapid Transfer Alignment of MEMS SINS Based on Adaptive Incremental Kalman Filter

Directory of Open Access Journals (Sweden)

Hairong Chu

2017-01-01

Full Text Available In airborne MEMS SINS transfer alignment, the error of MEMS IMU is highly environment-dependent and the parameters of the system model are also uncertain, which may lead to large error and bad convergence of the Kalman filter. In order to solve this problem, an improved adaptive incremental Kalman filter (AIKF algorithm is proposed. First, the model of SINS transfer alignment is defined based on the “Velocity and Attitude” matching method. Then the detailed algorithm progress of AIKF and its recurrence formulas are presented. The performance and calculation amount of AKF and AIKF are also compared. Finally, a simulation test is designed to verify the accuracy and the rapidity of the AIKF algorithm by comparing it with KF and AKF. The results show that the AIKF algorithm has better estimation accuracy and shorter convergence time, especially for the bias of the gyroscope and the accelerometer, which can meet the accuracy and rapidity requirement of transfer alignment.

A New Polar Transfer Alignment Algorithm with the Aid of a Star Sensor and Based on an Adaptive Unscented Kalman Filter

Directory of Open Access Journals (Sweden)

Jianhua Cheng

2017-10-01

Full Text Available Because of the harsh polar environment, the master strapdown inertial navigation system (SINS has low accuracy and the system model information becomes abnormal. In this case, existing polar transfer alignment (TA algorithms which use the measurement information provided by master SINS would lose their effectiveness. In this paper, a new polar TA algorithm with the aid of a star sensor and based on an adaptive unscented Kalman filter (AUKF is proposed to deal with the problems. Since the measurement information provided by master SINS is inaccurate, the accurate information provided by the star sensor is chosen as the measurement. With the compensation of lever-arm effect and the model of star sensor, the nonlinear navigation equations are derived. Combined with the attitude matching method, the filter models for polar TA are designed. An AUKF is introduced to solve the abnormal information of system model. Then, the AUKF is used to estimate the states of TA. Results have demonstrated that the performance of the new polar TA algorithm is better than the state-of-the-art polar TA algorithms. Therefore, the new polar TA algorithm proposed in this paper is effectively to ensure and improve the accuracy of TA in the harsh polar environment.

A New Polar Transfer Alignment Algorithm with the Aid of a Star Sensor and Based on an Adaptive Unscented Kalman Filter.

Science.gov (United States)

Cheng, Jianhua; Wang, Tongda; Wang, Lu; Wang, Zhenmin

2017-10-23

Because of the harsh polar environment, the master strapdown inertial navigation system (SINS) has low accuracy and the system model information becomes abnormal. In this case, existing polar transfer alignment (TA) algorithms which use the measurement information provided by master SINS would lose their effectiveness. In this paper, a new polar TA algorithm with the aid of a star sensor and based on an adaptive unscented Kalman filter (AUKF) is proposed to deal with the problems. Since the measurement information provided by master SINS is inaccurate, the accurate information provided by the star sensor is chosen as the measurement. With the compensation of lever-arm effect and the model of star sensor, the nonlinear navigation equations are derived. Combined with the attitude matching method, the filter models for polar TA are designed. An AUKF is introduced to solve the abnormal information of system model. Then, the AUKF is used to estimate the states of TA. Results have demonstrated that the performance of the new polar TA algorithm is better than the state-of-the-art polar TA algorithms. Therefore, the new polar TA algorithm proposed in this paper is effectively to ensure and improve the accuracy of TA in the harsh polar environment.

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

Directory of Open Access Journals (Sweden)

Hazelhurst Scott

2010-03-01

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

Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series.

Science.gov (United States)

Yuan, Yuan; Chen, Yi-Ping Phoebe; Ni, Shengyu; Xu, Augix Guohua; Tang, Lin; Vingron, Martin; Somel, Mehmet; Khaitovich, Philipp

2011-08-18

Comparing biological time series data across different conditions, or different specimens, is a common but still challenging task. Algorithms aligning two time series represent a valuable tool for such comparisons. While many powerful computation tools for time series alignment have been developed, they do not provide significance estimates for time shift measurements. Here, we present an extended version of the original DTW algorithm that allows us to determine the significance of time shift estimates in time series alignments, the DTW-Significance (DTW-S) algorithm. The DTW-S combines important properties of the original algorithm and other published time series alignment tools: DTW-S calculates the optimal alignment for each time point of each gene, it uses interpolated time points for time shift estimation, and it does not require alignment of the time-series end points. As a new feature, we implement a simulation procedure based on parameters estimated from real time series data, on a series-by-series basis, allowing us to determine the false positive rate (FPR) and the significance of the estimated time shift values. We assess the performance of our method using simulation data and real expression time series from two published primate brain expression datasets. Our results show that this method can provide accurate and robust time shift estimates for each time point on a gene-by-gene basis. Using these estimates, we are able to uncover novel features of the biological processes underlying human brain development and maturation. The DTW-S provides a convenient tool for calculating accurate and robust time shift estimates at each time point for each gene, based on time series data. The estimates can be used to uncover novel biological features of the system being studied. The DTW-S is freely available as an R package TimeShift at http://www.picb.ac.cn/Comparative/data.html.

Incremental Ontology-Based Extraction and Alignment in Semi-structured Documents

Science.gov (United States)

Thiam, Mouhamadou; Bennacer, Nacéra; Pernelle, Nathalie; Lô, Moussa

SHIRIis an ontology-based system for integration of semi-structured documents related to a specific domain. The system’s purpose is to allow users to access to relevant parts of documents as answers to their queries. SHIRI uses RDF/OWL for representation of resources and SPARQL for their querying. It relies on an automatic, unsupervised and ontology-driven approach for extraction, alignment and semantic annotation of tagged elements of documents. In this paper, we focus on the Extract-Align algorithm which exploits a set of named entity and term patterns to extract term candidates to be aligned with the ontology. It proceeds in an incremental manner in order to populate the ontology with terms describing instances of the domain and to reduce the access to extern resources such as Web. We experiment it on a HTML corpus related to call for papers in computer science and the results that we obtain are very promising. These results show how the incremental behaviour of Extract-Align algorithm enriches the ontology and the number of terms (or named entities) aligned directly with the ontology increases.

Two-wavelength Lidar inversion algorithm for determining planetary boundary layer height

Science.gov (United States)

Liu, Boming; Ma, Yingying; Gong, Wei; Jian, Yang; Ming, Zhang

2018-02-01

This study proposes a two-wavelength Lidar inversion algorithm to determine the boundary layer height (BLH) based on the particles clustering. Color ratio and depolarization ratio are used to analyze the particle distribution, based on which the proposed algorithm can overcome the effects of complex aerosol layers to calculate the BLH. The algorithm is used to determine the top of the boundary layer under different mixing state. Experimental results demonstrate that the proposed algorithm can determine the top of the boundary layer even in a complex case. Moreover, it can better deal with the weak convection conditions. Finally, experimental data from June 2015 to December 2015 were used to verify the reliability of the proposed algorithm. The correlation between the results of the proposed algorithm and the manual method is R2 = 0.89 with a RMSE of 131 m and mean bias of 49 m; the correlation between the results of the ideal profile fitting method and the manual method is R2 = 0.64 with a RMSE of 270 m and a mean bias of 165 m; and the correlation between the results of the wavelet covariance transform method and manual method is R2 = 0.76, with a RMSE of 196 m and mean bias of 23 m. These findings indicate that the proposed algorithm has better reliability and stability than traditional algorithms.

Automatic gender determination from 3D digital maxillary tooth plaster models based on the random forest algorithm and discrete cosine transform.

Science.gov (United States)

Akkoç, Betül; Arslan, Ahmet; Kök, Hatice

2017-05-01

One of the first stages in the identification of an individual is gender determination. Through gender determination, the search spectrum can be reduced. In disasters such as accidents or fires, which can render identification somewhat difficult, durable teeth are an important source for identification. This study proposes a smart system that can automatically determine gender using 3D digital maxillary tooth plaster models. The study group was composed of 40 Turkish individuals (20 female, 20 male) between the ages of 21 and 24. Using the iterative closest point (ICP) algorithm, tooth models were aligned, and after the segmentation process, models were transformed into depth images. The local discrete cosine transform (DCT) was used in the process of feature extraction, and the random forest (RF) algorithm was used for the process of classification. Classification was performed using 30 different seeds for random generator values and 10-fold cross-validation. A value of 85.166% was obtained for average classification accuracy (CA) and a value of 91.75% for the area under the ROC curve (AUC). A multi-disciplinary study is performed here that includes computer sciences, medicine and dentistry. A smart system is proposed for the determination of gender from 3D digital models of maxillary tooth plaster models. This study has the capacity to extend the field of gender determination from teeth. Copyright © 2017 Elsevier B.V. All rights reserved.

MSuPDA: A Memory Efficient Algorithm for Sequence Alignment.

Science.gov (United States)

Khan, Mohammad Ibrahim; Kamal, Md Sarwar; Chowdhury, Linkon

2016-03-01

Space complexity is a million dollar question in DNA sequence alignments. In this regard, memory saving under pushdown automata can help to reduce the occupied spaces in computer memory. Our proposed process is that anchor seed (AS) will be selected from given data set of nucleotide base pairs for local sequence alignment. Quick splitting techniques will separate the AS from all the DNA genome segments. Selected AS will be placed to pushdown automata's (PDA) input unit. Whole DNA genome segments will be placed into PDA's stack. AS from input unit will be matched with the DNA genome segments from stack of PDA. Match, mismatch and indel of nucleotides will be popped from the stack under the control unit of pushdown automata. During the POP operation on stack, it will free the memory cell occupied by the nucleotide base pair.

Initial Alignment for SINS Based on Pseudo-Earth Frame in Polar Regions.

Science.gov (United States)

Gao, Yanbin; Liu, Meng; Li, Guangchun; Guang, Xingxing

2017-06-16

An accurate initial alignment must be required for inertial navigation system (INS). The performance of initial alignment directly affects the following navigation accuracy. However, the rapid convergence of meridians and the small horizontalcomponent of rotation of Earth make the traditional alignment methods ineffective in polar regions. In this paper, from the perspective of global inertial navigation, a novel alignment algorithm based on pseudo-Earth frame and backward process is proposed to implement the initial alignment in polar regions. Considering that an accurate coarse alignment of azimuth is difficult to obtain in polar regions, the dynamic error modeling with large azimuth misalignment angle is designed. At the end of alignment phase, the strapdown attitude matrix relative to local geographic frame is obtained without influence of position errors and cumbersome computation. As a result, it would be more convenient to access the following polar navigation system. Then, it is also expected to unify the polar alignment algorithm as much as possible, thereby further unifying the form of external reference information. Finally, semi-physical static simulation and in-motion tests with large azimuth misalignment angle assisted by unscented Kalman filter (UKF) validate the effectiveness of the proposed method.

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

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.

An Overview of DNA Microarray Grid Alignment and Foreground Separation Approaches

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Bajcsy Peter

2006-01-01

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

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.

Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix

DEFF Research Database (Denmark)

Havgaard, Jakob Hull; Torarinsson, Elfar; Gorodkin, Jan

2007-01-01

and backtracked in a normal fashion. Finally, the FOLDALIGN algorithm has also been updated with a better memory implementation and an improved energy model. With these improvements in the algorithm, the FOLDALIGN software package provides the molecular biologist with an efficient and user-friendly tool...... the advantage of providing the constraints dynamically. This has been included in a new implementation of the FOLDALIGN algorithm for pairwise local or global structural alignment of RNA sequences. It is shown that time and memory requirements are dramatically lowered while overall performance is maintained....... Furthermore, a new divide and conquer method is introduced to limit the memory requirement during global alignment and backtrack of local alignment. All branch points in the computed RNA structure are found and used to divide the structure into smaller unbranched segments. Each segment is then realigned...

Accurate and robust brain image alignment using boundary-based registration.

Science.gov (United States)

Greve, Douglas N; Fischl, Bruce

2009-10-15

The fine spatial scales of the structures in the human brain represent an enormous challenge to the successful integration of information from different images for both within- and between-subject analysis. While many algorithms to register image pairs from the same subject exist, visual inspection shows that their accuracy and robustness to be suspect, particularly when there are strong intensity gradients and/or only part of the brain is imaged. This paper introduces a new algorithm called Boundary-Based Registration, or BBR. The novelty of BBR is that it treats the two images very differently. The reference image must be of sufficient resolution and quality to extract surfaces that separate tissue types. The input image is then aligned to the reference by maximizing the intensity gradient across tissue boundaries. Several lower quality images can be aligned through their alignment with the reference. Visual inspection and fMRI results show that BBR is more accurate than correlation ratio or normalized mutual information and is considerably more robust to even strong intensity inhomogeneities. BBR also excels at aligning partial-brain images to whole-brain images, a domain in which existing registration algorithms frequently fail. Even in the limit of registering a single slice, we show the BBR results to be robust and accurate.

Long Read Alignment with Parallel MapReduce Cloud Platform

Science.gov (United States)

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

2015-01-01

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

Dynamic programming algorithms for biological sequence comparison.

Science.gov (United States)

Pearson, W R; Miller, W

1992-01-01

Efficient dynamic programming algorithms are available for a broad class of protein and DNA sequence comparison problems. These algorithms require computer time proportional to the product of the lengths of the two sequences being compared [O(N2)] but require memory space proportional only to the sum of these lengths [O(N)]. Although the requirement for O(N2) time limits use of the algorithms to the largest computers when searching protein and DNA sequence databases, many other applications of these algorithms, such as calculation of distances for evolutionary trees and comparison of a new sequence to a library of sequence profiles, are well within the capabilities of desktop computers. In particular, the results of library searches with rapid searching programs, such as FASTA or BLAST, should be confirmed by performing a rigorous optimal alignment. Whereas rapid methods do not overlook significant sequence similarities, FASTA limits the number of gaps that can be inserted into an alignment, so that a rigorous alignment may extend the alignment substantially in some cases. BLAST does not allow gaps in the local regions that it reports; a calculation that allows gaps is very likely to extend the alignment substantially. Although a Monte Carlo evaluation of the statistical significance of a similarity score with a rigorous algorithm is much slower than the heuristic approach used by the RDF2 program, the dynamic programming approach should take less than 1 hr on a 386-based PC or desktop Unix workstation. For descriptive purposes, we have limited our discussion to methods for calculating similarity scores and distances that use gap penalties of the form g = rk. Nevertheless, programs for the more general case (g = q+rk) are readily available. Versions of these programs that run either on Unix workstations, IBM-PC class computers, or the Macintosh can be obtained from either of the authors.

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

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Solayar GN

2017-07-01

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

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.

Real-time driver fatigue detection based on face alignment

Science.gov (United States)

Tao, Huanhuan; Zhang, Guiying; Zhao, Yong; Zhou, Yi

2017-07-01

The performance and robustness of fatigue detection largely decrease if the driver with glasses. To address this issue, this paper proposes a practical driver fatigue detection method based on face alignment at 3000 FPS algorithm. Firstly, the eye regions of the driver are localized by exploiting 6 landmarks surrounding each eye. Secondly, the HOG features of the extracted eye regions are calculated and put into SVM classifier to recognize the eye state. Finally, the value of PERCLOS is calculated to determine whether the driver is drowsy or not. An alarm will be generated if the eye is closed for a specified period of time. The accuracy and real-time on testing videos with different drivers demonstrate that the proposed algorithm is robust and obtain better accuracy for driver fatigue detection compared with some previous method.

Heuristic for Solving the Multiple Alignment Sequence Problem

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Roman Anselmo Mora Gutiérrez

2011-03-01

Full Text Available In this paper we developed a new algorithm for solving the problem of multiple sequence alignment (AM S, which is a hybrid metaheuristic based on harmony search and simulated annealing. The hybrid was validated with the methodology of Julie Thompson. This is a basic algorithm and and results obtained during this stage are encouraging.

Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

Directory of Open Access Journals (Sweden)

Toh Hiroyuki

2008-04-01

Full Text Available Abstract Background Structural alignment of RNAs is becoming important, since the discovery of functional non-coding RNAs (ncRNAs. Recent studies, mainly based on various approximations of the Sankoff algorithm, have resulted in considerable improvement in the accuracy of pairwise structural alignment. In contrast, for the cases with more than two sequences, the practical merit of structural alignment remains unclear as compared to traditional sequence-based methods, although the importance of multiple structural alignment is widely recognized. Results We took a different approach from a straightforward extension of the Sankoff algorithm to the multiple alignments from the viewpoints of accuracy and time complexity. As a new option of the MAFFT alignment program, we developed a multiple RNA alignment framework, X-INS-i, which builds a multiple alignment with an iterative method incorporating structural information through two components: (1 pairwise structural alignments by an external pairwise alignment method such as SCARNA or LaRA and (2 a new objective function, Four-way Consistency, derived from the base-pairing probability of every sub-aligned group at every multiple alignment stage. Conclusion The BRAliBASE benchmark showed that X-INS-i outperforms other methods currently available in the sum-of-pairs score (SPS criterion. As a basis for predicting common secondary structure, the accuracy of the present method is comparable to or rather higher than those of the current leading methods such as RNA Sampler. The X-INS-i framework can be used for building a multiple RNA alignment from any combination of algorithms for pairwise RNA alignment and base-pairing probability. The source code is available at the webpage found in the Availability and requirements section.

A Practical Guide to Multi-image Alignment

OpenAIRE

Aguerrebere, Cecilia; Delbracio, Mauricio; Bartesaghi, Alberto; Sapiro, Guillermo

2018-01-01

Multi-image alignment, bringing a group of images into common register, is an ubiquitous problem and the first step of many applications in a wide variety of domains. As a result, a great amount of effort is being invested in developing efficient multi-image alignment algorithms. Little has been done, however, to answer fundamental practical questions such as: what is the comparative performance of existing methods? is there still room for improvement? under which conditions should one techni...

Simulation of high-resolution X-ray microscopic images for improved alignment

International Nuclear Information System (INIS)

Song Xiangxia; Zhang Xiaobo; Liu Gang; Cheng Xianchao; Li Wenjie; Guan Yong; Liu Ying; Xiong Ying; Tian Yangchao

2011-01-01

The introduction of precision optical elements to X-ray microscopes necessitates fine realignment to achieve optimal high-resolution imaging. In this paper, we demonstrate a numerical method for simulating image formation that facilitates alignment of the source, condenser, objective lens, and CCD camera. This algorithm, based on ray-tracing and Rayleigh-Sommerfeld diffraction theory, is applied to simulate the X-ray microscope beamline U7A of National Synchrotron Radiation Laboratory (NSRL). The simulations and imaging experiments show that the algorithm is useful for guiding experimental adjustments. Our alignment simulation method is an essential tool for the transmission X-ray microscope (TXM) with optical elements and may also be useful for the alignment of optical components in other modes of microscopy.

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.

Statistical alignment: computational properties, homology testing and goodness-of-fit

DEFF Research Database (Denmark)

Hein, J; Wiuf, Carsten; Møller, Martin

2000-01-01

The model of insertions and deletions in biological sequences, first formulated by Thorne, Kishino, and Felsenstein in 1991 (the TKF91 model), provides a basis for performing alignment within a statistical framework. Here we investigate this model.Firstly, we show how to accelerate the statistical...... alignment algorithms several orders of magnitude. The main innovations are to confine likelihood calculations to a band close to the similarity based alignment, to get good initial guesses of the evolutionary parameters and to apply an efficient numerical optimisation algorithm for finding the maximum...... analysis.Secondly, we propose a new homology test based on this model, where homology means that an ancestor to a sequence pair can be found finitely far back in time. This test has statistical advantages relative to the traditional shuffle test for proteins.Finally, we describe a goodness-of-fit test...

SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics.

Science.gov (United States)

Will, Sebastian; Otto, Christina; Miladi, Milad; Möhl, Mathias; Backofen, Rolf

2015-08-01

RNA-Seq experiments have revealed a multitude of novel ncRNAs. The gold standard for their analysis based on simultaneous alignment and folding suffers from extreme time complexity of [Formula: see text]. Subsequently, numerous faster 'Sankoff-style' approaches have been suggested. Commonly, the performance of such methods relies on sequence-based heuristics that restrict the search space to optimal or near-optimal sequence alignments; however, the accuracy of sequence-based methods breaks down for RNAs with sequence identities below 60%. Alignment approaches like LocARNA that do not require sequence-based heuristics, have been limited to high complexity ([Formula: see text] quartic time). Breaking this barrier, we introduce the novel Sankoff-style algorithm 'sparsified prediction and alignment of RNAs based on their structure ensembles (SPARSE)', which runs in quadratic time without sequence-based heuristics. To achieve this low complexity, on par with sequence alignment algorithms, SPARSE features strong sparsification based on structural properties of the RNA ensembles. Following PMcomp, SPARSE gains further speed-up from lightweight energy computation. Although all existing lightweight Sankoff-style methods restrict Sankoff's original model by disallowing loop deletions and insertions, SPARSE transfers the Sankoff algorithm to the lightweight energy model completely for the first time. Compared with LocARNA, SPARSE achieves similar alignment and better folding quality in significantly less time (speedup: 3.7). At similar run-time, it aligns low sequence identity instances substantially more accurate than RAF, which uses sequence-based heuristics. © The Author 2015. Published by Oxford University Press.

Anatomically Plausible Surface Alignment and Reconstruction

DEFF Research Database (Denmark)

Paulsen, Rasmus R.; Larsen, Rasmus

2010-01-01

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

Development and application of a modified dynamic time warping algorithm (DTW-S to analyses of primate brain expression time series

Directory of Open Access Journals (Sweden)

Vingron Martin

2011-08-01

Full Text Available Abstract Background Comparing biological time series data across different conditions, or different specimens, is a common but still challenging task. Algorithms aligning two time series represent a valuable tool for such comparisons. While many powerful computation tools for time series alignment have been developed, they do not provide significance estimates for time shift measurements. Results Here, we present an extended version of the original DTW algorithm that allows us to determine the significance of time shift estimates in time series alignments, the DTW-Significance (DTW-S algorithm. The DTW-S combines important properties of the original algorithm and other published time series alignment tools: DTW-S calculates the optimal alignment for each time point of each gene, it uses interpolated time points for time shift estimation, and it does not require alignment of the time-series end points. As a new feature, we implement a simulation procedure based on parameters estimated from real time series data, on a series-by-series basis, allowing us to determine the false positive rate (FPR and the significance of the estimated time shift values. We assess the performance of our method using simulation data and real expression time series from two published primate brain expression datasets. Our results show that this method can provide accurate and robust time shift estimates for each time point on a gene-by-gene basis. Using these estimates, we are able to uncover novel features of the biological processes underlying human brain development and maturation. Conclusions The DTW-S provides a convenient tool for calculating accurate and robust time shift estimates at each time point for each gene, based on time series data. The estimates can be used to uncover novel biological features of the system being studied. The DTW-S is freely available as an R package TimeShift at http://www.picb.ac.cn/Comparative/data.html.

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

International Nuclear Information System (INIS)

Winkler, Hanspeter; Taylor, Kenneth A.

2006-01-01

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

Long Read Alignment with Parallel MapReduce Cloud Platform

Directory of Open Access Journals (Sweden)

Ahmed Abdulhakim Al-Absi

2015-01-01

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

Automatic laser beam alignment using blob detection for an environment monitoring spectroscopy

Science.gov (United States)

Khidir, Jarjees; Chen, Youhua; Anderson, Gary

2013-05-01

This paper describes a fully automated system to align an infra-red laser beam with a small retro-reflector over a wide range of distances. The component development and test were especially used for an open-path spectrometer gas detection system. Using blob detection under OpenCV library, an automatic alignment algorithm was designed to achieve fast and accurate target detection in a complex background environment. Test results are presented to show that the proposed algorithm has been successfully applied to various target distances and environment conditions.

Considerations in the identification of functional RNA structural elements in genomic alignments

Directory of Open Access Journals (Sweden)

Blencowe Benjamin J

2007-01-01

Full Text Available Abstract Background Accurate identification of novel, functional noncoding (nc RNA features in genome sequence has proven more difficult than for exons. Current algorithms identify and score potential RNA secondary structures on the basis of thermodynamic stability, conservation, and/or covariance in sequence alignments. Neither the algorithms nor the information gained from the individual inputs have been independently assessed. Furthermore, due to issues in modelling background signal, it has been difficult to gauge the precision of these algorithms on a genomic scale, in which even a seemingly small false-positive rate can result in a vast excess of false discoveries. Results We developed a shuffling algorithm, shuffle-pair.pl, that simultaneously preserves dinucleotide frequency, gaps, and local conservation in pairwise sequence alignments. We used shuffle-pair.pl to assess precision and recall of six ncRNA search tools (MSARI, QRNA, ddbRNA, RNAz, Evofold, and several variants of simple thermodynamic stability on a test set of 3046 alignments of known ncRNAs. Relative to mononucleotide shuffling, preservation of dinucleotide content in shuffling the alignments resulted in a drastic increase in estimated false-positive detection rates for ncRNA elements, precluding evaluation of higher order alignments, which cannot not be adequately shuffled maintaining both dinucleotides and alignment structure. On pairwise alignments, none of the covariance-based tools performed markedly better than thermodynamic scoring alone. Although the high false-positive rates call into question the veracity of any individual predicted secondary structural element in our analysis, we nevertheless identified intriguing global trends in human genome alignments. The distribution of ncRNA prediction scores in 75-base windows overlapping UTRs, introns, and intergenic regions analyzed using both thermodynamic stability and EvoFold (which has no thermodynamic component was

Location and Position Determination Algorithm For Humanoid Soccer Robot

Directory of Open Access Journals (Sweden)

Oei Kurniawan Utomo

2016-03-01

Full Text Available The algorithm of location and position determination was designed for humanoid soccer robot. The robots have to be able to control the ball effectively on the field of Indonesian Robot Soccer Competition which has a size of 900 cm x 600 cm. The algorithm of location and position determination uses parameters, such as the goalpost’s thickness, the compass value, and the robot’s head servo value. The goalpost’s thickness is detected using The Centre of Gravity method. The width of the goalpost detected is analyzed using the principles of camera geometry to determine the distance between the robot and the goalpost. The tangent value of head servo’s tilt angle is used to determine the distance between the robot and the ball. The distance between robot-goalpost and the distance between robot-ball are processed with the difference of head servo’s pan angle and compass value using trigonometric formulas to determine the coordinates of the robot and the ball in the Cartesian coordinates.

Interactive software tool to comprehend the calculation of optimal sequence alignments with dynamic programming.

Science.gov (United States)

Ibarra, Ignacio L; Melo, Francisco

2010-07-01

Dynamic programming (DP) is a general optimization strategy that is successfully used across various disciplines of science. In bioinformatics, it is widely applied in calculating the optimal alignment between pairs of protein or DNA sequences. These alignments form the basis of new, verifiable biological hypothesis. Despite its importance, there are no interactive tools available for training and education on understanding the DP algorithm. Here, we introduce an interactive computer application with a graphical interface, for the purpose of educating students about DP. The program displays the DP scoring matrix and the resulting optimal alignment(s), while allowing the user to modify key parameters such as the values in the similarity matrix, the sequence alignment algorithm version and the gap opening/extension penalties. We hope that this software will be useful to teachers and students of bioinformatics courses, as well as researchers who implement the DP algorithm for diverse applications. The software is freely available at: http:/melolab.org/sat. The software is written in the Java computer language, thus it runs on all major platforms and operating systems including Windows, Mac OS X and LINUX. All inquiries or comments about this software should be directed to Francisco Melo at fmelo@bio.puc.cl.

Face Alignment Using Boosting and Evolutionary Search

NARCIS (Netherlands)

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

2010-01-01

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

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

Science.gov (United States)

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

2010-07-01

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

SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics

Science.gov (United States)

Will, Sebastian; Otto, Christina; Miladi, Milad; Möhl, Mathias; Backofen, Rolf

2015-01-01

Motivation: RNA-Seq experiments have revealed a multitude of novel ncRNAs. The gold standard for their analysis based on simultaneous alignment and folding suffers from extreme time complexity of O(n6). Subsequently, numerous faster ‘Sankoff-style’ approaches have been suggested. Commonly, the performance of such methods relies on sequence-based heuristics that restrict the search space to optimal or near-optimal sequence alignments; however, the accuracy of sequence-based methods breaks down for RNAs with sequence identities below 60%. Alignment approaches like LocARNA that do not require sequence-based heuristics, have been limited to high complexity (≥ quartic time). Results: Breaking this barrier, we introduce the novel Sankoff-style algorithm ‘sparsified prediction and alignment of RNAs based on their structure ensembles (SPARSE)’, which runs in quadratic time without sequence-based heuristics. To achieve this low complexity, on par with sequence alignment algorithms, SPARSE features strong sparsification based on structural properties of the RNA ensembles. Following PMcomp, SPARSE gains further speed-up from lightweight energy computation. Although all existing lightweight Sankoff-style methods restrict Sankoff’s original model by disallowing loop deletions and insertions, SPARSE transfers the Sankoff algorithm to the lightweight energy model completely for the first time. Compared with LocARNA, SPARSE achieves similar alignment and better folding quality in significantly less time (speedup: 3.7). At similar run-time, it aligns low sequence identity instances substantially more accurate than RAF, which uses sequence-based heuristics. Availability and implementation: SPARSE is freely available at http://www.bioinf.uni-freiburg.de/Software/SPARSE. Contact: backofen@informatik.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25838465

Energy band alignment at ferroelectric/electrode interface determined by photoelectron spectroscopy

International Nuclear Information System (INIS)

Chen Feng; Wu Wen-Bin; Li Shun-Yi; Klein Andreas

2014-01-01

The most important interface-related quantities determined by band alignment are the barrier heights for charge transport, given by the Fermi level position at the interface. Taking Pb(Zr,Ti)O 3 (PZT) as a typical ferroelectric material and applying X-ray photoelectron spectroscopy (XPS), we briefly review the interface formation and barrier heights at the interfaces between PZT and electrodes made of various metals or conductive oxides. Polarization dependence of the Schottky barrier height at a ferroelectric/electrode interface is also directly observed using XPS. (topical review - magnetism, magnetic materials, and interdisciplinary research)

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. �

An algorithm for determining the rotation count of pulsars

Science.gov (United States)

Freire, Paulo C. C.; Ridolfi, Alessandro

2018-06-01

We present here a simple, systematic method for determining the correct global rotation count of a radio pulsar; an essential step for the derivation of an accurate phase-coherent ephemeris. We then build on this method by developing a new algorithm for determining the global rotational count for pulsars with sparse timing data sets. This makes it possible to obtain phase-coherent ephemerides for pulsars for which this has been impossible until now. As an example, we do this for PSR J0024-7205aa, an extremely faint Millisecond pulsar (MSP) recently discovered in the globular cluster 47 Tucanae. This algorithm has the potential to significantly reduce the number of observations and the amount of telescope time needed to follow up on new pulsar discoveries.

Internal alignment and position resolution of the silicon tracker of DAMPE determined with orbit data

Science.gov (United States)

Tykhonov, A.; Ambrosi, G.; Asfandiyarov, R.; Azzarello, P.; Bernardini, P.; Bertucci, B.; Bolognini, A.; Cadoux, F.; D'Amone, A.; De Benedittis, A.; De Mitri, I.; Di Santo, M.; Dong, Y. F.; Duranti, M.; D'Urso, D.; Fan, R. R.; Fusco, P.; Gallo, V.; Gao, M.; Gargano, F.; Garrappa, S.; Gong, K.; Ionica, M.; La Marra, D.; Lei, S. J.; Li, X.; Loparco, F.; Marsella, G.; Mazziotta, M. N.; Peng, W. X.; Qiao, R.; Salinas, M. M.; Surdo, A.; Vagelli, V.; Vitillo, S.; Wang, H. Y.; Wang, J. Z.; Wang, Z. M.; Wu, D.; Wu, X.; Zhang, F.; Zhang, J. Y.; Zhao, H.; Zimmer, S.

2018-06-01

The DArk Matter Particle Explorer (DAMPE) is a space-borne particle detector designed to probe electrons and gamma-rays in the few GeV to 10 TeV energy range, as well as cosmic-ray proton and nuclei components between 10 GeV and 100 TeV. The silicon-tungsten tracker-converter is a crucial component of DAMPE. It allows the direction of incoming photons converting into electron-positron pairs to be estimated, and the trajectory and charge (Z) of cosmic-ray particles to be identified. It consists of 768 silicon micro-strip sensors assembled in 6 double layers with a total active area of 6.6 m2. Silicon planes are interleaved with three layers of tungsten plates, resulting in about one radiation length of material in the tracker. Internal alignment parameters of the tracker have been determined on orbit, with non-showering protons and helium nuclei. We describe the alignment procedure and present the position resolution and alignment stability measurements.

Feature-based Alignment of Volumetric Multi-modal Images

Science.gov (United States)

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

2014-01-01

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

Tracker Alignment Performance Plots after Commissioning

CERN Document Server

CMS Collaboration

2017-01-01

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

An optimisation algorithm for determination of treatment margins around moving and deformable targets

International Nuclear Information System (INIS)

Redpath, Anthony Thomas; Muren, Ludvig Paul

2005-01-01

Purpose: Determining treatment margins for inter-fractional motion of moving and deformable clinical target volumes (CTVs) remains a major challenge. This paper describes and applies an optimisation algorithm designed to derive such margins. Material and methods: The algorithm works by expanding the CTV, as determined from a pre-treatment or planning scan, to enclose the CTV positions observed during treatment. CTV positions during treatment may be obtained using, for example, repeat CT scanning and/or repeat electronic portal imaging (EPI). The algorithm can be applied to both individual patients and to a set of patients. The margins derived will minimise the excess volume outside the envelope that encloses all observed CTV positions (the CTV envelope). Initially, margins are set such that the envelope is more than adequately covered when the planning CTV is expanded. The algorithm uses an iterative method where the margins are sampled randomly and are then either increased or decreased randomly. The algorithm is tested on a set of 19 bladder cancer patients that underwent weekly repeat CT scanning and EPI throughout their treatment course. Results: From repeated runs on individual patients, the algorithm produces margins within a range of ±2 mm that lie among the best results found with an exhaustive search approach, and that agree within 3 mm with margins determined by a manual approach on the same data. The algorithm could be used to determine margins to cover any specified geometrical uncertainty, and allows for the determination of reduced margins by relaxing the coverage criteria, for example disregarding extreme CTV positions, or an arbitrarily selected volume fraction of the CTV envelope, and/or patients with extreme geometrical uncertainties. Conclusion: An optimisation approach to margin determination is found to give reproducible results within the accuracy required. The major advantage with this algorithm is that it is completely empirical, and it is

K2 and K2*: efficient alignment-free sequence similarity measurement based on Kendall statistics.

Science.gov (United States)

Lin, Jie; Adjeroh, Donald A; Jiang, Bing-Hua; Jiang, Yue

2018-05-15

Alignment-free sequence comparison methods can compute the pairwise similarity between a huge number of sequences much faster than sequence-alignment based methods. We propose a new non-parametric alignment-free sequence comparison method, called K2, based on the Kendall statistics. Comparing to the other state-of-the-art alignment-free comparison methods, K2 demonstrates competitive performance in generating the phylogenetic tree, in evaluating functionally related regulatory sequences, and in computing the edit distance (similarity/dissimilarity) between sequences. Furthermore, the K2 approach is much faster than the other methods. An improved method, K2*, is also proposed, which is able to determine the appropriate algorithmic parameter (length) automatically, without first considering different values. Comparative analysis with the state-of-the-art alignment-free sequence similarity methods demonstrates the superiority of the proposed approaches, especially with increasing sequence length, or increasing dataset sizes. The K2 and K2* approaches are implemented in the R language as a package and is freely available for open access (http://community.wvu.edu/daadjeroh/projects/K2/K2_1.0.tar.gz). yueljiang@163.com. Supplementary data are available at Bioinformatics online.

Inner detector alignment and top-quark mass measurement with the ATLAS detector

CERN Document Server

Moles-Valls, Regina

This thesis is divided in two parts: one related with the alignment of the ATLAS Inner Detector tracking system and other with the measurement of the top-quark mass. Both topics are connected by the Globalχ2 fitting method. In order to measure the properties of the particles with high accuracy, the ID detector is composed by devices with high intrinsic resolution. If by any chance the position of the modules in the detector is known with worse precision than their intrinsic resolution this may introduce a distortion in the reconstructed trajectory of the particles or at least degrade the tracking resolution. The alignment is the responsible of determining the location of each module with high precision and avoiding therefore any bias in the physics results. During the commissioning of the detector, different alignment exercises were performed for preparing the Globalχ2 algorithm (the CSC , the FDR, weak modes studies,…). At the same time, the ATLAS detector was collecting million of cosmic rays which were...

Predicting Consensus Structures for RNA Alignments Via Pseudo-Energy Minimization

Directory of Open Access Journals (Sweden)

Junilda Spirollari

2009-01-01

Full Text Available Thermodynamic processes with free energy parameters are often used in algorithms that solve the free energy minimization problem to predict secondary structures of single RNA sequences. While results from these algorithms are promising, an observation is that single sequence-based methods have moderate accuracy and more information is needed to improve on RNA secondary structure prediction, such as covariance scores obtained from multiple sequence alignments. We present in this paper a new approach to predicting the consensus secondary structure of a set of aligned RNA sequences via pseudo-energy minimization. Our tool, called RSpredict, takes into account sequence covariation and employs effective heuristics for accuracy improvement. RSpredict accepts, as input data, a multiple sequence alignment in FASTA or ClustalW format and outputs the consensus secondary structure of the input sequences in both the Vienna style Dot Bracket format and the Connectivity Table format. Our method was compared with some widely used tools including KNetFold, Pfold and RNAalifold. A comprehensive test on different datasets including Rfam sequence alignments and a multiple sequence alignment obtained from our study on the Drosophila X chromosome reveals that RSpredict is competitive with the existing tools on the tested datasets. RSpredict is freely available online as a web server and also as a jar file for download at http:// datalab.njit.edu/biology/RSpredict.

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

Science.gov (United States)

Löytynoja, Ari

2012-01-01

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

The LabelHash algorithm for substructure matching

Directory of Open Access Journals (Sweden)

Bryant Drew H

2010-11-01

Full Text Available Abstract Background There is an increasing number of proteins with known structure but unknown function. Determining their function would have a significant impact on understanding diseases and designing new therapeutics. However, experimental protein function determination is expensive and very time-consuming. Computational methods can facilitate function determination by identifying proteins that have high structural and chemical similarity. Results We present LabelHash, a novel algorithm for matching substructural motifs to large collections of protein structures. The algorithm consists of two phases. In the first phase the proteins are preprocessed in a fashion that allows for instant lookup of partial matches to any motif. In the second phase, partial matches for a given motif are expanded to complete matches. The general applicability of the algorithm is demonstrated with three different case studies. First, we show that we can accurately identify members of the enolase superfamily with a single motif. Next, we demonstrate how LabelHash can complement SOIPPA, an algorithm for motif identification and pairwise substructure alignment. Finally, a large collection of Catalytic Site Atlas motifs is used to benchmark the performance of the algorithm. LabelHash runs very efficiently in parallel; matching a motif against all proteins in the 95% sequence identity filtered non-redundant Protein Data Bank typically takes no more than a few minutes. The LabelHash algorithm is available through a web server and as a suite of standalone programs at http://labelhash.kavrakilab.org. The output of the LabelHash algorithm can be further analyzed with Chimera through a plugin that we developed for this purpose. Conclusions LabelHash is an efficient, versatile algorithm for large-scale substructure matching. When LabelHash is running in parallel, motifs can typically be matched against the entire PDB on the order of minutes. The algorithm is able to identify

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.

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.

An algorithm for determination of peak regions and baseline elimination in spectroscopic data

International Nuclear Information System (INIS)

Morhac, Miroslav

2009-01-01

In the paper we propose a new algorithm for the determination of peaks containing regions and their separation from peak-free regions. Further based on this algorithm we propose a new background elimination algorithm which allows more accurate estimate of the background beneath the peaks than the algorithms known so far. The algorithm is based on a clipping operation with the window adjustable automatically to the widths of identified peak regions. The illustrative examples presented in the paper prove in favor of the proposed algorithms.

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

Science.gov (United States)

Kuziemko, Andrew; Honig, Barry; Petrey, Donald

2011-10-01

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

Attitude sensor alignment calibration for the solar maximum mission

Science.gov (United States)

Pitone, Daniel S.; Shuster, Malcolm D.

1990-01-01

An earlier heuristic study of the fine attitude sensors for the Solar Maximum Mission (SMM) revealed a temperature dependence of the alignment about the yaw axis of the pair of fixed-head star trackers relative to the fine pointing Sun sensor. Here, new sensor alignment algorithms which better quantify the dependence of the alignments on the temperature are developed and applied to the SMM data. Comparison with the results from the previous study reveals the limitations of the heuristic approach. In addition, some of the basic assumptions made in the prelaunch analysis of the alignments of the SMM are examined. The results of this work have important consequences for future missions with stringent attitude requirements and where misalignment variations due to variations in the temperature will be significant.

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

Directory of Open Access Journals (Sweden)

Mourad Ykhlef

2015-01-01

Full Text Available 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 they are applied to large dataset. Nowadays, some evolutionary algorithms, such as particle swarm optimization and genetic algorithm, were proposed and have been applied. In order to improve the speed of evolutionary algorithms convergence, we will propose a new kind of hybrid evolutionary algorithm that combines genetic algorithm (GA with particle swarm optimization (PSO to solve winner determination problem in multiunit double auction; we will refer to this algorithm as AUC-GAPSO.

Iterative local Chi2 alignment approach for the ATLAS SCT detector

CERN Document Server

Härtel, Roland

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

The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search

DEFF Research Database (Denmark)

Havgaard, Jakob Hull; Lyngsø, Rune B.; Gorodkin, Jan

2005-01-01

FOLDALIGN is a Sankoff-based algorithm for making structural alignments of RNA sequences. Here, we present a web server for making pairwise alignments between two RNA sequences, using the recently updated version of FOLDALIGN. The server can be used to scan two sequences for a common structural RNA...... motif of limited size, or the entire sequences can be aligned locally or globally. The web server offers a graphical interface, which makes it simple to make alignments and manually browse the results. the web server can be accessed at http://foldalign.kvl.dk...

Track based alignment of the CMS silicon tracker and its implication on physics performance

International Nuclear Information System (INIS)

Draeger, Jula

2011-08-01

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.)

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.)

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

Science.gov (United States)

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

2016-04-01

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

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

Control rod housing alignment

International Nuclear Information System (INIS)

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

1990-01-01

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

Control Algorithms for Large-scale Single-axis Photovoltaic Trackers

Directory of Open Access Journals (Sweden)

Dorian Schneider

2012-01-01

Full Text Available The electrical yield of large-scale photovoltaic power plants can be greatly improved by employing solar trackers. While fixed-tilt superstructures are stationary and immobile, trackers move the PV-module plane in order to optimize its alignment to the sun. This paper introduces control algorithms for single-axis trackers (SAT, including a discussion for optimal alignment and backtracking. The results are used to simulate and compare the electrical yield of fixed-tilt and SAT systems. The proposed algorithms have been field tested, and are in operation in solar parks worldwide.

An efficient multi-resolution GA approach to dental image alignment

Science.gov (United States)

Nassar, Diaa Eldin; Ogirala, Mythili; Adjeroh, Donald; Ammar, Hany

2006-02-01

Automating the process of postmortem identification of individuals using dental records is receiving an increased attention in forensic science, especially with the large volume of victims encountered in mass disasters. Dental radiograph alignment is a key step required for automating the dental identification process. In this paper, we address the problem of dental radiograph alignment using a Multi-Resolution Genetic Algorithm (MR-GA) approach. We use location and orientation information of edge points as features; we assume that affine transformations suffice to restore geometric discrepancies between two images of a tooth, we efficiently search the 6D space of affine parameters using GA progressively across multi-resolution image versions, and we use a Hausdorff distance measure to compute the similarity between a reference tooth and a query tooth subject to a possible alignment transform. Testing results based on 52 teeth-pair images suggest that our algorithm converges to reasonable solutions in more than 85% of the test cases, with most of the error in the remaining cases due to excessive misalignments.

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

Science.gov (United States)

Yumura, Takashi; Yamamoto, Wataru

2017-09-20

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

CATCHprofiles: Clustering and Alignment Tool for ChIP Profiles

DEFF Research Database (Denmark)

G. G. Nielsen, Fiona; Galschiøt Markus, Kasper; Møllegaard Friborg, Rune

2012-01-01

IP-profiling data and detect potentially meaningful patterns, the areas of enrichment must be aligned and clustered, which is an algorithmically and computationally challenging task. We have developed CATCHprofiles, a novel tool for exhaustive pattern detection in ChIP profiling data. CATCHprofiles is built upon...... a computationally efficient implementation for the exhaustive alignment and hierarchical clustering of ChIP profiling data. The tool features a graphical interface for examination and browsing of the clustering results. CATCHprofiles requires no prior knowledge about functional sites, detects known binding patterns...... it an invaluable tool for explorative research based on ChIP profiling data. CATCHprofiles and the CATCH algorithm run on all platforms and is available for free through the CATCH website: http://catch.cmbi.ru.nl/. User support is available by subscribing to the mailing list catch-users@bioinformatics.org....

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

International Nuclear Information System (INIS)

Potter, J.D.

1995-01-01

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

Nova laser alignment control system

International Nuclear Information System (INIS)

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

1984-01-01

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

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

Directory of Open Access Journals (Sweden)

Andrew Kuziemko

2011-10-01

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

Two-antenna GNSS Aided-INS Alignment Using Adaptive Control of Filter Noise Covariance

Directory of Open Access Journals (Sweden)

HAO Yushi

2018-04-01

Full Text Available This paper developed a theory of INS fine alignment in order to restrain the divergence of yaw angle,two antennas GNSS aided-INS integrated alignment algorithm was utilized.An attitude error measurement equation was conducted based on the relationship between baseline vectors calculated by two sensors and attitude error.The algorithm was executed by EKF using adaptive control of filter noise covariance.The experimental results showed that stability of the integrated system was improved under the system noise covariance adaptive control mechanism;The measurement noise covariance adaptive control mechanism can reduce the influence of measurement noise and improve the alignment absolute accuracy;Further improvement was achieved under the condition of minim bias of baseline length.The accuracy of roll and pitch was 0.02°,the accuracy of yaw was 0.04°.

Advanced Alignment of the ATLAS Inner Detector

CERN Document Server

Stahlman, JM; The ATLAS collaboration

2012-01-01

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

Sequential Optimization of Global Sequence Alignments Relative to Different Cost Functions

KAUST Repository

Odat, Enas M.

2011-05-01

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

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

International Nuclear Information System (INIS)

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

2009-01-01

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.

SOAP2: an improved ultrafast tool for short read alignment

DEFF Research Database (Denmark)

Li, Ruiqiang; Yu, Chang; Li, Yingrui

2009-01-01

SUMMARY: SOAP2 is a significantly improved version of the short oligonucleotide alignment program that both reduces computer memory usage and increases alignment speed at an unprecedented rate. We used a Burrows Wheeler Transformation (BWT) compression index to substitute the seed strategy...... for indexing the reference sequence in the main memory. We tested it on the whole human genome and found that this new algorithm reduced memory usage from 14.7 to 5.4 GB and improved alignment speed by 20-30 times. SOAP2 is compatible with both single- and paired-end reads. Additionally, this tool now supports...... multiple text and compressed file formats. A consensus builder has also been developed for consensus assembly and SNP detection from alignment of short reads on a reference genome. AVAILABILITY: http://soap.genomics.org.cn....

ClustalXeed: a GUI-based grid computation version for high performance and terabyte size multiple sequence alignment

Directory of Open Access Journals (Sweden)

Kim Taeho

2010-09-01

Full Text Available Abstract Background There is an increasing demand to assemble and align large-scale biological sequence data sets. The commonly used multiple sequence alignment programs are still limited in their ability to handle very large amounts of sequences because the system lacks a scalable high-performance computing (HPC environment with a greatly extended data storage capacity. Results We designed ClustalXeed, a software system for multiple sequence alignment with incremental improvements over previous versions of the ClustalX and ClustalW-MPI software. The primary advantage of ClustalXeed over other multiple sequence alignment software is its ability to align a large family of protein or nucleic acid sequences. To solve the conventional memory-dependency problem, ClustalXeed uses both physical random access memory (RAM and a distributed file-allocation system for distance matrix construction and pair-align computation. The computation efficiency of disk-storage system was markedly improved by implementing an efficient load-balancing algorithm, called "idle node-seeking task algorithm" (INSTA. The new editing option and the graphical user interface (GUI provide ready access to a parallel-computing environment for users who seek fast and easy alignment of large DNA and protein sequence sets. Conclusions ClustalXeed can now compute a large volume of biological sequence data sets, which were not tractable in any other parallel or single MSA program. The main developments include: 1 the ability to tackle larger sequence alignment problems than possible with previous systems through markedly improved storage-handling capabilities. 2 Implementing an efficient task load-balancing algorithm, INSTA, which improves overall processing times for multiple sequence alignment with input sequences of non-uniform length. 3 Support for both single PC and distributed cluster systems.

Application of genetic algorithm in radio ecological models parameter determination

Energy Technology Data Exchange (ETDEWEB)

Pantelic, G. [Institute of Occupatioanl Health and Radiological Protection ' Dr Dragomir Karajovic' , Belgrade (Serbia)

2006-07-01

The method of genetic algorithms was used to determine the biological half-life of 137 Cs in cow milk after the accident in Chernobyl. Methodologically genetic algorithms are based on the fact that natural processes tend to optimize themselves and therefore this method should be more efficient in providing optimal solutions in the modeling of radio ecological and environmental events. The calculated biological half-life of 137 Cs in milk is (32 {+-} 3) days and transfer coefficient from grass to milk is (0.019 {+-} 0.005). (authors)

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...

An algorithm of improving speech emotional perception for hearing aid

Science.gov (United States)

Xi, Ji; Liang, Ruiyu; Fei, Xianju

2017-07-01

In this paper, a speech emotion recognition (SER) algorithm was proposed to improve the emotional perception of hearing-impaired people. The algorithm utilizes multiple kernel technology to overcome the drawback of SVM: slow training speed. Firstly, in order to improve the adaptive performance of Gaussian Radial Basis Function (RBF), the parameter determining the nonlinear mapping was optimized on the basis of Kernel target alignment. Then, the obtained Kernel Function was used as the basis kernel of Multiple Kernel Learning (MKL) with slack variable that could solve the over-fitting problem. However, the slack variable also brings the error into the result. Therefore, a soft-margin MKL was proposed to balance the margin against the error. Moreover, the relatively iterative algorithm was used to solve the combination coefficients and hyper-plane equations. Experimental results show that the proposed algorithm can acquire an accuracy of 90% for five kinds of emotions including happiness, sadness, anger, fear and neutral. Compared with KPCA+CCA and PIM-FSVM, the proposed algorithm has the highest accuracy.

CMS Muon Alignment: System Description and first results

CERN Document Server

Sobron, M

2008-01-01

The CMS detector has been instrumented with a precise and complex opto-mechanical alignment subsystem that provides a common reference frame between Tracker and Muon detection systems by means of a net of laser beams. The system allows a continuous and accurate monitoring of the muon chambers positions with respect to the Tracker body. Preliminary results of operation during the test of the CMS 4T solenoid magnet, performed in 2006, are presented. These measurements complement the information provided by the use of survey techniques and the results of alignment algorithms based on muon tracks crossing the detector.

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

International Nuclear Information System (INIS)

Goettfert, Tobias

2010-01-01

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 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 χ 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.)

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.)

Measuring the visual salience of alignments by their non-accidentalness.

Science.gov (United States)

Blusseau, S; Carboni, A; Maiche, A; Morel, J M; Grompone von Gioi, R

2016-09-01

Quantitative approaches are part of the understanding of contour integration and the Gestalt law of good continuation. The present study introduces a new quantitative approach based on the a contrario theory, which formalizes the non-accidentalness principle for good continuation. This model yields an ideal observer algorithm, able to detect non-accidental alignments in Gabor patterns. More precisely, this parameterless algorithm associates with each candidate percept a measure, the Number of False Alarms (NFA), quantifying its degree of masking. To evaluate the approach, we compared this ideal observer with the human attentive performance on three experiments of straight contours detection in arrays of Gabor patches. The experiments showed a strong correlation between the detectability of the target stimuli and their degree of non-accidentalness, as measured by our model. What is more, the algorithm's detection curves were very similar to the ones of human subjects. This fact seems to validate our proposed measurement method as a convenient way to predict the visibility of alignments. This framework could be generalized to other Gestalts. Copyright © 2015 Elsevier Ltd. All rights reserved.

Exact Solutions for Internuclear Vectors and Backbone Dihedral Angles from NH Residual Dipolar Couplings in Two Media, and their Application in a Systematic Search Algorithm for Determining Protein Backbone Structure

International Nuclear Information System (INIS)

Wang Lincong; Donald, Bruce Randall

2004-01-01

We have derived a quartic equation for computing the direction of an internuclear vector from residual dipolar couplings (RDCs) measured in two aligning media, and two simple trigonometric equations for computing the backbone (φ,ψ) angles from two backbone vectors in consecutive peptide planes. These equations make it possible to compute, exactly and in constant time, the backbone (φ,ψ) angles for a residue from RDCs in two media on any single backbone vector type. Building upon these exact solutions we have designed a novel algorithm for determining a protein backbone substructure consisting of α-helices and β-sheets. Our algorithm employs a systematic search technique to refine the conformation of both α-helices and β-sheets and to determine their orientations using exclusively the angular restraints from RDCs. The algorithm computes the backbone substructure employing very sparse distance restraints between pairs of α-helices and β-sheets refined by the systematic search. The algorithm has been demonstrated on the protein human ubiquitin using only backbone NH RDCs, plus twelve hydrogen bonds and four NOE distance restraints. Further, our results show that both the global orientations and the conformations of α-helices and β-strands can be determined with high accuracy using only two RDCs per residue. The algorithm requires, as its input, backbone resonance assignments, the identification of α-helices and β-sheets as well as sparse NOE distance and hydrogen bond restraints.Abbreviations: NMR - nuclear magnetic resonance; RDC - residual dipolar coupling; NOE - nuclear Overhauser effect; SVD - singular value decomposition; DFS - depth-first search; RMSD - root mean square deviation; POF - principal order frame; PDB - protein data bank; SA - simulated annealing; MD - molecular dynamics

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

Spike Pattern Recognition for Automatic Collimation Alignment

CERN Document Server

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

2017-01-01

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

Methods in ALFA Alignment

CERN Document Server

Melendez, Jordan

2014-01-01

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

Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix.

Directory of Open Access Journals (Sweden)

Jakob H Havgaard

2007-10-01

Full Text Available It has become clear that noncoding RNAs (ncRNA play important roles in cells, and emerging studies indicate that there might be a large number of unknown ncRNAs in mammalian genomes. There exist computational methods that can be used to search for ncRNAs by comparing sequences from different genomes. One main problem with these methods is their computational complexity, and heuristics are therefore employed. Two heuristics are currently very popular: pre-folding and pre-aligning. However, these heuristics are not ideal, as pre-aligning is dependent on sequence similarity that may not be present and pre-folding ignores the comparative information. Here, pruning of the dynamical programming matrix is presented as an alternative novel heuristic constraint. All subalignments that do not exceed a length-dependent minimum score are discarded as the matrix is filled out, thus giving the advantage of providing the constraints dynamically. This has been included in a new implementation of the FOLDALIGN algorithm for pairwise local or global structural alignment of RNA sequences. It is shown that time and memory requirements are dramatically lowered while overall performance is maintained. Furthermore, a new divide and conquer method is introduced to limit the memory requirement during global alignment and backtrack of local alignment. All branch points in the computed RNA structure are found and used to divide the structure into smaller unbranched segments. Each segment is then realigned and backtracked in a normal fashion. Finally, the FOLDALIGN algorithm has also been updated with a better memory implementation and an improved energy model. With these improvements in the algorithm, the FOLDALIGN software package provides the molecular biologist with an efficient and user-friendly tool for searching for new ncRNAs. The software package is available for download at http://foldalign.ku.dk.

Prediction of molecular alignment of nucleic acids in aligned media

International Nuclear Information System (INIS)

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

2006-01-01

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

Automatic Image Alignment and Stitching of Medical Images with Seam Blending

OpenAIRE

Abhinav Kumar; Raja Sekhar Bandaru; B Madhusudan Rao; Saket Kulkarni; Nilesh Ghatpande

2010-01-01

This paper proposes an algorithm which automatically aligns and stitches the component medical images (fluoroscopic) with varying degrees of overlap into a single composite image. The alignment method is based on similarity measure between the component images. As applied here the technique is intensity based rather than feature based. It works well in domains where feature based methods have difficulty, yet more robust than traditional correlation. Component images are stitched together usin...

Application of genetic algorithm in radio ecological models parameter determination

International Nuclear Information System (INIS)

Pantelic, G.

2006-01-01

The method of genetic algorithms was used to determine the biological half-life of 137 Cs in cow milk after the accident in Chernobyl. Methodologically genetic algorithms are based on the fact that natural processes tend to optimize themselves and therefore this method should be more efficient in providing optimal solutions in the modeling of radio ecological and environmental events. The calculated biological half-life of 137 Cs in milk is (32 ± 3) days and transfer coefficient from grass to milk is (0.019 ± 0.005). (authors)

Desktop aligner for fabrication of multilayer microfluidic devices.

Science.gov (United States)

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

2015-07-01

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

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

DEFF Research Database (Denmark)

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

2005-01-01

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

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

International Nuclear Information System (INIS)

Xu, Dinghua; Ge, Meibao

2012-01-01

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. (paper)

Iterative Stable Alignment and Clustering of 2D Transmission Electron Microscope Images

Science.gov (United States)

Yang, Zhengfan; Fang, Jia; Chittuluru, Johnathan; Asturias, Francisco J.; Penczek, Pawel A.

2012-01-01

SUMMARY Identification of homogeneous subsets of images in a macromolecular electron microscopy (EM) image data set is a critical step in single-particle analysis. The task is handled by iterative algorithms, whose performance is compromised by the compounded limitations of image alignment and K-means clustering. Here we describe an approach, iterative stable alignment and clustering (ISAC) that, relying on a new clustering method and on the concepts of stability and reproducibility, can extract validated, homogeneous subsets of images. ISAC requires only a small number of simple parameters and, with minimal human intervention, can eliminate bias from two-dimensional image clustering and maximize the quality of group averages that can be used for ab initio three-dimensional structural determination and analysis of macromolecular conformational variability. Repeated testing of the stability and reproducibility of a solution within ISAC eliminates heterogeneous or incorrect classes and introduces critical validation to the process of EM image clustering. PMID:22325773

W-curve alignments for HIV-1 genomic comparisons.

Directory of Open Access Journals (Sweden)

Douglas J Cork

2010-06-01

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

W-curve alignments for HIV-1 genomic comparisons.

Science.gov (United States)

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

2010-06-01

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

KISS for STRAP: user extensions for a protein alignment editor.

Science.gov (United States)

Gille, Christoph; Lorenzen, Stephan; Michalsky, Elke; Frömmel, Cornelius

2003-12-12

The Structural Alignment Program STRAP is a comfortable comprehensive editor and analyzing tool for protein alignments. A wide range of functions related to protein sequences and protein structures are accessible with an intuitive graphical interface. Recent features include mapping of mutations and polymorphisms onto structures and production of high quality figures for publication. Here we address the general problem of multi-purpose program packages to keep up with the rapid development of bioinformatical methods and the demand for specific program functions. STRAP was remade implementing a novel design which aims at Keeping Interfaces in STRAP Simple (KISS). KISS renders STRAP extendable to bio-scientists as well as to bio-informaticians. Scientists with basic computer skills are capable of implementing statistical methods or embedding existing bioinformatical tools in STRAP themselves. For bio-informaticians STRAP may serve as an environment for rapid prototyping and testing of complex algorithms such as automatic alignment algorithms or phylogenetic methods. Further, STRAP can be applied as an interactive web applet to present data related to a particular protein family and as a teaching tool. JAVA-1.4 or higher. http://www.charite.de/bioinf/strap/

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

Science.gov (United States)

Faust, Gregory G; Hall, Ira M

2012-10-01

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

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.

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.

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

Science.gov (United States)

Soares, Inês; Goios, Ana; Amorim, António

2012-01-01

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

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

Directory of Open Access Journals (Sweden)

Alachiotis Nikolaos

2012-08-01

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

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.

Advanced Dispersed Fringe Sensing Algorithm for Coarse Phasing Segmented Mirror Telescopes

Science.gov (United States)

Spechler, Joshua A.; Hoppe, Daniel J.; Sigrist, Norbert; Shi, Fang; Seo, Byoung-Joon; Bikkannavar, Siddarayappa A.

2013-01-01

Segment mirror phasing, a critical step of segment mirror alignment, requires the ability to sense and correct the relative pistons between segments from up to a few hundred microns to a fraction of wavelength in order to bring the mirror system to its full diffraction capability. When sampling the aperture of a telescope, using auto-collimating flats (ACFs) is more economical. The performance of a telescope with a segmented primary mirror strongly depends on how well those primary mirror segments can be phased. One such process to phase primary mirror segments in the axial piston direction is dispersed fringe sensing (DFS). DFS technology can be used to co-phase the ACFs. DFS is essentially a signal fitting and processing operation. It is an elegant method of coarse phasing segmented mirrors. DFS performance accuracy is dependent upon careful calibration of the system as well as other factors such as internal optical alignment, system wavefront errors, and detector quality. Novel improvements to the algorithm have led to substantial enhancements in DFS performance. The Advanced Dispersed Fringe Sensing (ADFS) Algorithm is designed to reduce the sensitivity to calibration errors by determining the optimal fringe extraction line. Applying an angular extraction line dithering procedure and combining this dithering process with an error function while minimizing the phase term of the fitted signal, defines in essence the ADFS algorithm.

Performance Analysis of Combined Methods of Genetic Algorithm and K-Means Clustering in Determining the Value of Centroid

Science.gov (United States)

Adya Zizwan, Putra; Zarlis, Muhammad; Budhiarti Nababan, Erna

2017-12-01

The determination of Centroid on K-Means Algorithm directly affects the quality of the clustering results. Determination of centroid by using random numbers has many weaknesses. The GenClust algorithm that combines the use of Genetic Algorithms and K-Means uses a genetic algorithm to determine the centroid of each cluster. The use of the GenClust algorithm uses 50% chromosomes obtained through deterministic calculations and 50% is obtained from the generation of random numbers. This study will modify the use of the GenClust algorithm in which the chromosomes used are 100% obtained through deterministic calculations. The results of this study resulted in performance comparisons expressed in Mean Square Error influenced by centroid determination on K-Means method by using GenClust method, modified GenClust method and also classic K-Means.

Angular momentum alignment in molecular beam scattering

International Nuclear Information System (INIS)

Treffers, M.A.

1985-01-01

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

Heat-Treatment-Responsive Proteins in Different Developmental Stages of Tomato Pollen Detected by Targeted Mass Accuracy Precursor Alignment (tMAPA).

Science.gov (United States)

Chaturvedi, Palak; Doerfler, Hannes; Jegadeesan, Sridharan; Ghatak, Arindam; Pressman, Etan; Castillejo, Maria Angeles; Wienkoop, Stefanie; Egelhofer, Volker; Firon, Nurit; Weckwerth, Wolfram

2015-11-06

Recently, we have developed a quantitative shotgun proteomics strategy called mass accuracy precursor alignment (MAPA). The MAPA algorithm uses high mass accuracy to bin mass-to-charge (m/z) ratios of precursor ions from LC-MS analyses, determines their intensities, and extracts a quantitative sample versus m/z ratio data alignment matrix from a multitude of samples. Here, we introduce a novel feature of this algorithm that allows the extraction and alignment of proteotypic peptide precursor ions or any other target peptide from complex shotgun proteomics data for accurate quantification of unique proteins. This strategy circumvents the problem of confusing the quantification of proteins due to indistinguishable protein isoforms by a typical shotgun proteomics approach. We applied this strategy to a comparison of control and heat-treated tomato pollen grains at two developmental stages, post-meiotic and mature. Pollen is a temperature-sensitive tissue involved in the reproductive cycle of plants and plays a major role in fruit setting and yield. By LC-MS-based shotgun proteomics, we identified more than 2000 proteins in total for all different tissues. By applying the targeted MAPA data-processing strategy, 51 unique proteins were identified as heat-treatment-responsive protein candidates. The potential function of the identified candidates in a specific developmental stage is discussed.

GapMis: a tool for pairwise sequence alignment with a single gap.

Science.gov (United States)

Flouri, Tomás; Frousios, Kimon; Iliopoulos, Costas S; Park, Kunsoo; Pissis, Solon P; Tischler, German

2013-08-01

Pairwise sequence alignment has received a new motivation due to the advent of recent patents in next-generation sequencing technologies, particularly so for the application of re-sequencing---the assembly of a genome directed by a reference sequence. After the fast alignment between a factor of the reference sequence and a high-quality fragment of a short read by a short-read alignment programme, an important problem is to find the alignment between a relatively short succeeding factor of the reference sequence and the remaining low-quality part of the read allowing a number of mismatches and the insertion of a single gap in the alignment. We present GapMis, a tool for pairwise sequence alignment with a single gap. It is based on a simple algorithm, which computes a different version of the traditional dynamic programming matrix. The presented experimental results demonstrate that GapMis is more suitable and efficient than most popular tools for this task.

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

Science.gov (United States)

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

2017-07-10

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

Detector Alignment Studies for the CMS Experiment

CERN Document Server

Lampén, Tapio

2007-01-01

This thesis presen ts studies related to trac k-based alignmen t for the future CMS exp erimen t at CERN. Excellen t geometric alignmen t is crucial to fully bene t from the outstanding resolution of individual sensors. The large num ber of sensors mak es it dicult in CMS to utilize computationally demanding alignmen t algorithms. A computationally ligh t alignmen t algorithm, called the Hits and Impact Points algorithm (HIP), is dev elop ed and studied. It is based on minimization of the hit residuals. It can be applied to individual sensors or to comp osite objects. All six alignmen t parameters (three translations and three rotations), or their subgroup can be considered. The algorithm is exp ected to be particularly suitable for the alignmen t of the innermost part of CMS, the pixel detector, during its early operation, but can be easily utilized to align other parts of CMS also. The HIP algorithm is applied to sim ulated CMS data and real data measured with a test-b eam setup. The sim ulation studies dem...

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

Science.gov (United States)

Edgar, Robert C

2004-01-01

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

Application of fast Fourier transform cross-correlation and mass spectrometry data for accurate alignment of chromatograms.

Science.gov (United States)

Zheng, Yi-Bao; Zhang, Zhi-Min; Liang, Yi-Zeng; Zhan, De-Jian; Huang, Jian-Hua; Yun, Yong-Huan; Xie, Hua-Lin

2013-04-19

Chromatography has been established as one of the most important analytical methods in the modern analytical laboratory. However, preprocessing of the chromatograms, especially peak alignment, is usually a time-consuming task prior to extracting useful information from the datasets because of the small unavoidable differences in the experimental conditions caused by minor changes and drift. Most of the alignment algorithms are performed on reduced datasets using only the detected peaks in the chromatograms, which means a loss of data and introduces the problem of extraction of peak data from the chromatographic profiles. These disadvantages can be overcome by using the full chromatographic information that is generated from hyphenated chromatographic instruments. A new alignment algorithm called CAMS (Chromatogram Alignment via Mass Spectra) is present here to correct the retention time shifts among chromatograms accurately and rapidly. In this report, peaks of each chromatogram were detected based on Continuous Wavelet Transform (CWT) with Haar wavelet and were aligned against the reference chromatogram via the correlation of mass spectra. The aligning procedure was accelerated by Fast Fourier Transform cross correlation (FFT cross correlation). This approach has been compared with several well-known alignment methods on real chromatographic datasets, which demonstrates that CAMS can preserve the shape of peaks and achieve a high quality alignment result. Furthermore, the CAMS method was implemented in the Matlab language and available as an open source package at http://www.github.com/matchcoder/CAMS. Copyright © 2013. Published by Elsevier B.V.

Classical Methods and Calculation Algorithms for Determining Lime Requirements

Directory of Open Access Journals (Sweden)

André Guarçoni

Full Text Available ABSTRACT The methods developed for determination of lime requirements (LR are based on widely accepted principles. However, the formulas used for calculation have evolved little over recent decades, and in some cases there are indications of their inadequacy. The aim of this study was to compare the lime requirements calculated by three classic formulas and three algorithms, defining those most appropriate for supplying Ca and Mg to coffee plants and the smaller possibility of causing overliming. The database used contained 600 soil samples, which were collected in coffee plantings. The LR was estimated by the methods of base saturation, neutralization of Al3+, and elevation of Ca2+ and Mg2+ contents (two formulas and by the three calculation algorithms. Averages of the lime requirements were compared, determining the frequency distribution of the 600 lime requirements (LR estimated through each calculation method. In soils with low cation exchange capacity at pH 7, the base saturation method may fail to adequately supply the plants with Ca and Mg in many situations, while the method of Al3+ neutralization and elevation of Ca2+ and Mg2+ contents can result in the calculation of application rates that will increase the pH above the suitable range. Among the methods studied for calculating lime requirements, the algorithm that predicts reaching a defined base saturation, with adequate Ca and Mg supply and the maximum application rate limited to the H+Al value, proved to be the most efficient calculation method, and it can be recommended for use in numerous crops conditions.

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

Science.gov (United States)

Lizotte, Todd E.

2011-10-01

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

Black hole algorithm for determining model parameter in self-potential data

Science.gov (United States)

Sungkono; Warnana, Dwa Desa

2018-01-01

Analysis of self-potential (SP) data is increasingly popular in geophysical method due to its relevance in many cases. However, the inversion of SP data is often highly nonlinear. Consequently, local search algorithms commonly based on gradient approaches have often failed to find the global optimum solution in nonlinear problems. Black hole algorithm (BHA) was proposed as a solution to such problems. As the name suggests, the algorithm was constructed based on the black hole phenomena. This paper investigates the application of BHA to solve inversions of field and synthetic self-potential (SP) data. The inversion results show that BHA accurately determines model parameters and model uncertainty. This indicates that BHA is highly potential as an innovative approach for SP data inversion.

Adaptive Processing for Sequence Alignment

KAUST Repository

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

2012-01-01

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

Adaptive Processing for Sequence Alignment

KAUST Repository

Zidan, Mohammed A.

2012-01-26

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2016-11-10

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

Sequential Optimization of Global Sequence Alignments Relative to Different Cost Functions

KAUST Repository

Odat, Enas M.

2011-01-01

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

Aligning the unalignable: bacteriophage whole genome alignments.

Science.gov (United States)

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

2016-01-13

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

GATA: A graphic alignment tool for comparative sequenceanalysis

Energy Technology Data Exchange (ETDEWEB)

Nix, David A.; Eisen, Michael B.

2005-01-01

Several problems exist with current methods used to align DNA sequences for comparative sequence analysis. Most dynamic programming algorithms assume that conserved sequence elements are collinear. This assumption appears valid when comparing orthologous protein coding sequences. Functional constraints on proteins provide strong selective pressure against sequence inversions, and minimize sequence duplications and feature shuffling. For non-coding sequences this collinearity assumption is often invalid. For example, enhancers contain clusters of transcription factor binding sites that change in number, orientation, and spacing during evolution yet the enhancer retains its activity. Dotplot analysis is often used to estimate non-coding sequence relatedness. Yet dot plots do not actually align sequences and thus cannot account well for base insertions or deletions. Moreover, they lack an adequate statistical framework for comparing sequence relatedness and are limited to pairwise comparisons. Lastly, dot plots and dynamic programming text outputs fail to provide an intuitive means for visualizing DNA alignments.

Pattern analysis of aligned nanowires in a microchannel

International Nuclear Information System (INIS)

Jeon, Young Jin; Kang, Hyun Wook; Ko, Seung Hwan; Sung, Hyung Jin

2013-01-01

An image processing method for evaluating the quality of nanowire alignment in a microchannel is described. A solution containing nanowires flowing into a microchannel will tend to deposit the nanowires on the bottom surface of the channel via near-wall shear flows. The deposited nanowires generally form complex directional structures along the direction of flow, and the physical properties of these structures depend on the structural morphology, including the alignment quality. A quantitative analysis approach to characterizing the nanowire alignment is needed to estimate the useful features of the nanowire structures. This analysis consists of several image processing methods, including ridge detection, texton analysis and autocorrelation function (ACF) calculation. The ridge detection method improved the ACF by extracting nanowire frames 1–2 pixels in width. Dilation filters were introduced to permit a comparison of the ACF results calculated from different images, regardless of the nanowire orientation. An ACF based on the FFT was then calculated over a square interrogation window. The alignment angle probability distribution was obtained using texton analysis. Monte Carlo simulations of artificially generated images were carried out, and the new algorithm was applied to images collected using two types of microscopy. (paper)

TU-D-209-03: Alignment of the Patient Graphic Model Using Fluoroscopic Images for Skin Dose Mapping

Energy Technology Data Exchange (ETDEWEB)

Oines, A; Oines, A; Kilian-Meneghin, J; Karthikeyan, B; Rudin, S; Bednarek, D [University at Buffalo (SUNY) School of Med., Buffalo, NY (United States)

2016-06-15

Purpose: The Dose Tracking System (DTS) was developed to provide realtime feedback of skin dose and dose rate during interventional fluoroscopic procedures. A color map on a 3D graphic of the patient represents the cumulative dose distribution on the skin. Automated image correlation algorithms are described which use the fluoroscopic procedure images to align and scale the patient graphic for more accurate dose mapping. Methods: Currently, the DTS employs manual patient graphic selection and alignment. To improve the accuracy of dose mapping and automate the software, various methods are explored to extract information about the beam location and patient morphology from the procedure images. To match patient anatomy with a reference projection image, preprocessing is first used, including edge enhancement, edge detection, and contour detection. Template matching algorithms from OpenCV are then employed to find the location of the beam. Once a match is found, the reference graphic is scaled and rotated to fit the patient, using image registration correlation functions in Matlab. The algorithm runs correlation functions for all points and maps all correlation confidences to a surface map. The highest point of correlation is used for alignment and scaling. The transformation data is saved for later model scaling. Results: Anatomic recognition is used to find matching features between model and image and image registration correlation provides for alignment and scaling at any rotation angle with less than onesecond runtime, and at noise levels in excess of 150% of those found in normal procedures. Conclusion: The algorithm provides the necessary scaling and alignment tools to improve the accuracy of dose distribution mapping on the patient graphic with the DTS. Partial support from NIH Grant R01-EB002873 and Toshiba Medical Systems Corp.

TU-D-209-03: Alignment of the Patient Graphic Model Using Fluoroscopic Images for Skin Dose Mapping

International Nuclear Information System (INIS)

Oines, A; Oines, A; Kilian-Meneghin, J; Karthikeyan, B; Rudin, S; Bednarek, D

2016-01-01

Purpose: The Dose Tracking System (DTS) was developed to provide realtime feedback of skin dose and dose rate during interventional fluoroscopic procedures. A color map on a 3D graphic of the patient represents the cumulative dose distribution on the skin. Automated image correlation algorithms are described which use the fluoroscopic procedure images to align and scale the patient graphic for more accurate dose mapping. Methods: Currently, the DTS employs manual patient graphic selection and alignment. To improve the accuracy of dose mapping and automate the software, various methods are explored to extract information about the beam location and patient morphology from the procedure images. To match patient anatomy with a reference projection image, preprocessing is first used, including edge enhancement, edge detection, and contour detection. Template matching algorithms from OpenCV are then employed to find the location of the beam. Once a match is found, the reference graphic is scaled and rotated to fit the patient, using image registration correlation functions in Matlab. The algorithm runs correlation functions for all points and maps all correlation confidences to a surface map. The highest point of correlation is used for alignment and scaling. The transformation data is saved for later model scaling. Results: Anatomic recognition is used to find matching features between model and image and image registration correlation provides for alignment and scaling at any rotation angle with less than onesecond runtime, and at noise levels in excess of 150% of those found in normal procedures. Conclusion: The algorithm provides the necessary scaling and alignment tools to improve the accuracy of dose distribution mapping on the patient graphic with the DTS. Partial support from NIH Grant R01-EB002873 and Toshiba Medical Systems Corp.

Antares automatic beam alignment system

International Nuclear Information System (INIS)

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

1980-01-01

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

A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases.

Science.gov (United States)

Jain, Chirag; Dilthey, Alexander; Koren, Sergey; Aluru, Srinivas; Phillippy, Adam M

2018-04-30

Emerging single-molecule sequencing technologies from Pacific Biosciences and Oxford Nanopore have revived interest in long-read mapping algorithms. Alignment-based seed-and-extend methods demonstrate good accuracy, but face limited scalability, while faster alignment-free methods typically trade decreased precision for efficiency. In this article, we combine a fast approximate read mapping algorithm based on minimizers with a novel MinHash identity estimation technique to achieve both scalability and precision. In contrast to prior methods, we develop a mathematical framework that defines the types of mapping targets we uncover, establish probabilistic estimates of p-value and sensitivity, and demonstrate tolerance for alignment error rates up to 20%. With this framework, our algorithm automatically adapts to different minimum length and identity requirements and provides both positional and identity estimates for each mapping reported. For mapping human PacBio reads to the hg38 reference, our method is 290 × faster than Burrows-Wheeler Aligner-MEM with a lower memory footprint and recall rate of 96%. We further demonstrate the scalability of our method by mapping noisy PacBio reads (each ≥5 kbp in length) to the complete NCBI RefSeq database containing 838 Gbp of sequence and >60,000 genomes.

A tool for aligning event logs and prescriptive process models through automated planning

OpenAIRE

De Leoni, M.; Lanciano, G.; Marrella, A.

2017-01-01

In Conformance Checking, alignment is the problem of detecting and repairing nonconformity between the actual execution of a business process, as recorded in an event log, and the model of the same process. Literature proposes solutions for the alignment problem that are implementations of planning algorithms built ad-hoc for the specific problem. Unfortunately, in the era of big data, these ad-hoc implementations do not scale sufficiently compared with wellestablished planning systems. In th...

Alignment of ICNP? 2.0 Ontology and a proposed INCP? Brazilian Ontology1

OpenAIRE

Carvalho, Carina Maris Gaspar; Cubas, Marcia Regina; Malucelli, Andreia; da N?brega, Maria Miriam Lima

2014-01-01

OBJECTIVE: to align the International Classification for Nursing Practice (ICNP®) Version 2.0 ontology and a proposed INCP® Brazilian Ontology.METHOD: document-based, exploratory and descriptive study, the empirical basis of which was provided by the ICNP® 2.0 Ontology and the INCP® Brazilian Ontology. The ontology alignment was performed using a computer tool with algorithms to identify correspondences between concepts, which were organized and analyzed according to their presence or absence...

Alignment of the ATLAS Silicon Tracker and measurement of the top quark mass

CERN Document Server

Escobar, C; Marti i García, S

2010-01-01

The Large Hadron Collider (LHC) era started with its first proton-proton collisions produced in November 2009 at the CERN laboratory. In the coming decade, the high energy physics program will be dominated by the LHC and its experiments. Discoveries such as the Higgs or supersymmetric particles are some of the dreams that hopefully the LHC will bring us. This thesis is framed within the ATLAS experiment, which is one of the four large detectors located at the LHC. The work presented in this thesis is divided in two parts. The first part is dedicated to the alignment of the ATLAS silicon tracking detector using the GlobalChi2 algorithm, which is the actual baseline algorithm. It covers performance studies with Monte Carlo samples with a realistic detector description, with real cosmic rays as well as with first LHC collisions at 900 GeV. The main achievement was the production of a set of alignment constants for the real ATLAS detector. Those constants were obtained from the alignment of real cosmic ray data, ...

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

Directory of Open Access Journals (Sweden)

Inês Soares

2012-01-01

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

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

Science.gov (United States)

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

2017-01-29

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

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

Directory of Open Access Journals (Sweden)

Claros M Gonzalo

2010-06-01

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

Floyd-warshall algorithm to determine the shortest path based on android

Science.gov (United States)

Ramadiani; Bukhori, D.; Azainil; Dengen, N.

2018-04-01

The development of technology has made all areas of life easier now, one of which is the ease of obtaining geographic information. The use of geographic information may vary according to need, for example, the digital map learning, navigation systems, observations area, and much more. With the support of adequate infrastructure, almost no one will ever get lost to a destination even to foreign places or that have never been visited before. The reasons why many institutions and business entities use technology to improve services to consumers and to streamline the production process undertaken and so forth. Speaking of the efficient, there are many elements related to efficiency in navigation systems, and one of them is the efficiency in terms of distance. The shortest distance determination algorithm required in this research is used Floyd-Warshall Algorithm. Floyd-Warshall algorithm is the algorithm to find the fastest path and the shortest distance between 2 nodes, while the program is intended to find the path of more than 2 nodes.

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

Science.gov (United States)

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

2015-10-27

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

Multiple Whole Genome Alignments and Novel Biomedical Applicationsat the VISTA Portal

Energy Technology Data Exchange (ETDEWEB)

Brudno, Michael; Poliakov, Alexander; Minovitsky, Simon; Ratnere,Igor; Dubchak, Inna

2007-02-01

The VISTA portal for comparative genomics is designed togive biomedical scientists a unified set of tools to lead them from theraw DNA sequences through the alignment and annotation to thevisualization of the results. The VISTA portal also hosts alignments of anumber of genomes computed by our group, allowing users to study regionsof their interest without having to manually download the individualsequences. Here we describe various algorithmic and functionalimprovements implemented in the VISTA portal over the last two years. TheVISTA Portal is accessible at http://genome.lbl.gov/vista.

Minimal-effort planning of active alignment processes for beam-shaping optics

Science.gov (United States)

Haag, Sebastian; Schranner, Matthias; Müller, Tobias; Zontar, Daniel; Schlette, Christian; Losch, Daniel; Brecher, Christian; Roßmann, Jürgen

2015-03-01

In science and industry, the alignment of beam-shaping optics is usually a manual procedure. Many industrial applications utilizing beam-shaping optical systems require more scalable production solutions and therefore effort has been invested in research regarding the automation of optics assembly. In previous works, the authors and other researchers have proven the feasibility of automated alignment of beam-shaping optics such as collimation lenses or homogenization optics. Nevertheless, the planning efforts as well as additional knowledge from the fields of automation and control required for such alignment processes are immense. This paper presents a novel approach of planning active alignment processes of beam-shaping optics with the focus of minimizing the planning efforts for active alignment. The approach utilizes optical simulation and the genetic programming paradigm from computer science for automatically extracting features from a simulated data basis with a high correlation coefficient regarding the individual degrees of freedom of alignment. The strategy is capable of finding active alignment strategies that can be executed by an automated assembly system. The paper presents a tool making the algorithm available to end-users and it discusses the results of planning the active alignment of the well-known assembly of a fast-axis collimator. The paper concludes with an outlook on the transferability to other use cases such as application specific intensity distributions which will benefit from reduced planning efforts.

TotalReCaller: improved accuracy and performance via integrated alignment and base-calling.

Science.gov (United States)

Menges, Fabian; Narzisi, Giuseppe; Mishra, Bud

2011-09-01

Currently, re-sequencing approaches use multiple modules serially to interpret raw sequencing data from next-generation sequencing platforms, while remaining oblivious to the genomic information until the final alignment step. Such approaches fail to exploit the full information from both raw sequencing data and the reference genome that can yield better quality sequence reads, SNP-calls, variant detection, as well as an alignment at the best possible location in the reference genome. Thus, there is a need for novel reference-guided bioinformatics algorithms for interpreting analog signals representing sequences of the bases ({A, C, G, T}), while simultaneously aligning possible sequence reads to a source reference genome whenever available. Here, we propose a new base-calling algorithm, TotalReCaller, to achieve improved performance. A linear error model for the raw intensity data and Burrows-Wheeler transform (BWT) based alignment are combined utilizing a Bayesian score function, which is then globally optimized over all possible genomic locations using an efficient branch-and-bound approach. The algorithm has been implemented in soft- and hardware [field-programmable gate array (FPGA)] to achieve real-time performance. Empirical results on real high-throughput Illumina data were used to evaluate TotalReCaller's performance relative to its peers-Bustard, BayesCall, Ibis and Rolexa-based on several criteria, particularly those important in clinical and scientific applications. Namely, it was evaluated for (i) its base-calling speed and throughput, (ii) its read accuracy and (iii) its specificity and sensitivity in variant calling. A software implementation of TotalReCaller as well as additional information, is available at: http://bioinformatics.nyu.edu/wordpress/projects/totalrecaller/ fabian.menges@nyu.edu.

Track based alignment of the Mu3e detector

Energy Technology Data Exchange (ETDEWEB)

Hartenstein, Ulrich [Institut fuer Kernphysik, Universitaet Mainz (Germany)

2016-07-01

The Mu3e experiment searches for the lepton flavor violating decay μ{sup +} → e{sup +}e{sup -}e{sup +} with a sensitivity goal for the branching fraction of better than 10{sup -16}. This process is heavily supressed in the standard model of particle physics (BR < 10{sup -50}) which makes an observation of this decay a clear indication of new physics. For track reconstruction, four barrel shaped layers consisting of about 3000 high-voltage monolithic active pixel sensors (HV-MAPS) are used. The position, orientation and possible deformations of these sensors must be known to greater precision than the assembly tolerances. A track based alignment via the General Broken Lines fit and the Millepede-II algorithm will be used to achieve this precision in the final detector. The talk discusses a study of the required alignment precision and preparations for aligning the detector using a detailed simulation.

GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters.

Science.gov (United States)

Sela, Itamar; Ashkenazy, Haim; Katoh, Kazutaka; Pupko, Tal

2015-07-01

Inference of multiple sequence alignments (MSAs) is a critical part of phylogenetic and comparative genomics studies. However, from the same set of sequences different MSAs are often inferred, depending on the methodologies used and the assumed parameters. Much effort has recently been devoted to improving the ability to identify unreliable alignment regions. Detecting such unreliable regions was previously shown to be important for downstream analyses relying on MSAs, such as the detection of positive selection. Here we developed GUIDANCE2, a new integrative methodology that accounts for: (i) uncertainty in the process of indel formation, (ii) uncertainty in the assumed guide tree and (iii) co-optimal solutions in the pairwise alignments, used as building blocks in progressive alignment algorithms. We compared GUIDANCE2 with seven methodologies to detect unreliable MSA regions using extensive simulations and empirical benchmarks. We show that GUIDANCE2 outperforms all previously developed methodologies. Furthermore, GUIDANCE2 also provides a set of alternative MSAs which can be useful for downstream analyses. The novel algorithm is implemented as a web-server, available at: http://guidance.tau.ac.il. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Least Squares Approach to the Alignment of the Generic High Precision Tracking System

Science.gov (United States)

de Renstrom, Pawel Brückman; Haywood, Stephen

2006-04-01

A least squares method to solve a generic alignment problem of a high granularity tracking system is presented. The algorithm is based on an analytical linear expansion and allows for multiple nested fits, e.g. imposing a common vertex for groups of particle tracks is of particular interest. We present a consistent and complete recipe to impose constraints on either implicit or explicit parameters. The method has been applied to the full simulation of a subset of the ATLAS silicon tracking system. The ultimate goal is to determine ≈35,000 degrees of freedom (DoF's). We present a limited scale exercise exploring various aspects of the solution.

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

KAUST Repository

Chiu, Ming-Hui; Zhang, Chendong; Shiu, Hung-Wei; Chuu, Chih-Piao; Chen, Chang-Hsiao; Chang, Chih-Yuan S.; Chen, Chia-Hao; Chou, Mei-Yin; Shih, Chih-Kang; Li, Lain-Jong

2015-01-01

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.

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.

Efficient Constrained Local Model Fitting for Non-Rigid Face Alignment.

Science.gov (United States)

Lucey, Simon; Wang, Yang; Cox, Mark; Sridharan, Sridha; Cohn, Jeffery F

2009-11-01

Active appearance models (AAMs) have demonstrated great utility when being employed for non-rigid face alignment/tracking. The "simultaneous" algorithm for fitting an AAM achieves good non-rigid face registration performance, but has poor real time performance (2-3 fps). The "project-out" algorithm for fitting an AAM achieves faster than real time performance (> 200 fps) but suffers from poor generic alignment performance. In this paper we introduce an extension to a discriminative method for non-rigid face registration/tracking referred to as a constrained local model (CLM). Our proposed method is able to achieve superior performance to the "simultaneous" AAM algorithm along with real time fitting speeds (35 fps). We improve upon the canonical CLM formulation, to gain this performance, in a number of ways by employing: (i) linear SVMs as patch-experts, (ii) a simplified optimization criteria, and (iii) a composite rather than additive warp update step. Most notably, our simplified optimization criteria for fitting the CLM divides the problem of finding a single complex registration/warp displacement into that of finding N simple warp displacements. From these N simple warp displacements, a single complex warp displacement is estimated using a weighted least-squares constraint. Another major advantage of this simplified optimization lends from its ability to be parallelized, a step which we also theoretically explore in this paper. We refer to our approach for fitting the CLM as the "exhaustive local search" (ELS) algorithm. Experiments were conducted on the CMU Multi-PIE database.

Validation of the CLIC alignment strategy on short range

CERN Document Server

Mainaud Durand, H; Griffet, S; Kemppinen, J; Rude, V; Sosin, M

2012-01-01

The pre-alignment of CLIC consists of aligning the components of linacs and beam delivery systems (BDS) in the most accurate possible way, so that a first pilot beam can circulate and allow the implementation of the beam based alignment. Taking into account the precision and accuracy needed: 10 µm rms over sliding windows of 200m, this pre-alignment must be active and it can be divided into two parts: the determination of a straight reference over 20 km, thanks to a metrological network and the determination of the component positions with respect to this reference, and their adjustment. The second part is the object of the paper, describing the steps of the proposed strategy: firstly the fiducialisation of the different components of CLIC; secondly, the alignment of these components on common supports and thirdly the active alignment of these supports using sensors and actuators. These steps have been validated on a test setup over a length of 4m, and the obtained results are analysed.

A novel image toggle tool for comparison of serial mammograms: automatic density normalization and alignment-development of the tool and initial experience.

Science.gov (United States)

Honda, Satoshi; Tsunoda, Hiroko; Fukuda, Wataru; Saida, Yukihisa

2014-12-01

The purpose is to develop a new image toggle tool with automatic density normalization (ADN) and automatic alignment (AA) for comparing serial digital mammograms (DMGs). We developed an ADN and AA process to compare the images of serial DMGs. In image density normalization, a linear interpolation was applied by taking two points of high- and low-brightness areas. The alignment was calculated by determining the point of the greatest correlation while shifting the alignment between the current and prior images. These processes were performed on a PC with a 3.20-GHz Xeon processor and 8 GB of main memory. We selected 12 suspected breast cancer patients who had undergone screening DMGs in the past. Automatic processing was retrospectively performed on these images. Two radiologists subjectively evaluated them. The process of the developed algorithm took approximately 1 s per image. In our preliminary experience, two images could not be aligned approximately. When they were aligned, image toggling allowed detection of differences between examinations easily. We developed a new tool to facilitate comparative reading of DMGs on a mammography viewing system. Using this tool for toggling comparisons might improve the interpretation efficiency of serial DMGs.

SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.

Science.gov (United States)

Liu, Kevin; Warnow, Tandy J; Holder, Mark T; Nelesen, Serita M; Yu, Jiaye; Stamatakis, Alexandros P; Linder, C Randal

2012-01-01

Highly accurate estimation of phylogenetic trees for large data sets is difficult, in part because multiple sequence alignments must be accurate for phylogeny estimation methods to be accurate. Coestimation of alignments and trees has been attempted but currently only SATé estimates reasonably accurate trees and alignments for large data sets in practical time frames (Liu K., Raghavan S., Nelesen S., Linder C.R., Warnow T. 2009b. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science. 324:1561-1564). Here, we present a modification to the original SATé algorithm that improves upon SATé (which we now call SATé-I) in terms of speed and of phylogenetic and alignment accuracy. SATé-II uses a different divide-and-conquer strategy than SATé-I and so produces smaller more closely related subsets than SATé-I; as a result, SATé-II produces more accurate alignments and trees, can analyze larger data sets, and runs more efficiently than SATé-I. Generally, SATé is a metamethod that takes an existing multiple sequence alignment method as an input parameter and boosts the quality of that alignment method. SATé-II-boosted alignment methods are significantly more accurate than their unboosted versions, and trees based upon these improved alignments are more accurate than trees based upon the original alignments. Because SATé-I used maximum likelihood (ML) methods that treat gaps as missing data to estimate trees and because we found a correlation between the quality of tree/alignment pairs and ML scores, we explored the degree to which SATé's performance depends on using ML with gaps treated as missing data to determine the best tree/alignment pair. We present two lines of evidence that using ML with gaps treated as missing data to optimize the alignment and tree produces very poor results. First, we show that the optimization problem where a set of unaligned DNA sequences is given and the output is the tree and alignment of

Multidimensional Scaling Localization Algorithm in Wireless Sensor Networks

Directory of Open Access Journals (Sweden)

Zhang Dongyang

2014-02-01

Full Text Available Due to the localization algorithm in large-scale wireless sensor network exists shortcomings both in positioning accuracy and time complexity compared to traditional localization algorithm, this paper presents a fast multidimensional scaling location algorithm. By positioning algorithm for fast multidimensional scaling, fast mapping initialization, fast mapping and coordinate transform can get schematic coordinates of node, coordinates Initialize of MDS algorithm, an accurate estimate of the node coordinates and using the PRORUSTES to analysis alignment of the coordinate and final position coordinates of nodes etc. There are four steps, and the thesis gives specific implementation steps of the algorithm. Finally, compared with stochastic algorithms and classical MDS algorithm experiment, the thesis takes application of specific examples. Experimental results show that: the proposed localization algorithm has fast multidimensional scaling positioning accuracy in ensuring certain circumstances, but also greatly improves the speed of operation.

Curve aligning approach for gait authentication based on a wearable accelerometer

International Nuclear Information System (INIS)

Sun, Hu; Yuao, Tao

2012-01-01

Gait authentication based on a wearable accelerometer is a novel biometric which can be used for identity identification, medical rehabilitation and early detection of neurological disorders. The method for matching gait patterns tells heavily on authentication performances. In this paper, curve aligning is introduced as a new method for matching gait patterns and it is compared with correlation and dynamic time warping (DTW). A support vector machine (SVM) is proposed to fuse pattern-matching methods in a decision level. Accelerations collected from ankles of 22 walking subjects are processed for authentications in our experiments. The fusion of curve aligning with backward–forward accelerations and DTW with vertical accelerations promotes authentication performances substantially and consistently. This fusion algorithm is tested repeatedly. Its mean and standard deviation of equal error rates are 0.794% and 0.696%, respectively, whereas among all presented non-fusion algorithms, the best one shows an EER of 3.03%. (paper)

AlignMe—a membrane protein sequence alignment web server

Science.gov (United States)

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

2014-01-01

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

Markov random field based automatic image alignment for electron tomography.

Science.gov (United States)

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

2008-03-01

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

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

Science.gov (United States)

Yin, Hongliang; Xu, Bo; Liu, Dezheng

2017-09-01

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

Fast centroid algorithm for determining the surface plasmon resonance angle using the fixed-boundary method

International Nuclear Information System (INIS)

Zhan, Shuyue; Wang, Xiaoping; Liu, Yuling

2011-01-01

To simplify the algorithm for determining the surface plasmon resonance (SPR) angle for special applications and development trends, a fast method for determining an SPR angle, called the fixed-boundary centroid algorithm, has been proposed. Two experiments were conducted to compare three centroid algorithms from the aspects of the operation time, sensitivity to shot noise, signal-to-noise ratio (SNR), resolution, and measurement range. Although the measurement range of this method was narrower, the other performance indices were all better than the other two centroid methods. This method has outstanding performance, high speed, good conformity, low error and a high SNR and resolution. It thus has the potential to be widely adopted

Evaluation of train-speed control algorithms

Energy Technology Data Exchange (ETDEWEB)

Slavik, M.M. [BKS Advantech (Pty.) Ltd., Pretoria (South Africa)

2000-07-01

A relatively simple and fast simulator has been developed and used for the preliminary testing of train cruise-control algorithms. The simulation is done in software on a PC. The simulator is used to gauge the consequences and feasibility of a cruise-control strategy prior to more elaborate testing and evaluation. The tool was used to design and pre-test a train-cruise control algorithm called NSS, which does not require knowledge of exact train mass, vertical alignment, or actual braking force. Only continuous measurements on the speed of the train and electrical current are required. With this modest input, the NSS algorithm effected speed changes smoothly and efficiently for a wide range of operating conditions. (orig.)

Computer vision applications for coronagraphic optical alignment and image processing.

Science.gov (United States)

Savransky, Dmitry; Thomas, Sandrine J; Poyneer, Lisa A; Macintosh, Bruce A

2013-05-10

Modern coronagraphic systems require very precise alignment between optical components and can benefit greatly from automated image processing. We discuss three techniques commonly employed in the fields of computer vision and image analysis as applied to the Gemini Planet Imager, a new facility instrument for the Gemini South Observatory. We describe how feature extraction and clustering methods can be used to aid in automated system alignment tasks, and also present a search algorithm for finding regular features in science images used for calibration and data processing. Along with discussions of each technique, we present our specific implementation and show results of each one in operation.

A New Algorithm for Determining Ultimate Pit Limits Based on Network Optimization

Directory of Open Access Journals (Sweden)

Ali Asghar Khodayari

2013-12-01

Full Text Available One of the main concerns of the mining industry is to determine ultimate pit limits. Final pit is a collection of blocks, which can be removed with maximum profit while following restrictions on the slope of the mine’s walls. The size, location and final shape of an open-pit are very important in designing the location of waste dumps, stockpiles, processing plants, access roads and other surface facilities as well as in developing a production program. There are numerous methods for designing ultimate pit limits. Some of these methods, such as floating cone algorithm, are heuristic and do not guarantee to generate optimum pit limits. Other methods, like Lerchs–Grossmann algorithm, are rigorous and always generate the true optimum pit limits. In this paper, a new rigorous algorithm is introduced. The main logic in this method is that only positive blocks, which can pay costs of their overlying non-positive blocks, are able to appear in the final pit. Those costs may be paid either by positive block itself or jointly with other positive blocks, which have the same overlying negative blocks. This logic is formulated using a network model as a Linear Programming (LP problem. This algorithm can be applied to two- and three-dimension block models. Since there are many commercial programs available for solving LP problems, pit limits in large block models can be determined easily by using this method.

Fractal MapReduce decomposition of sequence alignment

Directory of Open Access Journals (Sweden)

Almeida Jonas S

2012-05-01

Full Text Available Abstract Background The dramatic fall in the cost of genomic sequencing, and the increasing convenience of distributed cloud computing resources, positions the MapReduce coding pattern as a cornerstone of scalable bioinformatics algorithm development. In some cases an algorithm will find a natural distribution via use of map functions to process vectorized components, followed by a reduce of aggregate intermediate results. However, for some data analysis procedures such as sequence analysis, a more fundamental reformulation may be required. Results In this report we describe a solution to sequence comparison that can be thoroughly decomposed into multiple rounds of map and reduce operations. The route taken makes use of iterated maps, a fractal analysis technique, that has been found to provide a "alignment-free" solution to sequence analysis and comparison. That is, a solution that does not require dynamic programming, relying on a numeric Chaos Game Representation (CGR data structure. This claim is demonstrated in this report by calculating the length of the longest similar segment by inspecting only the USM coordinates of two analogous units: with no resort to dynamic programming. Conclusions The procedure described is an attempt at extreme decomposition and parallelization of sequence alignment in anticipation of a volume of genomic sequence data that cannot be met by current algorithmic frameworks. The solution found is delivered with a browser-based application (webApp, highlighting the browser's emergence as an environment for high performance distributed computing. Availability Public distribution of accompanying software library with open source and version control at http://usm.github.com. Also available as a webApp through Google Chrome's WebStore http://chrome.google.com/webstore: search with "usm".

High performance deformable image registration algorithms for manycore processors

CERN Document Server

Shackleford, James; Sharp, Gregory

2013-01-01

High Performance Deformable Image Registration Algorithms for Manycore Processors develops highly data-parallel image registration algorithms suitable for use on modern multi-core architectures, including graphics processing units (GPUs). Focusing on deformable registration, we show how to develop data-parallel versions of the registration algorithm suitable for execution on the GPU. Image registration is the process of aligning two or more images into a common coordinate frame and is a fundamental step to be able to compare or fuse data obtained from different sensor measurements. E

GraphCrunch 2: Software tool for network modeling, alignment and clustering.

Science.gov (United States)

Kuchaiev, Oleksii; Stevanović, Aleksandar; Hayes, Wayne; Pržulj, Nataša

2011-01-19

Recent advancements in experimental biotechnology have produced large amounts of protein-protein interaction (PPI) data. The topology of PPI networks is believed to have a strong link to their function. Hence, the abundance of PPI data for many organisms stimulates the development of computational techniques for the modeling, comparison, alignment, and clustering of networks. In addition, finding representative models for PPI networks will improve our understanding of the cell just as a model of gravity has helped us understand planetary motion. To decide if a model is representative, we need quantitative comparisons of model networks to real ones. However, exact network comparison is computationally intractable and therefore several heuristics have been used instead. Some of these heuristics are easily computable "network properties," such as the degree distribution, or the clustering coefficient. An important special case of network comparison is the network alignment problem. Analogous to sequence alignment, this problem asks to find the "best" mapping between regions in two networks. It is expected that network alignment might have as strong an impact on our understanding of biology as sequence alignment has had. Topology-based clustering of nodes in PPI networks is another example of an important network analysis problem that can uncover relationships between interaction patterns and phenotype. We introduce the GraphCrunch 2 software tool, which addresses these problems. It is a significant extension of GraphCrunch which implements the most popular random network models and compares them with the data networks with respect to many network properties. Also, GraphCrunch 2 implements the GRAph ALigner algorithm ("GRAAL") for purely topological network alignment. GRAAL can align any pair of networks and exposes large, dense, contiguous regions of topological and functional similarities far larger than any other existing tool. Finally, GraphCruch 2 implements an

GraphCrunch 2: Software tool for network modeling, alignment and clustering

Directory of Open Access Journals (Sweden)

Hayes Wayne

2011-01-01

Full Text Available Abstract Background Recent advancements in experimental biotechnology have produced large amounts of protein-protein interaction (PPI data. The topology of PPI networks is believed to have a strong link to their function. Hence, the abundance of PPI data for many organisms stimulates the development of computational techniques for the modeling, comparison, alignment, and clustering of networks. In addition, finding representative models for PPI networks will improve our understanding of the cell just as a model of gravity has helped us understand planetary motion. To decide if a model is representative, we need quantitative comparisons of model networks to real ones. However, exact network comparison is computationally intractable and therefore several heuristics have been used instead. Some of these heuristics are easily computable "network properties," such as the degree distribution, or the clustering coefficient. An important special case of network comparison is the network alignment problem. Analogous to sequence alignment, this problem asks to find the "best" mapping between regions in two networks. It is expected that network alignment might have as strong an impact on our understanding of biology as sequence alignment has had. Topology-based clustering of nodes in PPI networks is another example of an important network analysis problem that can uncover relationships between interaction patterns and phenotype. Results We introduce the GraphCrunch 2 software tool, which addresses these problems. It is a significant extension of GraphCrunch which implements the most popular random network models and compares them with the data networks with respect to many network properties. Also, GraphCrunch 2 implements the GRAph ALigner algorithm ("GRAAL" for purely topological network alignment. GRAAL can align any pair of networks and exposes large, dense, contiguous regions of topological and functional similarities far larger than any other

BFAST: an alignment tool for large scale genome resequencing.

Directory of Open Access Journals (Sweden)

Nils Homer

2009-11-01

Full Text Available The new generation of massively parallel DNA sequencers, combined with the challenge of whole human genome resequencing, result in the need for rapid and accurate alignment of billions of short DNA sequence reads to a large reference genome. Speed is obviously of great importance, but equally important is maintaining alignment accuracy of short reads, in the 25-100 base range, in the presence of errors and true biological variation.We introduce a new algorithm specifically optimized for this task, as well as a freely available implementation, BFAST, which can align data produced by any of current sequencing platforms, allows for user-customizable levels of speed and accuracy, supports paired end data, and provides for efficient parallel and multi-threaded computation on a computer cluster. The new method is based on creating flexible, efficient whole genome indexes to rapidly map reads to candidate alignment locations, with arbitrary multiple independent indexes allowed to achieve robustness against read errors and sequence variants. The final local alignment uses a Smith-Waterman method, with gaps to support the detection of small indels.We compare BFAST to a selection of large-scale alignment tools -- BLAT, MAQ, SHRiMP, and SOAP -- in terms of both speed and accuracy, using simulated and real-world datasets. We show BFAST can achieve substantially greater sensitivity of alignment in the context of errors and true variants, especially insertions and deletions, and minimize false mappings, while maintaining adequate speed compared to other current methods. We show BFAST can align the amount of data needed to fully resequence a human genome, one billion reads, with high sensitivity and accuracy, on a modest computer cluster in less than 24 hours. BFAST is available at (http://bfast.sourceforge.net.

Flexible, fast and accurate sequence alignment profiling on GPGPU with PaSWAS.

Directory of Open Access Journals (Sweden)

Sven Warris

Full Text Available To obtain large-scale sequence alignments in a fast and flexible way is an important step in the analyses of next generation sequencing data. Applications based on the Smith-Waterman (SW algorithm are often either not fast enough, limited to dedicated tasks or not sufficiently accurate due to statistical issues. Current SW implementations that run on graphics hardware do not report the alignment details necessary for further analysis.With the Parallel SW Alignment Software (PaSWAS it is possible (a to have easy access to the computational power of NVIDIA-based general purpose graphics processing units (GPGPUs to perform high-speed sequence alignments, and (b retrieve relevant information such as score, number of gaps and mismatches. The software reports multiple hits per alignment. The added value of the new SW implementation is demonstrated with two test cases: (1 tag recovery in next generation sequence data and (2 isotype assignment within an immunoglobulin 454 sequence data set. Both cases show the usability and versatility of the new parallel Smith-Waterman implementation.

Flexible, fast and accurate sequence alignment profiling on GPGPU with PaSWAS.

Science.gov (United States)

Warris, Sven; Yalcin, Feyruz; Jackson, Katherine J L; Nap, Jan Peter

2015-01-01

To obtain large-scale sequence alignments in a fast and flexible way is an important step in the analyses of next generation sequencing data. Applications based on the Smith-Waterman (SW) algorithm are often either not fast enough, limited to dedicated tasks or not sufficiently accurate due to statistical issues. Current SW implementations that run on graphics hardware do not report the alignment details necessary for further analysis. With the Parallel SW Alignment Software (PaSWAS) it is possible (a) to have easy access to the computational power of NVIDIA-based general purpose graphics processing units (GPGPUs) to perform high-speed sequence alignments, and (b) retrieve relevant information such as score, number of gaps and mismatches. The software reports multiple hits per alignment. The added value of the new SW implementation is demonstrated with two test cases: (1) tag recovery in next generation sequence data and (2) isotype assignment within an immunoglobulin 454 sequence data set. Both cases show the usability and versatility of the new parallel Smith-Waterman implementation.

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

GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping.

Science.gov (United States)

Alser, Mohammed; Hassan, Hasan; Xin, Hongyi; Ergin, Oguz; Mutlu, Onur; Alkan, Can

2017-11-01

High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments -called short reads- that cause significant computational burden. To analyze the entire genome, each of the billions of short reads must be mapped to a reference genome based on the similarity between a read and 'candidate' locations in that reference genome. The similarity measurement, called alignment, formulated as an approximate string matching problem, is the computational bottleneck because: (i) it is implemented using quadratic-time dynamic programming algorithms and (ii) the majority of candidate locations in the reference genome do not align with a given read due to high dissimilarity. Calculating the alignment of such incorrect candidate locations consumes an overwhelming majority of a modern read mapper's execution time. Therefore, it is crucial to develop a fast and effective filter that can detect incorrect candidate locations and eliminate them before invoking computationally costly alignment algorithms. We propose GateKeeper, a new hardware accelerator that functions as a pre-alignment step that quickly filters out most incorrect candidate locations. GateKeeper is the first design to accelerate pre-alignment using Field-Programmable Gate Arrays (FPGAs), which can perform pre-alignment much faster than software. When implemented on a single FPGA chip, GateKeeper maintains high accuracy (on average >96%) while providing, on average, 90-fold and 130-fold speedup over the state-of-the-art software pre-alignment techniques, Adjacency Filter and Shifted Hamming Distance (SHD), respectively. The addition of GateKeeper as a pre-alignment step can reduce the verification time of the mrFAST mapper by a factor of 10. https://github.com/BilkentCompGen/GateKeeper. mohammedalser@bilkent.edu.tr or onur.mutlu@inf.ethz.ch or calkan@cs.bilkent.edu.tr. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press

Research on localization and alignment technology for transfer cask

Energy Technology Data Exchange (ETDEWEB)

Wang, Jingchuan, E-mail: jchwang@sjtu.edu.cn [Department of Automation, Shanghai Jiao Tong University, Shanghai (China); Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai (China); Yang, Ming; Chen, Weidong [Department of Automation, Shanghai Jiao Tong University, Shanghai (China); Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai (China)

2015-10-15

Highlights: • A method for the alignment between TB and HCB based on localizability is proposed. • A localization method based on the localizability estimation is proposed to realize the cask's localization accurately and ensures the transfer cask's accurate docking in the front of the window of Tokmak Building. • The experimental results show that the proposed algorithm works well in the indoor simulation environment. This system will be test in EAST of China. - Abstract: According to the long length characteristics of transfer cask compared to the environment space between Tokmak Building (TB) and HCB (Hot Cell Building), this paper proposes an autonomous localization and alignment method for the internal components transportation and replacement. A localization method based on the localizability estimation is used to realize the cask's localization and navigation accurately. Once the cask arrives at the front of the TB window, the position and attitude measurement system is used to detect the relative alignment error between the seal door of pallet and the window of TB real-time. The alignment between seal door and TB window could be realized based on this offset. The simulation experiment based on the real model is designed according to the real TB situation. The experiment results show that the proposed localization and alignment method can be used for transfer cask.

An additional reference axis improves femoral rotation alignment in image-free computer navigation assisted total knee arthroplasty.

Science.gov (United States)

Inui, Hiroshi; Taketomi, Shuji; Nakamura, Kensuke; Sanada, Takaki; Tanaka, Sakae; Nakagawa, Takumi

2013-05-01

Few studies have demonstrated improvement in accuracy of rotational alignment using image-free navigation systems mainly due to the inconsistent registration of anatomical landmarks. We have used an image-free navigation for total knee arthroplasty, which adopts the average algorithm between two reference axes (transepicondylar axis and axis perpendicular to the Whiteside axis) for femoral component rotation control. We hypothesized that addition of another axis (condylar twisting axis measured on a preoperative radiograph) would improve the accuracy. One group using the average algorithm (double-axis group) was compared with the other group using another axis to confirm the accuracy of the average algorithm (triple-axis group). Femoral components were more accurately implanted for rotational alignment in the triple-axis group (ideal: triple-axis group 100%, double-axis group 82%, P<0.05). Copyright © 2013 Elsevier Inc. All rights reserved.

Alignment of time-resolved data from high throughput experiments.

Science.gov (United States)

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

2016-12-01

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

Biologically inspired EM image alignment and neural reconstruction.

Science.gov (United States)

Knowles-Barley, Seymour; Butcher, Nancy J; Meinertzhagen, Ian A; Armstrong, J Douglas

2011-08-15

Three-dimensional reconstruction of consecutive serial-section transmission electron microscopy (ssTEM) images of neural tissue currently requires many hours of manual tracing and annotation. Several computational techniques have already been applied to ssTEM images to facilitate 3D reconstruction and ease this burden. Here, we present an alternative computational approach for ssTEM image analysis. We have used biologically inspired receptive fields as a basis for a ridge detection algorithm to identify cell membranes, synaptic contacts and mitochondria. Detected line segments are used to improve alignment between consecutive images and we have joined small segments of membrane into cell surfaces using a dynamic programming algorithm similar to the Needleman-Wunsch and Smith-Waterman DNA sequence alignment procedures. A shortest path-based approach has been used to close edges and achieve image segmentation. Partial reconstructions were automatically generated and used as a basis for semi-automatic reconstruction of neural tissue. The accuracy of partial reconstructions was evaluated and 96% of membrane could be identified at the cost of 13% false positive detections. An open-source reference implementation is available in the Supplementary information. seymour.kb@ed.ac.uk; douglas.armstrong@ed.ac.uk Supplementary data are available at Bioinformatics online.

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

Science.gov (United States)

Wang, Wei; Chen, Xiyuan

2018-02-23

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

A Trust Region Aggressive Space Mapping Algorithm for EM

DEFF Research Database (Denmark)

Bakr., M.; Bandler, J. W.; Biernacki, R.

1998-01-01

A robust new algorithm for electromagnetic (EM) optimization of microwave circuits is presented. The algorithm (TRASM) integrates a trust region methodology with the aggressive space mapping (ASM). The trust region ensures that each iteration results in improved alignment between the coarse....... This suggested step exploits all the available EM simulations for improving the uniqueness of parameter extraction. The new algorithm was successfully used to design a number of microwave circuits. Examples include the EM optimization of a double-folded stub filter and of a high-temperature superconducting (HTS...

Tracing magnetic fields with aligned grains

International Nuclear Information System (INIS)

Lazarian, A.

2007-01-01

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

Micro-vision servo control of a multi-axis alignment system for optical fiber assembly

International Nuclear Information System (INIS)

Chen, Weihai; Yu, Fei; Qu, Jianliang; Chen, Wenjie; Zhang, Jianbin

2017-01-01

This paper describes a novel optical fiber assembly system featuring a multi-axis alignment function based on micro-vision feedback control. It consists of an active parallel alignment mechanism, a passive compensation mechanism, a micro-gripper and a micro-vision servo control system. The active parallel alignment part is a parallelogram-based design with remote-center-of-motion (RCM) function to achieve precise rotation without fatal lateral motion. The passive mechanism, with five degrees of freedom (5-DOF), is used to implement passive compensation for multi-axis errors. A specially designed 1-DOF micro-gripper mounted onto the active parallel alignment platform is adopted to grasp and rotate the optical fiber. A micro-vision system equipped with two charge-coupled device (CCD) cameras is introduced to observe the small field of view and obtain multi-axis errors for servo feedback control. The two CCD cameras are installed in an orthogonal arrangement—thus the errors can be easily measured via the captured images. Meanwhile, a series of tracking and measurement algorithms based on specific features of the target objects are developed. Details of the force and displacement sensor information acquisition in the assembly experiment are also provided. An experiment demonstrates the validity of the proposed visual algorithm by achieving the task of eliminating errors and inserting an optical fiber to the U-groove accurately. (paper)

Flexible, fast and accurate sequence alignment profiling on GPGPU with PaSWAS

NARCIS (Netherlands)

Warris, S.; Yalcin, F.; Jackson, K.J.; Nap, J.P.H.

2015-01-01

Motivation To obtain large-scale sequence alignments in a fast and flexible way is an important step in the analyses of next generation sequencing data. Applications based on the Smith-Waterman (SW) algorithm are often either not fast enough, limited to dedicated tasks or not sufficiently accurate

Surveying alignment-free features for Ortholog detection in related yeast proteomes by using supervised big data classifiers.

Science.gov (United States)

Galpert, Deborah; Fernández, Alberto; Herrera, Francisco; Antunes, Agostinho; Molina-Ruiz, Reinaldo; Agüero-Chapin, Guillermin

2018-05-03

The development of new ortholog detection algorithms and the improvement of existing ones are of major importance in functional genomics. We have previously introduced a successful supervised pairwise ortholog classification approach implemented in a big data platform that considered several pairwise protein features and the low ortholog pair ratios found between two annotated proteomes (Galpert, D et al., BioMed Research International, 2015). The supervised models were built and tested using a Saccharomycete yeast benchmark dataset proposed by Salichos and Rokas (2011). Despite several pairwise protein features being combined in a supervised big data approach; they all, to some extent were alignment-based features and the proposed algorithms were evaluated on a unique test set. Here, we aim to evaluate the impact of alignment-free features on the performance of supervised models implemented in the Spark big data platform for pairwise ortholog detection in several related yeast proteomes. The Spark Random Forest and Decision Trees with oversampling and undersampling techniques, and built with only alignment-based similarity measures or combined with several alignment-free pairwise protein features showed the highest classification performance for ortholog detection in three yeast proteome pairs. Although such supervised approaches outperformed traditional methods, there were no significant differences between the exclusive use of alignment-based similarity measures and their combination with alignment-free features, even within the twilight zone of the studied proteomes. Just when alignment-based and alignment-free features were combined in Spark Decision Trees with imbalance management, a higher success rate (98.71%) within the twilight zone could be achieved for a yeast proteome pair that underwent a whole genome duplication. The feature selection study showed that alignment-based features were top-ranked for the best classifiers while the runners-up were

Group sparse multiview patch alignment framework with view consistency for image classification.

Science.gov (United States)

Gui, Jie; Tao, Dacheng; Sun, Zhenan; Luo, Yong; You, Xinge; Tang, Yuan Yan

2014-07-01

No single feature can satisfactorily characterize the semantic concepts of an image. Multiview learning aims to unify different kinds of features to produce a consensual and efficient representation. This paper redefines part optimization in the patch alignment framework (PAF) and develops a group sparse multiview patch alignment framework (GSM-PAF). The new part optimization considers not only the complementary properties of different views, but also view consistency. In particular, view consistency models the correlations between all possible combinations of any two kinds of view. In contrast to conventional dimensionality reduction algorithms that perform feature extraction and feature selection independently, GSM-PAF enjoys joint feature extraction and feature selection by exploiting l(2,1)-norm on the projection matrix to achieve row sparsity, which leads to the simultaneous selection of relevant features and learning transformation, and thus makes the algorithm more discriminative. Experiments on two real-world image data sets demonstrate the effectiveness of GSM-PAF for image classification.

An Iterative Algorithm to Determine the Dynamic User Equilibrium in a Traffic Simulation Model

Science.gov (United States)

Gawron, C.

An iterative algorithm to determine the dynamic user equilibrium with respect to link costs defined by a traffic simulation model is presented. Each driver's route choice is modeled by a discrete probability distribution which is used to select a route in the simulation. After each simulation run, the probability distribution is adapted to minimize the travel costs. Although the algorithm does not depend on the simulation model, a queuing model is used for performance reasons. The stability of the algorithm is analyzed for a simple example network. As an application example, a dynamic version of Braess's paradox is studied.

Uncertainty evaluation in the self-alignment test of the upper plate of a press

International Nuclear Information System (INIS)

Lourenço, Alexandre S; E Sousa, J Alves

2015-01-01

This paper describes a method to evaluate uncertainty of the self-alignment test of the upper plate of a press according to EN 12390-4:2000. The method, the algorithms and the sources of uncertainty are described

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.

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

International Nuclear Information System (INIS)

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

2015-01-01

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

SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing.

Science.gov (United States)

Tsuchiya, Mariko; Amano, Kojiro; Abe, Masaya; Seki, Misato; Hase, Sumitaka; Sato, Kengo; Sakakibara, Yasubumi

2016-06-15

Deep sequencing of the transcripts of regulatory non-coding RNA generates footprints of post-transcriptional processes. After obtaining sequence reads, the short reads are mapped to a reference genome, and specific mapping patterns can be detected called read mapping profiles, which are distinct from random non-functional degradation patterns. These patterns reflect the maturation processes that lead to the production of shorter RNA sequences. Recent next-generation sequencing studies have revealed not only the typical maturation process of miRNAs but also the various processing mechanisms of small RNAs derived from tRNAs and snoRNAs. We developed an algorithm termed SHARAKU to align two read mapping profiles of next-generation sequencing outputs for non-coding RNAs. In contrast with previous work, SHARAKU incorporates the primary and secondary sequence structures into an alignment of read mapping profiles to allow for the detection of common processing patterns. Using a benchmark simulated dataset, SHARAKU exhibited superior performance to previous methods for correctly clustering the read mapping profiles with respect to 5'-end processing and 3'-end processing from degradation patterns and in detecting similar processing patterns in deriving the shorter RNAs. Further, using experimental data of small RNA sequencing for the common marmoset brain, SHARAKU succeeded in identifying the significant clusters of read mapping profiles for similar processing patterns of small derived RNA families expressed in the brain. The source code of our program SHARAKU is available at http://www.dna.bio.keio.ac.jp/sharaku/, and the simulated dataset used in this work is available at the same link. Accession code: The sequence data from the whole RNA transcripts in the hippocampus of the left brain used in this work is available from the DNA DataBank of Japan (DDBJ) Sequence Read Archive (DRA) under the accession number DRA004502. yasu@bio.keio.ac.jp Supplementary data are available

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.

Determination of material constants of vertically aligned carbon nanotube structures in compressions

International Nuclear Information System (INIS)

Li, Yupeng; Kang, Junmo; Choi, Jae-Boong; Nam, Jae-Do; Suhr, Jonghwan

2015-01-01

Different chemical vapour deposition (CVD) fabrication conditions lead to a wide range of variation in the microstructure and morphologies of carbon nanotubes (CNTs), which actually determine the compressive mechanical properties of CNTs. However, the underlying relationship between the structure/morphology and mechanical properties of CNTs is not fully understood. In this study, we characterized and compared the structural and morphological properties of three kinds of vertically aligned carbon nanotube (VACNT) arrays from different CVD fabrication methods and performed monotonic compressive tests for each VACNT array. The compressive stress–strain responses and plastic deformation were first compared and analyzed with nanotube buckling behaviours. To quantify the compressive properties of the VACNT arrays, a strain density energy function was used to determine their intrinsic material constants. Then, the structural and morphological effects on the quantified material constants of the VACNTs were statistically investigated and analogized to cellular materials with an open-cell model. The statistical analysis shows that density, defect degree, and the moment of inertia of the CNTs are key factors in the improvement of the compressive mechanical properties of VACNT arrays. This approach could allow a model-driven CNT synthesis for engineering their mechanical behaviours. (paper)

Determination of the electrical resistivity of vertically aligned carbon nanotubes by scanning probe microscopy

Science.gov (United States)

Ageev, O. A.; Il'in, O. I.; Rubashkina, M. V.; Smirnov, V. A.; Fedotov, A. A.; Tsukanova, O. G.

2015-07-01

Techniques are developed to determine the resistance per unit length and the electrical resistivity of vertically aligned carbon nanotubes (VA CNTs) using atomic force microscopy (AFM) and scanning tunneling microscopy (STM). These techniques are used to study the resistance of VA CNTs. The resistance of an individual VA CNT calculated with the AFM-based technique is shown to be higher than the resistance of VA CNTs determined by the STM-based technique by a factor of 200, which is related to the influence of the resistance of the contact of an AFM probe to VA CNTs. The resistance per unit length and the electrical resistivity of an individual VA CNT 118 ± 39 nm in diameter and 2.23 ± 0.37 μm in height that are determined by the STM-based technique are 19.28 ± 3.08 kΩ/μm and 8.32 ± 3.18 × 10-4 Ω m, respectively. The STM-based technique developed to determine the resistance per unit length and the electrical resistivity of VA CNTs can be used to diagnose the electrical parameters of VA CNTs and to create VA CNT-based nanoelectronic elements.

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, ...

Polar transfer alignment of shipborne SINS with a large misalignment angle

International Nuclear Information System (INIS)

Cheng, Jianhua; Wang, Tongda; Guan, Dongxue; Li, Meiling

2016-01-01

Existing polar transfer alignment (TA) algorithms are designed based on linear Kalman filters (KF) to estimate misalignment angles. In the case of a large misalignment angle, these algorithms cannot be applied in order to achieve accurate TA. In this paper, a TA algorithm based on an unscented Kalman filter (UKF) is proposed to solve the problem of the large misalignment angle in the polar region. Based on a large misalignment angle, nonlinear navigation error equations, which are the UKF dynamic models, are derived under grid frames. This paper chooses the velocity plus attitude matching method as the TA matching method and errors of velocity and attitude as observations. The misalignment angle can be estimated by the designed UKF. The simulation results have demonstrated that the polar TA algorithm can be effective in improving the TA accuracy, especially when large misalignment angles occur. (paper)

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

Science.gov (United States)

Kawata, Masaaki; Sato, Chikara

2007-06-01

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

Self-learning computers for surgical planning and prediction of postoperative alignment.

Science.gov (United States)

Lafage, Renaud; Pesenti, Sébastien; Lafage, Virginie; Schwab, Frank J

2018-02-01

In past decades, the role of sagittal alignment has been widely demonstrated in the setting of spinal conditions. As several parameters can be affected, identifying the driver of the deformity is the cornerstone of a successful treatment approach. Despite the importance of restoring sagittal alignment for optimizing outcome, this task remains challenging. Self-learning computers and optimized algorithms are of great interest in spine surgery as in that they facilitate better planning and prediction of postoperative alignment. Nowadays, computer-assisted tools are part of surgeons' daily practice; however, the use of such tools remains to be time-consuming. NARRATIVE REVIEW AND RESULTS: Computer-assisted methods for the prediction of postoperative alignment consist of a three step analysis: identification of anatomical landmark, definition of alignment objectives, and simulation of surgery. Recently, complex rules for the prediction of alignment have been proposed. Even though this kind of work leads to more personalized objectives, the number of parameters involved renders it difficult for clinical use, stressing the importance of developing computer-assisted tools. The evolution of our current technology, including machine learning and other types of advanced algorithms, will provide powerful tools that could be useful in improving surgical outcomes and alignment prediction. These tools can combine different types of advanced technologies, such as image recognition and shape modeling, and using this technique, computer-assisted methods are able to predict spinal shape. The development of powerful computer-assisted methods involves the integration of several sources of information such as radiographic parameters (X-rays, MRI, CT scan, etc.), demographic information, and unusual non-osseous parameters (muscle quality, proprioception, gait analysis data). In using a larger set of data, these methods will aim to mimic what is actually done by spine surgeons, leading

The aligned K-center problem

KAUST Repository

Braß, Peter

2011-04-01

In this paper we study several instances of the aligned k-center problem where the goal is, given a set of points S in the plane and a parameter k ≥ 1, to find k disks with centers on a line ℓ such that their union covers S and the maximum radius of the disks is minimized. This problem is a constrained version of the well-known k-center problem in which the centers are constrained to lie in a particular region such as a segment, a line, or a polygon. We first consider the simplest version of the problem where the line ℓ is given in advance; we can solve this problem in time O(n log2 n). In the case where only the direction of ℓ is fixed, we give an O(n2 log 2 n)-time algorithm. When ℓ is an arbitrary line, we give a randomized algorithm with expected running time O(n4 log2 n). Then we present (1+ε)-approximation algorithms for these three problems. When we denote T(k, ε) = (k/ε2+(k/ε) log k) log(1/ε), these algorithms run in O(n log k + T(k, ε)) time, O(n log k + T(k, ε)/ε) time, and O(n log k + T(k, ε)/ε2) time, respectively. For k = O(n1/3/log n), we also give randomized algorithms with expected running times O(n + (k/ε2) log(1/ε)), O(n+(k/ε3) log(1/ε)), and O(n + (k/ε4) log(1/ε)), respectively. © 2011 World Scientific Publishing Company.

Image correlation method for DNA sequence alignment.

Science.gov (United States)

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

2012-01-01

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

An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data

Directory of Open Access Journals (Sweden)

Dommisse Roger

2011-10-01

Full Text Available Abstract Background Nuclear magnetic resonance spectroscopy (NMR is a powerful technique to reveal and compare quantitative metabolic profiles of biological tissues. However, chemical and physical sample variations make the analysis of the data challenging, and typically require the application of a number of preprocessing steps prior to data interpretation. For example, noise reduction, normalization, baseline correction, peak picking, spectrum alignment and statistical analysis are indispensable components in any NMR analysis pipeline. Results We introduce a novel suite of informatics tools for the quantitative analysis of NMR metabolomic profile data. The core of the processing cascade is a novel peak alignment algorithm, called hierarchical Cluster-based Peak Alignment (CluPA. The algorithm aligns a target spectrum to the reference spectrum in a top-down fashion by building a hierarchical cluster tree from peak lists of reference and target spectra and then dividing the spectra into smaller segments based on the most distant clusters of the tree. To reduce the computational time to estimate the spectral misalignment, the method makes use of Fast Fourier Transformation (FFT cross-correlation. Since the method returns a high-quality alignment, we can propose a simple methodology to study the variability of the NMR spectra. For each aligned NMR data point the ratio of the between-group and within-group sum of squares (BW-ratio is calculated to quantify the difference in variability between and within predefined groups of NMR spectra. This differential analysis is related to the calculation of the F-statistic or a one-way ANOVA, but without distributional assumptions. Statistical inference based on the BW-ratio is achieved by bootstrapping the null distribution from the experimental data. Conclusions The workflow performance was evaluated using a previously published dataset. Correlation maps, spectral and grey scale plots show clear

An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data.

Science.gov (United States)

Vu, Trung N; Valkenborg, Dirk; Smets, Koen; Verwaest, Kim A; Dommisse, Roger; Lemière, Filip; Verschoren, Alain; Goethals, Bart; Laukens, Kris

2011-10-20

Nuclear magnetic resonance spectroscopy (NMR) is a powerful technique to reveal and compare quantitative metabolic profiles of biological tissues. However, chemical and physical sample variations make the analysis of the data challenging, and typically require the application of a number of preprocessing steps prior to data interpretation. For example, noise reduction, normalization, baseline correction, peak picking, spectrum alignment and statistical analysis are indispensable components in any NMR analysis pipeline. We introduce a novel suite of informatics tools for the quantitative analysis of NMR metabolomic profile data. The core of the processing cascade is a novel peak alignment algorithm, called hierarchical Cluster-based Peak Alignment (CluPA). The algorithm aligns a target spectrum to the reference spectrum in a top-down fashion by building a hierarchical cluster tree from peak lists of reference and target spectra and then dividing the spectra into smaller segments based on the most distant clusters of the tree. To reduce the computational time to estimate the spectral misalignment, the method makes use of Fast Fourier Transformation (FFT) cross-correlation. Since the method returns a high-quality alignment, we can propose a simple methodology to study the variability of the NMR spectra. For each aligned NMR data point the ratio of the between-group and within-group sum of squares (BW-ratio) is calculated to quantify the difference in variability between and within predefined groups of NMR spectra. This differential analysis is related to the calculation of the F-statistic or a one-way ANOVA, but without distributional assumptions. Statistical inference based on the BW-ratio is achieved by bootstrapping the null distribution from the experimental data. The workflow performance was evaluated using a previously published dataset. Correlation maps, spectral and grey scale plots show clear improvements in comparison to other methods, and the down

Alignment of the ATLAS Inner Detector Tracking System

CERN Document Server

Lacuesta, V; The ATLAS collaboration

2010-01-01

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

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

Directory of Open Access Journals (Sweden)

Michal Brylinski

2014-09-01

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

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.

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...

Evolution of shiva laser alignment systems

International Nuclear Information System (INIS)

Boyd, R.D.

1980-07-01

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

InfoRoute: the CISMeF Context-specific Search Algorithm.

Science.gov (United States)

Merabti, Tayeb; Lelong, Romain; Darmoni, Stefan

2015-01-01

The aim of this paper was to present a practical InfoRoute algorithm and applications developed by CISMeF to perform a contextual information retrieval across multiple medical websites in different health domains. The algorithm was developed to treat multiple types of queries: natural, Boolean and advanced. The algorithm also generates multiple types of queries: Boolean query, PubMed query or Advanced query. Each query can be extended via an inter alignments relationship from UMLS and HeTOP portal. A web service and two web applications have been developed based on the InfoRoute algorithm to generate links-query across multiple websites, i.e.: "PubMed" or "ClinicalTrials.org". The InfoRoute algorithm is a useful tool to perform contextual information retrieval across multiple medical websites in both English and French.

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.

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.

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.

Intramedullary versus extramedullary alignment of the tibial component in the Triathlon knee

LENUS (Irish Health Repository)

Cashman, James P

2011-08-20

Abstract Background Long term survivorship in total knee arthroplasty is significantly dependant on prosthesis alignment. Our aim was determine which alignment guide was more accurate in positioning of the tibial component in total knee arthroplasty. We also aimed to assess whether there was any difference in short term patient outcome. Method A comparison of intramedullary versus extramedullary alignment jig was performed. Radiological alignment of tibial components and patient outcomes of 103 Triathlon total knee arthroplasties were analysed. Results Use of the intramedullary was found to be significantly more accurate in determining coronal alignment (p = 0.02) while use of the extramedullary jig was found to give more accurate results in sagittal alignment (p = 0.04). There was no significant difference in WOMAC or SF-36 at six months. Conclusion Use of an intramedullary jig is preferable for positioning of the tibial component using this knee system.

The GEM Detector projective alignment simulation system

International Nuclear Information System (INIS)

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

1993-01-01

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

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.

Georgia science curriculum alignment and accountability: A blueprint for student success

Science.gov (United States)

Reining-Gray, Kimberly M.

Current trends and legislation in education indicate an increased dependency on standardized test results as a measure for learner success. This study analyzed test data in an effort to assess the impact of curriculum alignment on learner success as well as teacher perceptions of the changes in classroom instruction due to curriculum alignment. Qualitative and quantitative design methods were used to determine the impact of science curriculum alignment in grades 9-12. To determine the impact of science curriculum alignment from the Quality Core Curriculum (QCC) to the Georgia Performance Standards (GPS) test data and teacher opinion surveys from one Georgia School system were examined. Standardized test scores before and after curriculum alignment were analyzed as well as teacher perception survey data regarding the impact of curriculum change. A quantitative teacher perception survey was administered to science teachers in the school system to identify significant changes in teacher perceptions or teaching strategies following curriculum realignment. Responses to the survey were assigned Likert scale values for analysis purposes. Selected teachers were also interviewed using panel-approved questions to further determine teacher opinions of curriculum realignment and the impact on student success and teaching strategies. Results of this study indicate significant changes related to curriculum alignment. Teachers reported a positive change in teaching strategies and instructional delivery as a result of curriculum alignment and implementation. Student scores also showed improvement, but more research is recommended in this area.

Climatic zonation and land suitability determination for saffron in Khorasan-Razavi province using data mining algorithms

Directory of Open Access Journals (Sweden)

mehdi Bashiri

2017-12-01

Full Text Available Yield prediction for agricultural crops plays an important role in export-import planning, purchase guarantees, pricing, secure profits and increasing in agricultural productivity. Crop yield is affected by several parameters especially climate. In this study, the saffron yield in the Khorasan-Razavi province was evaluated by different classification algorithms including artificial neural networks, regression models, local linear trees, decision trees, discriminant analysis, random forest, support vector machine and nearest neighbor analysis. These algorithms analyzed data for 20 years (1989-2009 including 11 climatological parameters. The results showed that a few numbers of climatological parameters affect the saffron yield. The minimum, mean and maximum of temperature, had the highest positive correlations and the relative humidity of 6.5h, sunny hours, relative humidity of 18.5h, evaporation, relative humidity of 12.5h and absolute humidity had the highest negative correlations with saffron cultivation areas, respectively. In addition, in classification of saffron cultivation areas, the discriminant analysis and support vector machine had higher accuracies. The correlation between saffron cultivation area and saffron yield values was relatively high (r=0.38. The nearest neighbor analysis had the best prediction accuracy for classification of cultivation areas. For this algorithm the coefficients of determination were 1 and 0.944 for training and testing stages, respectively. However, the algorithms accuracy for prediction of crop yield from climatological parameters was low (the average coefficients of determination equal to 0.48 and 0.05 for training and testing stages. The best algorithm i.e. nearest neighbor analysis had coefficients of determination equal to 1 and 0.177 for saffron yield prediction. Results showed that, using climatological parameters and data mining algorithms can classify cultivation areas. By this way it is possible

Sensing Characteristics of A Precision Aligner Using Moire Gratings for Precision Alignment System

Institute of Scientific and Technical Information of China (English)

ZHOU Lizhong; Hideo Furuhashi; Yoshiyuki Uchida

2001-01-01

Sensing characteristics of a precision aligner using moire gratings for precision alignment sysem has been investigated. A differential moire alignment system and a modified alignment system were used. The influence of the setting accuracy of the gap length and inclination of gratings on the alignment accuracy has been studied experimentally and theoretically. Setting accuracy of the gap length less than 2.5μm is required in modified moire alignment. There is no influence of the gap length on the alignment accuracy in the differential alignment system. The inclination affects alignment accuracies in both differential and modified moire alignment systems.

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.

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

Science.gov (United States)

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

2012-06-01

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

Optimal alignment of mirror based pentaprisms for scanning deflectometric devices

Energy Technology Data Exchange (ETDEWEB)

Barber, Samuel K.; Geckeler, Ralf D.; Yashchuk, Valeriy V.; Gubarev, Mikhail V.; Buchheim, Jana; Siewert, Frank; Zeschke, Thomas

2011-03-04

In the recent work [Proc. of SPIE 7801, 7801-2/1-12 (2010), Opt. Eng. 50(5) (2011), in press], we have reported on improvement of the Developmental Long Trace Profiler (DLTP), a slope measuring profiler available at the Advanced Light Source Optical Metrology Laboratory, achieved by replacing the bulk pentaprism with a mirror based pentaprism (MBPP). An original experimental procedure for optimal mutual alignment of the MBPP mirrors has been suggested and verified with numerical ray tracing simulations. It has been experimentally shown that the optimally aligned MBPP allows the elimination of systematic errors introduced by inhomogeneity of the optical material and fabrication imperfections of the bulk pentaprism. In the present article, we provide the analytical derivation and verification of easily executed optimal alignment algorithms for two different designs of mirror based pentaprisms. We also provide an analytical description for the mechanism for reduction of the systematic errors introduced by a typical high quality bulk pentaprism. It is also shown that residual misalignments of an MBPP introduce entirely negligible systematic errors in surface slope measurements with scanning deflectometric devices.

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 ...

Algorithm for selection of optimized EPR distance restraints for de novo protein structure determination

Science.gov (United States)

Kazmier, Kelli; Alexander, Nathan S.; Meiler, Jens; Mchaourab, Hassane S.

2010-01-01

A hybrid protein structure determination approach combining sparse Electron Paramagnetic Resonance (EPR) distance restraints and Rosetta de novo protein folding has been previously demonstrated to yield high quality models (Alexander et al., 2008). However, widespread application of this methodology to proteins of unknown structures is hindered by the lack of a general strategy to place spin label pairs in the primary sequence. In this work, we report the development of an algorithm that optimally selects spin labeling positions for the purpose of distance measurements by EPR. For the α-helical subdomain of T4 lysozyme (T4L), simulated restraints that maximize sequence separation between the two spin labels while simultaneously ensuring pairwise connectivity of secondary structure elements yielded vastly improved models by Rosetta folding. 50% of all these models have the correct fold compared to only 21% and 8% correctly folded models when randomly placed restraints or no restraints are used, respectively. Moreover, the improvements in model quality require a limited number of optimized restraints, the number of which is determined by the pairwise connectivities of T4L α-helices. The predicted improvement in Rosetta model quality was verified by experimental determination of distances between spin labels pairs selected by the algorithm. Overall, our results reinforce the rationale for the combined use of sparse EPR distance restraints and de novo folding. By alleviating the experimental bottleneck associated with restraint selection, this algorithm sets the stage for extending computational structure determination to larger, traditionally elusive protein topologies of critical structural and biochemical importance. PMID:21074624

GenNon-h: Generating multiple sequence alignments on nonhomogeneous phylogenetic trees

Directory of Open Access Journals (Sweden)

Kedzierska Anna M

2012-08-01

Full Text Available Abstract Background A number of software packages are available to generate DNA multiple sequence alignments (MSAs evolved under continuous-time Markov processes on phylogenetic trees. On the other hand, methods of simulating the DNA MSA directly from the transition matrices do not exist. Moreover, existing software restricts to the time-reversible models and it is not optimized to generate nonhomogeneous data (i.e. placing distinct substitution rates at different lineages. Results We present the first package designed to generate MSAs evolving under discrete-time Markov processes on phylogenetic trees, directly from probability substitution matrices. Based on the input model and a phylogenetic tree in the Newick format (with branch lengths measured as the expected number of substitutions per site, the algorithm produces DNA alignments of desired length. GenNon-h is publicly available for download. Conclusion The software presented here is an efficient tool to generate DNA MSAs on a given phylogenetic tree. GenNon-h provides the user with the nonstationary or nonhomogeneous phylogenetic data that is well suited for testing complex biological hypotheses, exploring the limits of the reconstruction algorithms and their robustness to such models.

ACCURACY COMPARISON OF ALGORITHMS FOR DETERMINATION OF IMAGE CENTER COORDINATES IN OPTOELECTRONIC DEVICES

Directory of Open Access Journals (Sweden)

N. A. Starasotnikau

2018-01-01

Full Text Available Accuracy in determination of coordinates for image having simple shapes is considered as one of important and significant parameters in metrological optoelectronic systems such as autocollimators, stellar sensors, Shack-Hartmann sensors, schemes for geometric calibration of digital cameras for aerial and space imagery, various tracking systems. The paper describes a mathematical model for a measuring stand based on a collimator which projects a test-object onto a photodetector of an optoelectronic device. The mathematical model takes into account characteristic noises for photodetectors: a shot noise of the desired signal (photon and a shot noise of a dark signal, readout and spatial heterogeneity of CCD (charge-coupled device matrix elements. In order to reduce noise effect it is proposed to apply the Wiener filter for smoothing an image and its unambiguous identification and also enter a threshold according to brightness level. The paper contains a comparison of two algorithms for determination of coordinates in accordance with energy gravity center and contour. Sobel, Pruitt, Roberts, Laplacian Gaussian, Canni detectors have been used for determination of the test-object contour. The essence of the algorithm for determination of coordinates lies in search for an image contour in the form of a circle with its subsequent approximation and determination of the image center. An error calculation has been made while determining coordinates of a gravity center for test-objects of various diameters: 5, 10, 20, 30, 40, 50 pixels of a photodetector and also signalto-noise ratio values: 200, 100, 70, 20, 10. Signal-to-noise ratio has been calculated as a difference between maximum image intensity of the test-object and the background which is divided by mean-square deviation of the background. The accuracy for determination of coordinates has been improved by 0.5-1 order in case when there was an increase in a signal-to-noise ratio. Accuracy

Determination of point of maximum likelihood in failure domain using genetic algorithms

International Nuclear Information System (INIS)

Obadage, A.S.; Harnpornchai, N.

2006-01-01

The point of maximum likelihood in a failure domain yields the highest value of the probability density function in the failure domain. The maximum-likelihood point thus represents the worst combination of random variables that contribute in the failure event. In this work Genetic Algorithms (GAs) with an adaptive penalty scheme have been proposed as a tool for the determination of the maximum likelihood point. The utilization of only numerical values in the GAs operation makes the algorithms applicable to cases of non-linear and implicit single and multiple limit state function(s). The algorithmic simplicity readily extends its application to higher dimensional problems. When combined with Monte Carlo Simulation, the proposed methodology will reduce the computational complexity and at the same time will enhance the possibility in rare-event analysis under limited computational resources. Since, there is no approximation done in the procedure, the solution obtained is considered accurate. Consequently, GAs can be used as a tool for increasing the computational efficiency in the element and system reliability analyses

Electrical alignment of antenna coordinate system in a planar near-field setup

DEFF Research Database (Denmark)

Mynster, Anders P.; Nielsen, Jeppe Majlund; Pivnenko, Sergey

2011-01-01

In this paper, a simple and efficient electrical alignment procedure known as flip-test is adapted and applied to check and correct two errors in the mechanical setup of a planar near-field system: the mis-pointing of the z-axis of the antenna coordinate system with respect to the scan plane...... and the displacement of the center point of the scan plane with respect to the z-axis of the antenna coordinate system. Simulations of the errors and their correction algorithms were carried out with different models of antennas composed of Hertzian dipoles and an optimum algorithm was then selected. The proposed...

Selecting local constraint for alignment of batch process data with dynamic time warping

DEFF Research Database (Denmark)

Spooner, Max Peter; Kold, David; Kulahci, Murat

2017-01-01

” may be interpreted as a progress signature of the batch which may be appended to the aligned data for further analysis. For the warping function to be a realistic reflection of the progress of a batch, it is necessary to impose some constraints on the dynamic time warping algorithm, to avoid...

Design and implementation of a hybrid MPI-CUDA model for the Smith-Waterman algorithm.

Science.gov (United States)

Khaled, Heba; Faheem, Hossam El Deen Mostafa; El Gohary, Rania

2015-01-01

This paper provides a novel hybrid model for solving the multiple pair-wise sequence alignment problem combining message passing interface and CUDA, the parallel computing platform and programming model invented by NVIDIA. The proposed model targets homogeneous cluster nodes equipped with similar Graphical Processing Unit (GPU) cards. The model consists of the Master Node Dispatcher (MND) and the Worker GPU Nodes (WGN). The MND distributes the workload among the cluster working nodes and then aggregates the results. The WGN performs the multiple pair-wise sequence alignments using the Smith-Waterman algorithm. We also propose a modified implementation to the Smith-Waterman algorithm based on computing the alignment matrices row-wise. The experimental results demonstrate a considerable reduction in the running time by increasing the number of the working GPU nodes. The proposed model achieved a performance of about 12 Giga cell updates per second when we tested against the SWISS-PROT protein knowledge base running on four nodes.

THE ALGORITHM OF DETERMINATION OF EYE FUNDUS VESSELS BLOOD FLOW CHARACTERISTICS ON VIDEOSEQUENCE

Directory of Open Access Journals (Sweden)

O. V. Nedzvedz

2018-01-01

Full Text Available The method of determination of the dynamic characteristics like the vessel diameter change, the linear and volume blood velocities in the vessels of the eye fundus is considered. Such characteristics allow to determine blood flow changes in the microvasculature affecting the blood flow in the brain, kidneys and coronary vessels. Developed algorithm includes four stages: the video sequence stabilization, the vessels segmentation with the help of a neural network, the determination of the instantaneous velocity in the vessels based on the optical flow and the analysis of the results.

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...

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.

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

Science.gov (United States)

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

2017-08-01

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

On developing B-spline registration algorithms for multi-core processors

International Nuclear Information System (INIS)

Shackleford, J A; Kandasamy, N; Sharp, G C

2010-01-01

Spline-based deformable registration methods are quite popular within the medical-imaging community due to their flexibility and robustness. However, they require a large amount of computing time to obtain adequate results. This paper makes two contributions towards accelerating B-spline-based registration. First, we propose a grid-alignment scheme and associated data structures that greatly reduce the complexity of the registration algorithm. Based on this grid-alignment scheme, we then develop highly data parallel designs for B-spline registration within the stream-processing model, suitable for implementation on multi-core processors such as graphics processing units (GPUs). Particular attention is focused on an optimal method for performing analytic gradient computations in a data parallel fashion. CPU and GPU versions are validated for execution time and registration quality. Performance results on large images show that our GPU algorithm achieves a speedup of 15 times over the single-threaded CPU implementation whereas our multi-core CPU algorithm achieves a speedup of 8 times over the single-threaded implementation. The CPU and GPU versions achieve near-identical registration quality in terms of RMS differences between the generated vector fields.

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

Science.gov (United States)

Cao, Hu; Lu, Yonggang

2017-01-01

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

Alignment Condition-Based Robust Adaptive Iterative Learning Control of Uncertain Robot System

Directory of Open Access Journals (Sweden)

Guofeng Tong

2014-04-01

Full Text Available This paper proposes an adaptive iterative learning control strategy integrated with saturation-based robust control for uncertain robot system in presence of modelling uncertainties, unknown parameter, and external disturbance under alignment condition. An important merit is that it achieves adaptive switching of gain matrix both in conventional PD-type feedforward control and robust adaptive control in the iteration domain simultaneously. The analysis of convergence of proposed control law is based on Lyapunov's direct method under alignment initial condition. Simulation results demonstrate the faster learning rate and better robust performance with proposed algorithm by comparing with other existing robust controllers. The actual experiment on three-DOF robot manipulator shows its better practical effectiveness.

Electric field-induced astrocyte alignment directs neurite outgrowth.

Science.gov (United States)

Alexander, John K; Fuss, Babette; Colello, Raymond J

2006-05-01

The extension and directionality of neurite outgrowth are key to achieving successful target connections during both CNS development and during the re-establishment of connections lost after neural trauma. The degree of axonal elongation depends, in large part, on the spatial arrangement of astrocytic processes rich in growth-promoting proteins. Because astrocytes in culture align their processes on exposure to an electrical field of physiological strength, we sought to determine the extent to which aligned astrocytes affect neurite outgrowth. To this end, dorsal root ganglia cells were seeded onto cultured rat astrocytes that were pre-aligned by exposure to an electric field of physiological strength (500 mV mm(-1)). Using confocal microscopy and digital image analysis, we found that neurite outgrowth at 24 hours and at 48 hours is enhanced significantly and directed consistently along the aligned astrocyte processes. Moreover, this directed neurite outgrowth is maintained when grown on fixed, aligned astrocytes. Collectively, these results indicate that endogenous electric fields present within the developing CNS might act to align astrocyte processes, which can promote and direct neurite growth. Furthermore, these results demonstrate a simple method to produce an aligned cellular substrate, which might be used to direct regenerating neurites.

Alignment and orientation in ion/endash/atom collisions

International Nuclear Information System (INIS)

Kimura, M.; Lane, N.F.

1987-01-01

Recent progress in the theoretical study of alignment and orientation in atom-atom and ion-atom collisions at intermediate energies is reviewed. Recent systematic studies of the alignment and orientation of electronic charge cloud distributions of excited states resulting from such collisions clearly have provided more detailed information about the underlying collision dynamics. However, since accurate determination of these parameters is quite difficult, both theoretically and experimentally, a close collaboration between theory and experiment is necessary for a deeper understanding of the collision dynamics. A more complete approach, where the full density matrix is determined, is also discussed

A comparative study of two different clear aligner systems.

Science.gov (United States)

Ercoli, Federica; Tepedino, Michele; Parziale, Vincenzo; Luzi, Cesare

2014-05-02

This study aims to compare the 'Nuvola®' system with 'Fantasmino®' system, examine their material properties, and define the indications for use of the aligners. Two groups of patients were selected and were respectively treated with Nuvola® aligner and Fantasmino® system. The goal of treatment has been achieved with the two systems. The two types of aligners have shown differences during the treatment. Fantasmino® system has elastic properties of high performance, but its size does not encourage compliance throughout the day. Nuvola® system determines good tooth movement and its size facilitates the patient's collaboration. In both aligner systems, difficulties were found in the correction of torque information and rotations.

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

DEFF Research Database (Denmark)

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

2017-01-01

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

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

Science.gov (United States)

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

2014-07-01

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

Laser beam alignment and profilometry using diagnostic fluorescent safety mirrors

Science.gov (United States)

Lizotte, Todd E.

2011-03-01

There are a wide range of laser beam delivery systems in use for various purposes; including industrial and medical applications. Virtually all such beam delivery systems for practical purposes employ optical systems comprised of mirrors and lenses to shape, focus and guide the laser beam down to the material being processed. The goal of the laser beam delivery is to set the optimum parameters and to "fold" the beam path to reduce the mechanical length of the optical system, thereby allowing a physically compact system. In many cases, even a compact system can incorporate upwards of six mirrors and a comparable number of lenses all needing alignment so they are collinear. One of the major requirements for use of such systems in industry is a method of safe alignment. The alignment process requires that the aligner determine where the beam strikes each element. The aligner should also preferably be able to determine the shape or pattern of the laser beam at that point and its relative power. These alignments are further compounded in that the laser beams generated are not visible to the unaided human eye. Such beams are also often of relatively high power levels, and are thereby a significant hazard to the eyes of the aligner. Obvious an invisible beam makes it nearly impossible to align laser system without some form of optical assistance. The predominant method of visually aligning the laser beam delivery is the use of thermal paper, paper cards or fluorescing card material. The use of paper products which have limited power handling capability or coated plastics can produce significant debris and contaminants within the beam line that ultimately damage the optics. The use of the cards can also create significant laser light scatter jeopardizing the safety of the person aligning the system. This paper covers a new safety mirror design for use with at various UV and Near IR wavelengths (193 nm to 1064 nm) within laser beam delivery systems and how its use can

Noisy: Identification of problematic columns in multiple sequence alignments

Directory of Open Access Journals (Sweden)

Grünewald Stefan

2008-06-01

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

Reverse alignment "mirror image" visualization as a laparoscopic training tool improves task performance.

Science.gov (United States)

Dunnican, Ward J; Singh, T Paul; Ata, Ashar; Bendana, Emma E; Conlee, Thomas D; Dolce, Charles J; Ramakrishnan, Rakesh

2010-06-01

Reverse alignment (mirror image) visualization is a disconcerting situation occasionally faced during laparoscopic operations. This occurs when the camera faces back at the surgeon in the opposite direction from which the surgeon's body and instruments are facing. Most surgeons will attempt to optimize trocar and camera placement to avoid this situation. The authors' objective was to determine whether the intentional use of reverse alignment visualization during laparoscopic training would improve performance. A standard box trainer was configured for reverse alignment, and 34 medical students and junior surgical residents were randomized to train with either forward alignment (DIRECT) or reverse alignment (MIRROR) visualization. Enrollees were tested on both modalities before and after a 4-week structured training program specific to their modality. Student's t test was used to determine differences in task performance between the 2 groups. Twenty-one participants completed the study (10 DIRECT, 11 MIRROR). There were no significant differences in performance time between DIRECT or MIRROR participants during forward or reverse alignment initial testing. At final testing, DIRECT participants had improved times only in forward alignment performance; they demonstrated no significant improvement in reverse alignment performance. MIRROR participants had significant time improvement in both forward and reverse alignment performance at final testing. Reverse alignment imaging for laparoscopic training improves task performance for both reverse alignment and forward alignment tasks. This may be translated into improved performance in the operating room when faced with reverse alignment situations. Minimal lab training can account for drastic adaptation to this environment.

Procedure, algorithm and criterions of determination of a burnup of a irradiated nuclear fuel in process of overloading

International Nuclear Information System (INIS)

Bilej, D.V.; Fridman, N.A.; Maslov, O.V.; Maksimov, M.V.

2001-01-01

The procedure, algorithm and criterions of determination of a burnup of the irradiated nuclear fuel in process of overloading are described. The feature of the procedure, algorithm and criterions consists in the account of initial enrichment and cooling time nuclear fuel after irradiation

Determining Optimal Replacement Policy with an Availability Constraint via Genetic Algorithms

OpenAIRE

Zong, Shengliang; Chai, Guorong; Su, Yana

2017-01-01

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 requi...

Advanced metaheuristic algorithms for laser optimization

International Nuclear Information System (INIS)

Tomizawa, H.

2010-01-01

A laser is one of the most important experimental tools. In synchrotron radiation field, lasers are widely used for experiments with Pump-Probe techniques. Especially for Xray-FELs, a laser has important roles as a seed light source or photo-cathode-illuminating light source to generate a high brightness electron bunch. The controls of laser pulse characteristics are required for many kinds of experiments. However, the laser should be tuned and customized for each requirement by laser experts. The automatic tuning of laser is required to realize with some sophisticated algorithms. The metaheuristic algorithm is one of the useful candidates to find one of the best solutions as acceptable as possible. The metaheuristic laser tuning system is expected to save our human resources and time for the laser preparations. I have shown successful results on a metaheuristic algorithm based on a genetic algorithm to optimize spatial (transverse) laser profiles and a hill climbing method extended with a fuzzy set theory to choose one of the best laser alignments automatically for each experimental requirement. (author)

3D head pose estimation and tracking using particle filtering and ICP algorithm

KAUST Repository

Ben Ghorbel, Mahdi; Baklouti, Malek; Couvet, Serge

2010-01-01

This paper addresses the issue of 3D head pose estimation and tracking. Existing approaches generally need huge database, training procedure, manual initialization or use face feature extraction manually extracted. We propose a framework for estimating the 3D head pose in its fine level and tracking it continuously across multiple Degrees of Freedom (DOF) based on ICP and particle filtering. We propose to approach the problem, using 3D computational techniques, by aligning a face model to the 3D dense estimation computed by a stereo vision method, and propose a particle filter algorithm to refine and track the posteriori estimate of the position of the face. This work comes with two contributions: the first concerns the alignment part where we propose an extended ICP algorithm using an anisotropic scale transformation. The second contribution concerns the tracking part. We propose the use of the particle filtering algorithm and propose to constrain the search space using ICP algorithm in the propagation step. The results show that the system is able to fit and track the head properly, and keeps accurate the results on new individuals without a manual adaptation or training. © Springer-Verlag Berlin Heidelberg 2010.

Algorithm for determining two-periodic steady-states in AC machines directly in time domain

Directory of Open Access Journals (Sweden)

Sobczyk Tadeusz J.

2016-09-01

Full Text Available This paper describes an algorithm for finding steady states in AC machines for the cases of their two-periodic nature. The algorithm enables to specify the steady-state solution identified directly in time domain despite of the fact that two-periodic waveforms are not repeated in any finite time interval. The basis for such an algorithm is a discrete differential operator that specifies the temporary values of the derivative of the two-periodic function in the selected set of points on the basis of the values of that function in the same set of points. It allows to develop algebraic equations defining the steady state solution reached in a chosen point set for the nonlinear differential equations describing the AC machines when electrical and mechanical equations should be solved together. That set of those values allows determining the steady state solution at any time instant up to infinity. The algorithm described in this paper is competitive with respect to the one known in literature an approach based on the harmonic balance method operated in frequency domain.