WorldWideScience

Sample records for high accuracy alignment

  1. 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.

  2. A New Three-Dimensional High-Accuracy Automatic Alignment System For Single-Mode Fibers

    Science.gov (United States)

    Yun-jiang, Rao; Shang-lian, Huang; Ping, Li; Yu-mei, Wen; Jun, Tang

    1990-02-01

    In order to achieve the low-loss splices of single-mode fibers, a new three-dimension high-accuracy automatic alignment system for single -mode fibers has been developed, which includes a new-type three-dimension high-resolution microdisplacement servo stage driven by piezoelectric elements, a new high-accuracy measurement system for the misalignment error of the fiber core-axis, and a special single chip microcomputer processing system. The experimental results show that alignment accuracy of ±0.1 pin with a movable stroke of -±20μm has been obtained. This new system has more advantages than that reported.

  3. PACMAN Project: A New Solution for the High-accuracy Alignment of Accelerator Components

    CERN Document Server

    Mainaud Durand, Helene; Buzio, Marco; Caiazza, Domenico; Catalán Lasheras, Nuria; Cherif, Ahmed; Doytchinov, Iordan; Fuchs, Jean-Frederic; Gaddi, Andrea; Galindo Munoz, Natalia; Gayde, Jean-Christophe; Kamugasa, Solomon; Modena, Michele; Novotny, Peter; Russenschuck, Stephan; Sanz, Claude; Severino, Giordana; Tshilumba, David; Vlachakis, Vasileios; Wendt, Manfred; Zorzetti, Silvia

    2016-01-01

    The beam alignment requirements for the next generation of lepton colliders have become increasingly challenging. As an example, the alignment requirements for the three major collider components of the CLIC linear collider are as follows. Before the first beam circulates, the Beam Position Monitors (BPM), Accelerating Structures (AS)and quadrupoles will have to be aligned up to 10 μm w.r.t. a straight line over 200 m long segments, along the 20 km of linacs. PACMAN is a study on Particle Accelerator Components' Metrology and Alignment to the Nanometre scale. It is an Innovative Doctoral Program, funded by the EU and hosted by CERN, providing high quality training to 10 Early Stage Researchers working towards a PhD thesis. The technical aim of the project is to improve the alignment accuracy of the CLIC components by developing new methods and tools addressing several steps of alignment simultaneously, to gain time and accuracy. The tools and methods developed will be validated on a test bench. This paper pr...

  4. Multiple sequence alignment accuracy and phylogenetic inference.

    Science.gov (United States)

    Ogden, T Heath; Rosenberg, Michael S

    2006-04-01

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

  5. 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

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

    Science.gov (United States)

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

    2012-07-15

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

  7. 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/

  8. High-accuracy alignment based on atmospherical dispersion - technological approaches and solutions for the dual-wavelength transmitter

    International Nuclear Information System (INIS)

    Burkhard, Boeckem

    1999-01-01

    In the course of the progressive developments of sophisticated geodetic systems utilizing electromagnetic waves in the visible or near IR-range a more detailed knowledge of the propagation medium and coevally solutions of atmospherically induced limitations will become important. An alignment system based on atmospherical dispersion, called a dispersometer, is a metrological solution to the atmospherically induced limitations, in optical alignment and direction observations of high accuracy. In the dispersometer we are using the dual-wavelength method for dispersive air to obtain refraction compensated angle measurements, the detrimental impact of atmospheric turbulence notwithstanding. The principle of the dual-wavelength method utilizes atmospherical dispersion, i.e. the wavelength dependence of the refractive index. The difference angle between two light beams of different wavelengths, which is called the dispersion angle Δβ, is to first approximation proportional to the refraction angle: β IR ν(β blue - β IR ) = ν Δβ, this equation implies that the dispersion angle has to be measured at least 42 times more accurate than the desired accuracy of the refraction angle for the wavelengths used in the present dispersometer. This required accuracy constitutes one major difficulty for the instrumental performance in applying the dispersion effect. However, the dual-wavelength method can only be successfully used in an optimized transmitter-receiver combination. Beyond the above mentioned resolution requirement for the detector, major difficulties in instrumental realization arise in the availability of a suitable dual-wavelength laser light source, laser light modulation with a very high extinction ratio and coaxial emittance of mono-mode radiation at both wavelengths. Therefore, this paper focuses on the solutions of the dual-wavelength transmitter introducing a new hardware approach and a complete re-design of the in [1] proposed conception of the dual

  9. Accuracy of binary black hole waveform models for aligned-spin binaries

    Science.gov (United States)

    Kumar, Prayush; Chu, Tony; Fong, Heather; Pfeiffer, Harald P.; Boyle, Michael; Hemberger, Daniel A.; Kidder, Lawrence E.; Scheel, Mark A.; Szilagyi, Bela

    2016-05-01

    Coalescing binary black holes are among the primary science targets for second generation ground-based gravitational wave detectors. Reliable gravitational waveform models are central to detection of such systems and subsequent parameter estimation. This paper performs a comprehensive analysis of the accuracy of recent waveform models for binary black holes with aligned spins, utilizing a new set of 84 high-accuracy numerical relativity simulations. Our analysis covers comparable mass binaries (mass-ratio 1 ≤q ≤3 ), and samples independently both black hole spins up to a dimensionless spin magnitude of 0.9 for equal-mass binaries and 0.85 for unequal mass binaries. Furthermore, we focus on the high-mass regime (total mass ≳50 M⊙ ). The two most recent waveform models considered (PhenomD and SEOBNRv2) both perform very well for signal detection, losing less than 0.5% of the recoverable signal-to-noise ratio ρ , except that SEOBNRv2's efficiency drops slightly for both black hole spins aligned at large magnitude. For parameter estimation, modeling inaccuracies of the SEOBNRv2 model are found to be smaller than systematic uncertainties for moderately strong GW events up to roughly ρ ≲15 . PhenomD's modeling errors are found to be smaller than SEOBNRv2's, and are generally irrelevant for ρ ≲20 . Both models' accuracy deteriorates with increased mass ratio, and when at least one black hole spin is large and aligned. The SEOBNRv2 model shows a pronounced disagreement with the numerical relativity simulation in the merger phase, for unequal masses and simultaneously both black hole spins very large and aligned. Two older waveform models (PhenomC and SEOBNRv1) are found to be distinctly less accurate than the more recent PhenomD and SEOBNRv2 models. Finally, we quantify the bias expected from all four waveform models during parameter estimation for several recovered binary parameters: chirp mass, mass ratio, and effective spin.

  10. High-resolution accelerator alignment using x-ray optics

    Directory of Open Access Journals (Sweden)

    Bingxin Yang

    2006-03-01

    Full Text Available We propose a novel alignment technique utilizing the x-ray beam of an undulator in conjunction with pinholes and position-sensitive detectors for positioning components of the accelerator, undulator, and beam line in an x-ray free-electron laser. Two retractable pinholes at each end of the undulator define a stable and reproducible x-ray beam axis (XBA. Targets are precisely positioned on the XBA using a pinhole camera technique. Position-sensitive detectors responding to both x-ray and electron beams enable direct transfer of the position setting from the XBA to the electron beam. This system has the potential to deliver superior alignment accuracy (1–3   μm for target pinholes in the transverse directions over a long distance (200 m or longer. It can be used to define the beam axis of the electron-beam–based alignment, enabling high reproducibility of the latter. This x-ray–based concept should complement the electron-beam–based alignment and the existing survey methods to raise the alignment accuracy of long accelerators to an unprecedented level. Further improvement of the transverse accuracy using x-ray zone plates will be discussed. We also propose a concurrent measurement scheme during accelerator operation to allow real-time feedback for transverse position correction.

  11. Passive photonic alignment with submicrometer repeatability and accuracy

    NARCIS (Netherlands)

    Gurp, J.F.C.; Tichem, M; Staufer, U.; Zhao, J.

    2013-01-01

    In this paper, we report on passive alignment with submicrometer accuracy of two photonic chips on a silicon optical bench. An effective design principle to minimize the tolerance chain is presented and applied to a case study. The chips have been successfully manufactured and an experimental setup

  12. Accuracy of target localisation and alignment in stereotactic radiosurgery at Royal Prince Alfred Hospital

    International Nuclear Information System (INIS)

    Downes, S.

    1996-01-01

    Full text: Over the last 30 years, stereotactic radiosurgery has become an effective clinical tool in the treatment of intra-cranial lesions. The use of high doses to a specific target volume in a single fraction and the proximity of critical organs requires very accurate geometric localisation of the various cranial structures (using CT, MRI and angiography imaging) and accurate alignment of the target volume prior to treatment. The purpose of this paper was to determine the accuracy of localising cranial structures using computed tomography and angiographic imaging modalities and to determine the accuracy of aligning the treatment isocentre to the specified coordinates. The sum of these two errors will give the total deviation of the treated target from the actual target. Measurements were made using an anthropomorphic (ART) phantom of an adult male and a cerrobend target. The ART phantom was immobilised using the Brown-Roberts-Wells (BRW) ring. The cerrobend target was inserted into the skull at 10 different positions. Each of these 10 positions were scanned using CT and angiographic imaging and localised using the stereotactic planning software. For each test position, the ART phantom was placed on the treatment couch and aligned to the treatment coordinates determined using localisation (CT and angiography). A-P and lateral port films were then made of the target. The distance between the centre of the cerrobend target (intended target) and the centre of radiation (actual target) was the total error in localisation and alignment of the target. For computed tomography, the measurements showed the average error in localisation and alignment of the target was ±0.7mm. In terms of coordinate axis, the average error was: A-P axis = ±0.5mm, Lateral(left-right) Axis = ±0.3mm, Vertical(inferior superior) Axis ±0.4mm. From these measurements it was shown that using the stereotactic radiosurgery planning system and hardware, cranial lesions could be localised and

  13. Improving the accuracy of protein secondary structure prediction using structural alignment

    Directory of Open Access Journals (Sweden)

    Gallin Warren J

    2006-06-01

    Full Text Available Abstract Background The accuracy of protein secondary structure prediction has steadily improved over the past 30 years. Now many secondary structure prediction methods routinely achieve an accuracy (Q3 of about 75%. We believe this accuracy could be further improved by including structure (as opposed to sequence database comparisons as part of the prediction process. Indeed, given the large size of the Protein Data Bank (>35,000 sequences, the probability of a newly identified sequence having a structural homologue is actually quite high. Results We have developed a method that performs structure-based sequence alignments as part of the secondary structure prediction process. By mapping the structure of a known homologue (sequence ID >25% onto the query protein's sequence, it is possible to predict at least a portion of that query protein's secondary structure. By integrating this structural alignment approach with conventional (sequence-based secondary structure methods and then combining it with a "jury-of-experts" system to generate a consensus result, it is possible to attain very high prediction accuracy. Using a sequence-unique test set of 1644 proteins from EVA, this new method achieves an average Q3 score of 81.3%. Extensive testing indicates this is approximately 4–5% better than any other method currently available. Assessments using non sequence-unique test sets (typical of those used in proteome annotation or structural genomics indicate that this new method can achieve a Q3 score approaching 88%. Conclusion By using both sequence and structure databases and by exploiting the latest techniques in machine learning it is possible to routinely predict protein secondary structure with an accuracy well above 80%. A program and web server, called PROTEUS, that performs these secondary structure predictions is accessible at http://wishart.biology.ualberta.ca/proteus. For high throughput or batch sequence analyses, the PROTEUS programs

  14. An automatic and accurate x-ray tube focal spot/grid alignment system for mobile radiography: System description and alignment accuracy

    International Nuclear Information System (INIS)

    Gauntt, David M.; Barnes, Gary T.

    2010-01-01

    Purpose: A mobile radiography automatic grid alignment system (AGAS) has been developed by modifying a commercially available mobile unit. The objectives of this article are to describe the modifications and operation and to report on the accuracy with which the focal spot is aligned to the grid and the time required to achieve the alignment. Methods: The modifications include an optical target arm attached to the grid tunnel, a video camera attached to the collimator, a motion control system with six degrees of freedom to position the collimator and x-ray tube, and a computer to control the system. The video camera and computer determine the grid position, and then the motion control system drives the x-ray focal spot to the center of the grid focal axis. The accuracy of the alignment of the focal spot with the grid and the time required to achieve alignment were measured both in laboratory tests and in clinical use. Results: For a typical exam, the modified unit automatically aligns the focal spot with the grid in less than 10 s, with an accuracy of better than 4 mm. The results of the speed and accuracy tests in clinical use were similar to the results in laboratory tests. Comparison patient chest images are presented--one obtained with a standard mobile radiographic unit without a grid and the other obtained with the modified unit and a 15:1 grid. The 15:1 grid images demonstrate a marked improvement in image quality compared to the nongrid images with no increase in patient dose. Conclusions: The mobile radiography AGAS produces images of significantly improved quality compared to nongrid images with alignment times of less than 10 s and no increase in patient dose.

  15. High accuracy prediction of beta-turns and their types using propensities and multiple alignments.

    Science.gov (United States)

    Fuchs, Patrick F J; Alix, Alain J P

    2005-06-01

    We have developed a method that predicts both the presence and the type of beta-turns, using a straightforward approach based on propensities and multiple alignments. The propensities were calculated classically, but the way to use them for prediction was completely new: starting from a tetrapeptide sequence on which one wants to evaluate the presence of a beta-turn, the propensity for a given residue is modified by taking into account all the residues present in the multiple alignment at this position. The evaluation of a score is then done by weighting these propensities by the use of Position-specific score matrices generated by PSI-BLAST. The introduction of secondary structure information predicted by PSIPRED or SSPRO2 as well as taking into account the flanking residues around the tetrapeptide improved the accuracy greatly. This latter evaluated on a database of 426 reference proteins (previously used on other studies) by a sevenfold crossvalidation gave very good results with a Matthews Correlation Coefficient (MCC) of 0.42 and an overall prediction accuracy of 74.8%; this places our method among the best ones. A jackknife test was also done, which gave results within the same range. This shows that it is possible to reach neural networks accuracy with considerably less computional cost and complexity. Furthermore, propensities remain excellent descriptors of amino acid tendencies to belong to beta-turns, which can be useful for peptide or protein engineering and design. For beta-turn type prediction, we reached the best accuracy ever published in terms of MCC (except for the irregular type IV) in the range of 0.25-0.30 for types I, II, and I' and 0.13-0.15 for types VIII, II', and IV. To our knowledge, our method is the only one available on the Web that predicts types I' and II'. The accuracy evaluated on two larger databases of 547 and 823 proteins was not improved significantly. All of this was implemented into a Web server called COUDES (French acronym

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

    Science.gov (United States)

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

    2010-10-01

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

  17. Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.

    Directory of Open Access Journals (Sweden)

    Shunichi Kosugi

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

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

    Directory of Open Access Journals (Sweden)

    Yong-Gang Zhang

    2014-01-01

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

  19. In-plane laser forming for high precision alignment

    NARCIS (Netherlands)

    Folkersma, Ger; Römer, Gerardus Richardus, Bernardus, Engelina; Brouwer, Dannis Michel; Huis in 't Veld, Bert

    2014-01-01

    Laser microforming is extensively used to align components with submicrometer accuracy, often after assembly. While laser-bending sheet metal is the most common laser-forming mechanism, the in-plane upsetting mechanism is preferred when a high actuator stiffness is required. A three-bridge planar

  20. 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.

  1. TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction.

    Science.gov (United States)

    Chang, Jia-Ming; Di Tommaso, Paolo; Notredame, Cedric

    2014-06-01

    Multiple sequence alignment (MSA) is a key modeling procedure when analyzing biological sequences. Homology and evolutionary modeling are the most common applications of MSAs. Both are known to be sensitive to the underlying MSA accuracy. In this work, we show how this problem can be partly overcome using the transitive consistency score (TCS), an extended version of the T-Coffee scoring scheme. Using this local evaluation function, we show that one can identify the most reliable portions of an MSA, as judged from BAliBASE and PREFAB structure-based reference alignments. We also show how this measure can be used to improve phylogenetic tree reconstruction using both an established simulated data set and a novel empirical yeast data set. For this purpose, we describe a novel lossless alternative to site filtering that involves overweighting the trustworthy columns. Our approach relies on the T-Coffee framework; it uses libraries of pairwise alignments to evaluate any third party MSA. Pairwise projections can be produced using fast or slow methods, thus allowing a trade-off between speed and accuracy. We compared TCS with Heads-or-Tails, GUIDANCE, Gblocks, and trimAl and found it to lead to significantly better estimates of structural accuracy and more accurate phylogenetic trees. The software is available from www.tcoffee.org/Projects/tcs. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  2. 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...

  3. Integrated three-dimensional digital assessment of accuracy of anterior tooth movement using clear aligners

    OpenAIRE

    Zhang, Xiao-Juan; He, Li; Guo, Hong-Ming; Tian, Jie; Bai, Yu-Xing; Li, Song

    2015-01-01

    Objective To assess the accuracy of anterior tooth movement using clear aligners in integrated three-dimensional digital models. Methods Cone-beam computed tomography was performed before and after treatment with clear aligners in 32 patients. Plaster casts were laser-scanned for virtual setup and aligner fabrication. Differences in predicted and achieved root and crown positions of anterior teeth were compared on superimposed maxillofacial digital images and virtual models and analyzed by St...

  4. A Computer Navigation System Analysis of the Accuracy of the Extramedullary (Tibial Alignment Technique in Total Knee Arthroplasty (TKA

    Directory of Open Access Journals (Sweden)

    EK Chee

    2010-07-01

    Full Text Available In total knee arthroplasty, mechanical alignment guides have improved the accuracy of implant alignment, but errors are not uncommon. In the present study, an image-free computer-assisted navigation system was used to analyse the accuracy of an extramedullary (tibial alignment system, which is based on predetermined, fixed anatomical landmarks. Comparisons were made between two surgeons, with different levels of competency in order to determine if experience affected the accuracy of extramedullary tibial jig placement, in either the coronal and sagittal planes or both planes. The results showed that the accuracy of the extramedullary tibial alignment system, in the coronal plane (in up to 80-87% of cases was much better than for posterior slope, and sagittal plane. Surgeon experience was not a significant factor.

  5. Refinement procedure for the image alignment in high-resolution electron tomography

    International Nuclear Information System (INIS)

    Houben, L.; Bar Sadan, M.

    2011-01-01

    High-resolution electron tomography from a tilt series of transmission electron microscopy images requires an accurate image alignment procedure in order to maximise the resolution of the tomogram. This is the case in particular for ultra-high resolution where even very small misalignments between individual images can dramatically reduce the fidelity of the resultant reconstruction. A tomographic-reconstruction based and marker-free method is proposed, which uses an iterative optimisation of the tomogram resolution. The method utilises a search algorithm that maximises the contrast in tomogram sub-volumes. Unlike conventional cross-correlation analysis it provides the required correlation over a large tilt angle separation and guarantees a consistent alignment of images for the full range of object tilt angles. An assessment based on experimental reconstructions shows that the marker-free procedure is competitive to the reference of marker-based procedures at lower resolution and yields sub-pixel accuracy even for simulated high-resolution data. -- Highlights: → Alignment procedure for electron tomography based on iterative tomogram contrast optimisation. → Marker-free, independent of object, little user interaction. → Accuracy competitive with fiducial marker methods and suited for high-resolution tomography.

  6. Fiducialisation and initial alignment of CLIC component with micrometric accuracy

    CERN Document Server

    Mainaud Durand, Helene; Buzio, Marco; Caiazza, Domenico; Catalan Lasheras, Nuria; Cherif, Ahmed; Doytchinov, Iordan Petrov; Fuchs, Jean-Frederic; Gaddi, Andrea; Galindo Munoz, Natalia; Gayde, Jean-Christophe; Kamugasa, Solomon William; Modena, Michele; Novotny, Peter; Sanz, Claude; Severino, Giordana; Russenschuck, Stephan; Tshilumba, David; Vlachakis, Vasileios; Wendt, Manfred; Zorzetti, Silvia; CERN. Geneva. ATS Department

    2016-01-01

    We propose a new solution to fiducialise the three major components of the CLIC collider: quadrupoles, beam-position monitors (BPM), and accelerating structures (AS). This solution is based on the use of a copper-beryllium (CuBe) wire to locate the reference position, i.e. the symmetry axes of the components (their magnetic, respectively electromagnetic centre axis), and to determine their position in the common support assembly defining a local coordinate system, with respect to the fiducials. These alignment targets will be used later to align the support assembly in the tunnel. With such a method, several accelerator components of different types, supported by a dedicated adjustment system, can be simultaneously fiducialised and pre-aligned using the same wire, enabling a micrometric accuracy with help of a 3D coordinate measurement machine (CMM). Alternative solutions based on frequency scanning interferometry (FSI) and micro-triangulation are also under development, to perform such fiducialisation and in...

  7. 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.

  8. High accuracy FIONA-AFM hybrid imaging

    International Nuclear Information System (INIS)

    Fronczek, D.N.; Quammen, C.; Wang, H.; Kisker, C.; Superfine, R.; Taylor, R.; Erie, D.A.; Tessmer, I.

    2011-01-01

    Multi-protein complexes are ubiquitous and play essential roles in many biological mechanisms. Single molecule imaging techniques such as electron microscopy (EM) and atomic force microscopy (AFM) are powerful methods for characterizing the structural properties of multi-protein and multi-protein-DNA complexes. However, a significant limitation to these techniques is the ability to distinguish different proteins from one another. Here, we combine high resolution fluorescence microscopy and AFM (FIONA-AFM) to allow the identification of different proteins in such complexes. Using quantum dots as fiducial markers in addition to fluorescently labeled proteins, we are able to align fluorescence and AFM information to ≥8 nm accuracy. This accuracy is sufficient to identify individual fluorescently labeled proteins in most multi-protein complexes. We investigate the limitations of localization precision and accuracy in fluorescence and AFM images separately and their effects on the overall registration accuracy of FIONA-AFM hybrid images. This combination of the two orthogonal techniques (FIONA and AFM) opens a wide spectrum of possible applications to the study of protein interactions, because AFM can yield high resolution (5-10 nm) information about the conformational properties of multi-protein complexes and the fluorescence can indicate spatial relationships of the proteins in the complexes. -- Research highlights: → Integration of fluorescent signals in AFM topography with high (<10 nm) accuracy. → Investigation of limitations and quantitative analysis of fluorescence-AFM image registration using quantum dots. → Fluorescence center tracking and display as localization probability distributions in AFM topography (FIONA-AFM). → Application of FIONA-AFM to a biological sample containing damaged DNA and the DNA repair proteins UvrA and UvrB conjugated to quantum dots.

  9. Integrated three-dimensional digital assessment of accuracy of anterior tooth movement using clear aligners.

    Science.gov (United States)

    Zhang, Xiao-Juan; He, Li; Guo, Hong-Ming; Tian, Jie; Bai, Yu-Xing; Li, Song

    2015-11-01

    To assess the accuracy of anterior tooth movement using clear aligners in integrated three-dimensional digital models. Cone-beam computed tomography was performed before and after treatment with clear aligners in 32 patients. Plaster casts were laser-scanned for virtual setup and aligner fabrication. Differences in predicted and achieved root and crown positions of anterior teeth were compared on superimposed maxillofacial digital images and virtual models and analyzed by Student's t-test. The mean discrepancies in maxillary and mandibular crown positions were 0.376 ± 0.041 mm and 0.398 ± 0.037 mm, respectively. Maxillary and mandibular root positions differed by 2.062 ± 0.128 mm and 1.941 ± 0.154 mm, respectively. Crowns but not roots of anterior teeth can be moved to designated positions using clear aligners, because these appliances cause tooth movement by tilting motion.

  10. 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.

  11. 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.

  12. Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space

    Directory of Open Access Journals (Sweden)

    Richard Wilton

    2015-03-01

    Full Text Available When computing alignments of DNA sequences to a large genome, a key element in achieving high processing throughput is to prioritize locations in the genome where high-scoring mappings might be expected. We formulated this task as a series of list-processing operations that can be efficiently performed on graphics processing unit (GPU hardware.We followed this approach in implementing a read aligner called Arioc that uses GPU-based parallel sort and reduction techniques to identify high-priority locations where potential alignments may be found. We then carried out a read-by-read comparison of Arioc’s reported alignments with the alignments found by several leading read aligners. With simulated reads, Arioc has comparable or better accuracy than the other read aligners we tested. With human sequencing reads, Arioc demonstrates significantly greater throughput than the other aligners we evaluated across a wide range of sensitivity settings. The Arioc software is available at https://github.com/RWilton/Arioc. It is released under a BSD open-source license.

  13. An improved image alignment procedure for high-resolution transmission electron microscopy.

    Science.gov (United States)

    Lin, Fang; Liu, Yan; Zhong, Xiaoyan; Chen, Jianghua

    2010-06-01

    Image alignment is essential for image processing methods such as through-focus exit-wavefunction reconstruction and image averaging in high-resolution transmission electron microscopy. Relative image displacements exist in any experimentally recorded image series due to the specimen drifts and image shifts, hence image alignment for correcting the image displacements has to be done prior to any further image processing. The image displacement between two successive images is determined by the correlation function of the two relatively shifted images. Here it is shown that more accurate image alignment can be achieved by using an appropriate aperture to filter the high-frequency components of the images being aligned, especially for a crystalline specimen with little non-periodic information. For the image series of crystalline specimens with little amorphous, the radius of the filter aperture should be as small as possible, so long as it covers the innermost lattice reflections. Testing with an experimental through-focus series of Si[110] images, the accuracies of image alignment with different correlation functions are compared with respect to the error functions in through-focus exit-wavefunction reconstruction based on the maximum-likelihood method. Testing with image averaging over noisy experimental images from graphene and carbon-nanotube samples, clear and sharp crystal lattice fringes are recovered after applying optimal image alignment. Copyright 2010 Elsevier Ltd. All rights reserved.

  14. Alignment for CSR

    International Nuclear Information System (INIS)

    Wang Shoujin; Man Kaidi; Guo Yizhen; Cai Guozhu; Guo Yuhui

    2002-01-01

    Cooled Storage Ring of Heavy Ion Research Facility in Lanzhou (HIRFL-CSR) belongs to China great scientific project in China. The alignment for it is very difficult because of very large area and very high accuracy. For the special case in HIRFL-CSR, some new methods and new instruments are used, including the construction of survey control network, the usage of laser tracker, and CSR alignment database system with applications developed to store and analyze data. The author describes the whole procedure of CSR alignment

  15. 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.

  16. Refinement procedure for the image alignment in high-resolution electron tomography.

    Science.gov (United States)

    Houben, L; Bar Sadan, M

    2011-01-01

    High-resolution electron tomography from a tilt series of transmission electron microscopy images requires an accurate image alignment procedure in order to maximise the resolution of the tomogram. This is the case in particular for ultra-high resolution where even very small misalignments between individual images can dramatically reduce the fidelity of the resultant reconstruction. A tomographic-reconstruction based and marker-free method is proposed, which uses an iterative optimisation of the tomogram resolution. The method utilises a search algorithm that maximises the contrast in tomogram sub-volumes. Unlike conventional cross-correlation analysis it provides the required correlation over a large tilt angle separation and guarantees a consistent alignment of images for the full range of object tilt angles. An assessment based on experimental reconstructions shows that the marker-free procedure is competitive to the reference of marker-based procedures at lower resolution and yields sub-pixel accuracy even for simulated high-resolution data. Copyright © 2011 Elsevier B.V. All rights reserved.

  17. 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

  18. Improved accuracy of component alignment with the implementation of image-free navigation in total knee arthroplasty.

    Science.gov (United States)

    Rosenberger, Ralf E; Hoser, Christian; Quirbach, Sebastian; Attal, Rene; Hennerbichler, Alfred; Fink, Christian

    2008-03-01

    Accuracy of implant positioning and reconstruction of the mechanical leg axis are major requirements for achieving good long-term results in total knee arthroplasty (TKA). The purpose of the present study was to determine whether image-free computer navigation technology has the potential to improve the accuracy of component alignment in TKA cohorts of experienced surgeons immediately and constantly. One hundred patients with primary arthritis of the knee underwent the unilateral total knee arthroplasty. The cohort of 50 TKAs implanted with conventional instrumentation was directly followed by the cohort of the very first 50 computer-assisted TKAs. All surgeries were performed by two senior surgeons. All patients received the Zimmer NexGen total knee prosthesis (Zimmer Inc., Warsaw, IN, USA). There was no variability regarding surgeons or surgical technique, except for the use of the navigation system (StealthStation) Treon plus Medtronic Inc., Minnesota, MI, USA). Accuracy of implant positioning was measured on postoperative long-leg standing radiographs and standard lateral X-rays with regard to the valgus angle and the coronal and sagittal component angles. In addition, preoperative deformities of the mechanical leg axis, tourniquet time, age, and gender were correlated. Statistical analyses were performed using the SPSS 15.0 (SPSS Inc., Chicago, IL, USA) software package. Independent t-tests were used, with significance set at P alignment between the two cohorts. To compute the rate of optimally implanted prostheses between the two groups we used the chi(2) test. The average postoperative radiological frontal mechanical alignment was 1.88 degrees of varus (range 6.1 degrees of valgus-10.1 degrees of varus; SD 3.68 degrees ) in the conventional cohort and 0.28 degrees of varus (range 3.7 degrees -6.0 degrees of varus; SD 1.97 degrees ) in the navigated cohort. Including all criteria for optimal implant alignment, 16 cases (32%) in the conventional cohort and 31

  19. Three-dimensional analysis of accuracy of patient-matched instrumentation in total knee arthroplasty: Evaluation of intraoperative techniques and postoperative alignment.

    Science.gov (United States)

    Kuwashima, Umito; Mizu-Uchi, Hideki; Okazaki, Ken; Hamai, Satoshi; Akasaki, Yukio; Murakami, Koji; Nakashima, Yasuharu

    2017-11-01

    It is questionable that the accuracies of patient-matched instrumentation (PMI) have been controversial, even though many surgeons follow manufacturers' recommendations. The purpose of this study was to evaluate the accuracy of intraoperative procedures and the postoperative alignment of the femoral side using PMI with 3-dimensional (3D) analysis. Eighteen knees that underwent total knee arthroplasty using MRI-based PMI were assessed. Intraoperative alignment and bone resection errors of the femoral side were evaluated with a CT-based navigation system. A conventional adjustable guide was used to compare cartilage data with that derived by PMI intraoperatively. Postoperative alignment was assessed using a 3D coordinate system with a computer-assisted design software. We also measured the postoperative alignments using conventional alignment guides with the 3D evaluation. Intraoperative coronal alignment with PMI was 90.9° ± 1.6°. Seventeen knees (94.4%) were within 3° of the optimal alignment. Intraoperative rotational alignment of the femoral guide position of PMI was 0.2° ± 1.6°compared with the adjustable guide, with 17 knees (94.4%) differing by 3° or less between the two methods. Maximum differences in coronal and rotation alignment before and after bone cutting were 2.0° and 2.8°, respectively. Postoperative coronal and rotational alignments were 89.4° ± 1.8° and -1.1° ± 1.3°, respectively. In both alignments, 94.4% of cases were within 3° of the optimal value. The PMI group had less outliers than conventional group in rotational alignment (p = 0.018). Our 3D analysis provided evidence that PMI system resulted in reasonably satisfactory alignments both intraoperatively and postoperatively. Surgeons should be aware that certain surgical techniques including bone cutting, and the associated errors may affect postoperative alignment despite accurate PMI positioning. Copyright © 2017 The Japanese Orthopaedic Association. Published by

  20. Development of a High Precision Edge Alignment System for Touch-Panel Glass Substrates

    Directory of Open Access Journals (Sweden)

    Hau-Wei Lee

    2014-06-01

    Full Text Available There are two kinds of alignment systems, marked and unmarked. The glass substrate for touch panels is categorized as an unmarked work piece. Vision based glass substrate alignment (GSA relies on the edge of the glass. Traditional GSA systems compensate first for angular and then for linear error. This reduces alignment accuracy and increases alignment time and edge detection usually takes longer than 10 ms. This study proposes an effortless edge detection method. This method is very simple and can significantly reduce the time taken to detect the edge to about 6 ms using a 1.3 megapixel image. In this study, a floating center idea is used to control the glass substrate on a high precision coplanar XXY alignment stage. According to the method, users can set the rotation center anywhere as long as it is on the working (xy plane. Tolerance prognosis is also considered in this study to help the operator decide if the substrate is usable or should be rejected. The experimental results show alignment repeatability of the x, y, and θ axes to be 1 μm, 1 μm, and 5 arcsec, respectively.

  1. 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

  2. Read-only high accuracy volume holographic optical correlator

    Science.gov (United States)

    Zhao, Tian; Li, Jingming; Cao, Liangcai; He, Qingsheng; Jin, Guofan

    2011-10-01

    A read-only volume holographic correlator (VHC) is proposed. After the recording of all of the correlation database pages by angular multiplexing, a stand-alone read-only high accuracy VHC will be separated from the VHC recording facilities which include the high-power laser and the angular multiplexing system. The stand-alone VHC has its own low power readout laser and very compact and simple structure. Since there are two lasers that are employed for recording and readout, respectively, the optical alignment tolerance of the laser illumination on the SLM is very sensitive. The twodimensional angular tolerance is analyzed based on the theoretical model of the volume holographic correlator. The experimental demonstration of the proposed read-only VHC is introduced and discussed.

  3. Accuracy of the Heidelberg Spectralis in the alignment between near-infrared image and tomographic scan in a model eye: a multicenter study.

    Science.gov (United States)

    Barteselli, Giulio; Bartsch, Dirk-Uwe; Viola, Francesco; Mojana, Francesca; Pellegrini, Marco; Hartmann, Kathrin I; Benatti, Eleonora; Leicht, Simon; Ratiglia, Roberto; Staurenghi, Giovanni; Weinreb, Robert N; Freeman, William R

    2013-09-01

    To evaluate temporal changes and predictors of accuracy in the alignment between simultaneous near-infrared image and optical coherence tomography (OCT) scan on the Heidelberg Spectralis using a model eye. Laboratory investigation. After calibrating the device, 6 sites performed weekly testing of the alignment for 12 weeks using a model eye. The maximum error was compared with multiple variables to evaluate predictors of inaccurate alignment. Variables included the number of weekly scanned patients, total number of OCT scans and B-scans performed, room temperature and its variation, and working time of the scanning laser. A 4-week extension study was subsequently performed to analyze short-term changes in the alignment. The average maximum error in the alignment was 15 ± 6 μm; the greatest error was 35 μm. The error increased significantly at week 1 (P = .01), specifically after the second imaging study (P alignment were temperature variation and scans per patient (P imaging study. To improve the accuracy, room temperature should be kept stable and unnecessary scans should be avoided. The alignment of the device does not need to be checked on a regular basis in the clinical setting, but it should be checked after every other patient for more precise research purposes. Published by Elsevier Inc.

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

    Science.gov (United States)

    Gajek, A.; Strzępek, P.

    2016-09-01

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

  5. High precision mirror alignment mechanism for use in synchrotron radiation beamlines

    International Nuclear Information System (INIS)

    Verma, Adu; Srivastava, P.K.; Das, Suraj; Nookaraju, Mogali

    2009-01-01

    The performance of a synchrotron radiation beamline is highly depends on parameters, crucially on the manufacturing accuracies of the optical elements and very good alignment of optical elements in the beam path. To develop a synchrotron beamline the misalignment effects have to be estimated and the mechanical components that hold optical elements have to be designed and developed within the specified tolerance limits. The translational inaccuracies result in shifting the image spot, which affect the flux throughput. The misorientation errors i.e. the rotation of optical elements about their mean position affects the image quality. The horizontal misorientation i.e. the rotation of an optical element about an axis passing through its centre and perpendicular to the plane containing the mirror has the most sever effect on the spectral resolution of the beamline, because of an increase in the dispersive spot size at the image plane. The design development and testing of a high precision mirror alignment mechanism is reported in this abstract. Though this mirror alignment mechanism is developed for the X-ray diffraction beamline on synchrotron radiation source Indus-2, 2.5 GeV, 300 mA, the design is general purpose and can be adapted for any other synchrotron facility or a similar ultra high vacuum environment. The mirror alignment mechanism is based on a constrained kinematic chain which provides the angular motions about three co-ordinate axes in the range of 0 to ±1° with the backlash free resolution of 1 arc second. The linear motions in three orthogonal directions are performed by other kinematic mounts in the range of 0 to ± 10 mm with a fine adjustment of 10 μm. The motions are transferred from air to ultra high vacuum through bellows. The ultra high vacuum chamber has been designed, fabricated and tested as per the ASME code. The rotational motions of the mirror alignment mechanism has been tested using a laser interferometer. (author)

  6. High Precision Survey and Alignment of Large Linear Accelerators

    CERN Document Server

    Prenting, J

    2004-01-01

    For the future linear accelerator TESLA the demanded accuracy for the alignment of the components is 0.5 mm horizontal and 0.2 mm vertical, both on each 600 m section. Other accelerators require similar accuracies. These demands can not be fulfilled with open-air geodetic methods, mainly because of refraction. Therefore the RTRS (Rapid Tunnel Reference Surveyor), a measurement train performing overlapping multipoint alignment on a reference network is being developed. Two refraction-free realizations of this concept are being developed at the moment: the first one (GeLiS) measures the horizontal co-ordinates using stretched wires, combined with photogrammetric split-image sensors in a distance measurement configuration. In areas of the tunnel where the accelerator is following the earth curvature GeLiS measures the height using a new hydrostatic leveling system. The second concept (LiCAS) is based on laser straightness monitors (LSM) combined with frequency scanning interferometry (FSI) in an evacuated system...

  7. GraphAlignment: Bayesian pairwise alignment of biological networks

    Directory of Open Access Journals (Sweden)

    Kolář Michal

    2012-11-01

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

  8. Face Alignment via Regressing Local Binary Features.

    Science.gov (United States)

    Ren, Shaoqing; Cao, Xudong; Wei, Yichen; Sun, Jian

    2016-03-01

    This paper presents a highly efficient and accurate regression approach for face alignment. Our approach has two novel components: 1) a set of local binary features and 2) a locality principle for learning those features. The locality principle guides us to learn a set of highly discriminative local binary features for each facial landmark independently. The obtained local binary features are used to jointly learn a linear regression for the final output. This approach achieves the state-of-the-art results when tested on the most challenging benchmarks to date. Furthermore, because extracting and regressing local binary features are computationally very cheap, our system is much faster than previous methods. It achieves over 3000 frames per second (FPS) on a desktop or 300 FPS on a mobile phone for locating a few dozens of landmarks. We also study a key issue that is important but has received little attention in the previous research, which is the face detector used to initialize alignment. We investigate several face detectors and perform quantitative evaluation on how they affect alignment accuracy. We find that an alignment friendly detector can further greatly boost the accuracy of our alignment method, reducing the error up to 16% relatively. To facilitate practical usage of face detection/alignment methods, we also propose a convenient metric to measure how good a detector is for alignment initialization.

  9. Chromatic bifocus alignment system for SR stepper

    International Nuclear Information System (INIS)

    Miyatake, Tsutomu

    1991-01-01

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

  10. High-throughput sequence alignment using Graphics Processing Units

    Directory of Open Access Journals (Sweden)

    Trapnell Cole

    2007-12-01

    Full Text Available Abstract Background The recent availability of new, less expensive high-throughput DNA sequencing technologies has yielded a dramatic increase in the volume of sequence data that must be analyzed. These data are being generated for several purposes, including genotyping, genome resequencing, metagenomics, and de novo genome assembly projects. Sequence alignment programs such as MUMmer have proven essential for analysis of these data, but researchers will need ever faster, high-throughput alignment tools running on inexpensive hardware to keep up with new sequence technologies. Results This paper describes MUMmerGPU, an open-source high-throughput parallel pairwise local sequence alignment program that runs on commodity Graphics Processing Units (GPUs in common workstations. MUMmerGPU uses the new Compute Unified Device Architecture (CUDA from nVidia to align multiple query sequences against a single reference sequence stored as a suffix tree. By processing the queries in parallel on the highly parallel graphics card, MUMmerGPU achieves more than a 10-fold speedup over a serial CPU version of the sequence alignment kernel, and outperforms the exact alignment component of MUMmer on a high end CPU by 3.5-fold in total application time when aligning reads from recent sequencing projects using Solexa/Illumina, 454, and Sanger sequencing technologies. Conclusion MUMmerGPU is a low cost, ultra-fast sequence alignment program designed to handle the increasing volume of data produced by new, high-throughput sequencing technologies. MUMmerGPU demonstrates that even memory-intensive applications can run significantly faster on the relatively low-cost GPU than on the CPU.

  11. 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.

  12. Liquid crystallinity driven highly aligned large graphene oxide composites

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-04-15

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

  13. 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

  14. 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.

  15. Efficient alignment-free DNA barcode analytics.

    Science.gov (United States)

    Kuksa, Pavel; Pavlovic, Vladimir

    2009-11-10

    In this work we consider barcode DNA analysis problems and address them using alternative, alignment-free methods and representations which model sequences as collections of short sequence fragments (features). The methods use fixed-length representations (spectrum) for barcode sequences to measure similarities or dissimilarities between sequences coming from the same or different species. The spectrum-based representation not only allows for accurate and computationally efficient species classification, but also opens possibility for accurate clustering analysis of putative species barcodes and identification of critical within-barcode loci distinguishing barcodes of different sample groups. New alignment-free methods provide highly accurate and fast DNA barcode-based identification and classification of species with substantial improvements in accuracy and speed over state-of-the-art barcode analysis methods. We evaluate our methods on problems of species classification and identification using barcodes, important and relevant analytical tasks in many practical applications (adverse species movement monitoring, sampling surveys for unknown or pathogenic species identification, biodiversity assessment, etc.) On several benchmark barcode datasets, including ACG, Astraptes, Hesperiidae, Fish larvae, and Birds of North America, proposed alignment-free methods considerably improve prediction accuracy compared to prior results. We also observe significant running time improvements over the state-of-the-art methods. Our results show that newly developed alignment-free methods for DNA barcoding can efficiently and with high accuracy identify specimens by examining only few barcode features, resulting in increased scalability and interpretability of current computational approaches to barcoding.

  16. An Automatic High Efficient Method for Dish Concentrator Alignment

    Directory of Open Access Journals (Sweden)

    Yong Wang

    2014-01-01

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

  17. 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

  18. How genome complexity can explain the difficulty of aligning reads to genomes.

    Science.gov (United States)

    Phan, Vinhthuy; Gao, Shanshan; Tran, Quang; Vo, Nam S

    2015-01-01

    Although it is frequently observed that aligning short reads to genomes becomes harder if they contain complex repeat patterns, there has not been much effort to quantify the relationship between complexity of genomes and difficulty of short-read alignment. Existing measures of sequence complexity seem unsuitable for the understanding and quantification of this relationship. We investigated several measures of complexity and found that length-sensitive measures of complexity had the highest correlation to accuracy of alignment. In particular, the rate of distinct substrings of length k, where k is similar to the read length, correlated very highly to alignment performance in terms of precision and recall. We showed how to compute this measure efficiently in linear time, making it useful in practice to estimate quickly the difficulty of alignment for new genomes without having to align reads to them first. We showed how the length-sensitive measures could provide additional information for choosing aligners that would align consistently accurately on new genomes. We formally established a connection between genome complexity and the accuracy of short-read aligners. The relationship between genome complexity and alignment accuracy provides additional useful information for selecting suitable aligners for new genomes. Further, this work suggests that the complexity of genomes sometimes should be thought of in terms of specific computational problems, such as the alignment of short reads to genomes.

  19. 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

  20. Seeking the perfect alignment

    CERN Multimedia

    2002-01-01

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

  1. 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.

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

    Directory of Open Access Journals (Sweden)

    Hartmann Stefanie

    2008-03-01

    sequences and gappy multiple sequence alignments can pose a major problem for phylogenetic analysis. The concern will be greatest for high-throughput phylogenomic analyses, in which Neighbor Joining is often the preferred method due to its computational efficiency. Both approaches can be used to increase the accuracy of phylogenetic inference from a gappy alignment. The choice between the two approaches will depend upon how robust the application is to the loss of sequences from the input set, with alignment masking generally giving a much greater improvement in accuracy but at the cost of discarding a larger number of the input sequences.

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

    Science.gov (United States)

    Hartmann, Stefanie; Vision, Todd J

    2008-03-26

    major problem for phylogenetic analysis. The concern will be greatest for high-throughput phylogenomic analyses, in which Neighbor Joining is often the preferred method due to its computational efficiency. Both approaches can be used to increase the accuracy of phylogenetic inference from a gappy alignment. The choice between the two approaches will depend upon how robust the application is to the loss of sequences from the input set, with alignment masking generally giving a much greater improvement in accuracy but at the cost of discarding a larger number of the input sequences.

  4. Alignment system for large high-power CO2 laser fusion systems

    International Nuclear Information System (INIS)

    Bausman, M.D.; Liberman, I.; Manning, J.P.; Singer, S.

    1977-01-01

    Aligning a pulsed CO 2 laser fusion system involves control systems which insure that the centers of beams follow a prescribed path to within 1 mm, that the pointing of the beams is correct to approximately 20 microradians, and that focal spot at the location of the experimental fusion target be placed to accuracies of 10 to 20 micrometers laterally and approximately 50 micrometers axially. These alignments are accomplished by a variety of sensing techniques which include thermal pinholes and quadrant detectors, Seebeck effect silicon detectors, and imaging autocollimating Hartmann test procedures employing ir vidicon systems

  5. High-accuracy local positioning network for the alignment of the Mu2e experiment.

    Energy Technology Data Exchange (ETDEWEB)

    Hejdukova, Jana B. [Czech Technical Univ., Prague (Czech Republic)

    2017-06-01

    This Diploma thesis describes the establishment of a high-precision local positioning network and accelerator alignment for the Mu2e physics experiment. The process of establishing new network consists of few steps: design of the network, pre-analysis, installation works, measurements of the network and making adjustments. Adjustments were performed using two approaches. First is a geodetic approach of taking into account the Earth’s curvature and the metrological approach of a pure 3D Cartesian system on the other side. The comparison of those two approaches is performed and evaluated in the results and compared with expected differences. The effect of the Earth’s curvature was found to be significant for this kind of network and should not be neglected. The measurements were obtained with Absolute Tracker AT401, leveling instrument Leica DNA03 and gyrotheodolite DMT Gyromat 2000. The coordinates of the points of the reference network were determined by the Least Square Meth od and the overall view is attached as Annexes.

  6. Image Alignment for Multiple Camera High Dynamic Range Microscopy.

    Science.gov (United States)

    Eastwood, Brian S; Childs, Elisabeth C

    2012-01-09

    This paper investigates the problem of image alignment for multiple camera high dynamic range (HDR) imaging. HDR imaging combines information from images taken with different exposure settings. Combining information from multiple cameras requires an alignment process that is robust to the intensity differences in the images. HDR applications that use a limited number of component images require an alignment technique that is robust to large exposure differences. We evaluate the suitability for HDR alignment of three exposure-robust techniques. We conclude that image alignment based on matching feature descriptors extracted from radiant power images from calibrated cameras yields the most accurate and robust solution. We demonstrate the use of this alignment technique in a high dynamic range video microscope that enables live specimen imaging with a greater level of detail than can be captured with a single camera.

  7. Self-Assembly of Chip-Size Components with Cavity Structures: High-Precision Alignment and Direct Bonding without Thermal Compression for Hetero Integration

    Directory of Open Access Journals (Sweden)

    Mitsumasa Koyanagi

    2011-02-01

    Full Text Available New surface mounting and packaging technologies, using self-assembly with chips having cavity structures, were investigated for three-dimensional (3D and hetero integration of complementary metal-oxide semiconductors (CMOS and microelectromechanical systems (MEMS. By the surface tension of small droplets of 0.5 wt% hydrogen fluoride (HF aqueous solution, the cavity chips, with a side length of 3 mm, were precisely aligned to hydrophilic bonding regions on the surface of plateaus formed on Si substrates. The plateaus have micro-channels to readily evaporate and fully remove the liquid from the cavities. The average alignment accuracy of the chips with a 1 mm square cavity was found to be 0.4 mm. The alignment accuracy depends, not only on the area of the bonding regions on the substrates and the length of chip periphery without the widths of channels in the plateaus, but also the area wetted by the liquid on the bonding regions. The precisely aligned chips were then directly bonded to the substrates at room temperature without thermal compression, resulting in a high shear bonding strength of more than 10 MPa.

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

    Directory of Open Access Journals (Sweden)

    Genki Terashi

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

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

    Science.gov (United States)

    Terashi, Genki; Takeda-Shitaka, Mayuko

    2015-01-01

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

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

    Science.gov (United States)

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

    2013-05-01

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

  11. Alignment system for SGII-Up laser facility

    Science.gov (United States)

    Gao, Yanqi; Cui, Yong; Li, Hong; Gong, Lei; Lin, Qiang; Liu, Daizhong; Zhu, Baoqiang; Ma, Weixin; Zhu, Jian; Lin, Zunqi

    2018-03-01

    The SGII-Up laser facility in Shanghai is one of the most important high-power laser facilities in China. It is designed to obtain 24 kJ (3ω) of energy with a square pulse of 3 ns using eight laser beams (two bundles). To satisfy the requirements for the safety, efficiency, and quality, an alignment system is developed for this facility. This alignment system can perform automatic alignment of the preamplifier system, main amplifier system, and harmonic conversion system within 30 min before every shot during the routine operation of the facility. In this article, an overview of the alignment system is first presented. Then, its alignment characteristics are discussed, along with the alignment process. Finally, experimental results, including the alignment results and the facility performance, are reported. The results show that the far-field beam pointing alignment accuracy is better than 3 μrad, and the alignment error of the near-field beam centering is no larger than 1 mm. These satisfy the design requirements very well.

  12. From Word Alignment to Word Senses, via Multilingual Wordnets

    Directory of Open Access Journals (Sweden)

    Dan Tufis

    2006-05-01

    Full Text Available Most of the successful commercial applications in language processing (text and/or speech dispense with any explicit concern on semantics, with the usual motivations stemming from the computational high costs required for dealing with semantics, in case of large volumes of data. With recent advances in corpus linguistics and statistical-based methods in NLP, revealing useful semantic features of linguistic data is becoming cheaper and cheaper and the accuracy of this process is steadily improving. Lately, there seems to be a growing acceptance of the idea that multilingual lexical ontologisms might be the key towards aligning different views on the semantic atomic units to be used in characterizing the general meaning of various and multilingual documents. Depending on the granularity at which semantic distinctions are necessary, the accuracy of the basic semantic processing (such as word sense disambiguation can be very high with relatively low complexity computing. The paper substantiates this statement by presenting a statistical/based system for word alignment and word sense disambiguation in parallel corpora. We describe a word alignment platform which ensures text pre-processing (tokenization, POS-tagging, lemmatization, chunking, sentence and word alignment as required by an accurate word sense disambiguation.

  13. Geometric accuracy of field alignment in fractionated stereotactic conformal radiotherapy of brain tumors

    International Nuclear Information System (INIS)

    Kortmann, Rolf D.; Becker, Gerd; Perelmouter, Jury; Buchgeister, Markus; Meisner, Christoph; Bamberg, Michael

    1999-01-01

    Purpose: To assess the accuracy of field alignment in patients undergoing three-dimensional (3D) conformal radiotherapy of brain tumors, and to evaluate the impact on the definition of planning target volume and control procedures. Methods and Materials: Geometric accuracy was analyzed in 20 patients undergoing fractionated stereotactic conformal radiotherapy for brain tumors. Rigid head fixation was achieved by using cast material. Transfer of stereotactic coordinates was performed by an external positioning device. The accuracy during treatment planning was quantitatively assessed by using repeated computed tomography (CT) examinations in treatment position (reproducibility of isocenter). Linear discrepancies were measured between treatment plan and CT examination. In addition, for each patient, a series of 20 verifications were taken in orthogonal projections. Linear discrepancies were measured between first and all subsequent verifications (accuracy during treatment delivery). Results: For the total group of patients, the distribution of deviations during treatment setup showed mean values between -0.3-1.2 mm, with standard deviations (SD) of 1.3-2.0 mm. During treatment delivery, the distribution of deviations revealed mean values between 0.7-0.8 mm, with SDs of 0.5-0.6 mm, respectively. For all patients, deviations for the transition to the treatment machine were similar to deviations during subsequent treatment delivery, with 95% of all absolute deviations between less than 2.8 and 4.6 mm. Conclusion: Random fluctuations of field displacements during treatment planning and delivery prevail. Therefore, our quantitative data should be considered when prescribing the safety margins of the planning target volume. Repeated CT examination are useful to detect operator errors and large random or systematic deviations before start of treatment. Control procedures during treatment delivery appear to be of limited importance. In addition, our findings should help to

  14. CORAL: aligning conserved core regions across domain families.

    Science.gov (United States)

    Fong, Jessica H; Marchler-Bauer, Aron

    2009-08-01

    Homologous protein families share highly conserved sequence and structure regions that are frequent targets for comparative analysis of related proteins and families. Many protein families, such as the curated domain families in the Conserved Domain Database (CDD), exhibit similar structural cores. To improve accuracy in aligning such protein families, we propose a profile-profile method CORAL that aligns individual core regions as gap-free units. CORAL computes optimal local alignment of two profiles with heuristics to preserve continuity within core regions. We benchmarked its performance on curated domains in CDD, which have pre-defined core regions, against COMPASS, HHalign and PSI-BLAST, using structure superpositions and comprehensive curator-optimized alignments as standards of truth. CORAL improves alignment accuracy on core regions over general profile methods, returning a balanced score of 0.57 for over 80% of all domain families in CDD, compared with the highest balanced score of 0.45 from other methods. Further, CORAL provides E-values to aid in detecting homologous protein families and, by respecting block boundaries, produces alignments with improved 'readability' that facilitate manual refinement. CORAL will be included in future versions of the NCBI Cn3D/CDTree software, which can be downloaded at http://www.ncbi.nlm.nih.gov/Structure/cdtree/cdtree.shtml. Supplementary data are available at Bioinformatics online.

  15. 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.

  16. Accuracy of field alignment in abdominal radiation therapy

    International Nuclear Information System (INIS)

    Kortmann, R. D.; Hess, C. F.; Meisner, C.; Schmidberger, H.; Bamberg, M.

    1996-01-01

    Purpose: To assess the accuracy of field alignment in a homogeneous group of patients undergoing radiotherapy of the abdomen (adjuvant treatment of the paraaortic region in Stage I testicular seminoma). To evaluate the predictive value of the first verification on field placement errors during subsequent treatment delivery. Methods and Materials: In 45 patients, linear and rotational discrepancies were measured between simulation and first check and between 10 consecutive verification films. Results: For the total group of patients, the distribution of all deviations showed mean values between 2.3 mm and -2.7 mm with standard deviations of 3.9 mm to 4.7 mm for linear discrepancies, and -0.5 deg. to 0.3 deg. with standard deviations of 1.2 deg. to 2.1 deg. for rotational discrepancies, respectively. For all patients, deviations for the transition from simulator to the treatment machine were similar to deviations during subsequent treatment delivery, with 95% of all absolute deviations < 10.0 mm and 4 deg. , respectively. When performing correlation analysis between deviations at first check and during treatment delivery, a correlation for lateral displacements and a borderline correlation for caudal displacements could be found. There was no correlation for cranial and rotational displacements. Conclusions: Although a trend of deviations for subsequent treatment delivery may be shown at first check, our analysis indicates that the first verification cannot reliably predict inaccuracies during treatment delivery. Random fluctuations of field displacements of up to 1.0 cm prevail. They must be considered when prescribing the safety margins of the planned target volume and determining cutoff points for corrective actions in abdominal radiation therapy

  17. 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.

  18. High-speed all-optical DNA local sequence alignment based on a three-dimensional artificial neural network.

    Science.gov (United States)

    Maleki, Ehsan; Babashah, Hossein; Koohi, Somayyeh; Kavehvash, Zahra

    2017-07-01

    This paper presents an optical processing approach for exploring a large number of genome sequences. Specifically, we propose an optical correlator for global alignment and an extended moiré matching technique for local analysis of spatially coded DNA, whose output is fed to a novel three-dimensional artificial neural network for local DNA alignment. All-optical implementation of the proposed 3D artificial neural network is developed and its accuracy is verified in Zemax. Thanks to its parallel processing capability, the proposed structure performs local alignment of 4 million sequences of 150 base pairs in a few seconds, which is much faster than its electrical counterparts, such as the basic local alignment search tool.

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

    International Nuclear Information System (INIS)

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

    2004-01-01

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

  20. Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline.

    Science.gov (United States)

    Dowsey, Andrew W; Dunn, Michael J; Yang, Guang-Zhong

    2008-04-01

    The quest for high-throughput proteomics has revealed a number of challenges in recent years. Whilst substantial improvements in automated protein separation with liquid chromatography and mass spectrometry (LC/MS), aka 'shotgun' proteomics, have been achieved, large-scale open initiatives such as the Human Proteome Organization (HUPO) Brain Proteome Project have shown that maximal proteome coverage is only possible when LC/MS is complemented by 2D gel electrophoresis (2-DE) studies. Moreover, both separation methods require automated alignment and differential analysis to relieve the bioinformatics bottleneck and so make high-throughput protein biomarker discovery a reality. The purpose of this article is to describe a fully automatic image alignment framework for the integration of 2-DE into a high-throughput differential expression proteomics pipeline. The proposed method is based on robust automated image normalization (RAIN) to circumvent the drawbacks of traditional approaches. These use symbolic representation at the very early stages of the analysis, which introduces persistent errors due to inaccuracies in modelling and alignment. In RAIN, a third-order volume-invariant B-spline model is incorporated into a multi-resolution schema to correct for geometric and expression inhomogeneity at multiple scales. The normalized images can then be compared directly in the image domain for quantitative differential analysis. Through evaluation against an existing state-of-the-art method on real and synthetically warped 2D gels, the proposed analysis framework demonstrates substantial improvements in matching accuracy and differential sensitivity. High-throughput analysis is established through an accelerated GPGPU (general purpose computation on graphics cards) implementation. Supplementary material, software and images used in the validation are available at http://www.proteomegrid.org/rain/.

  1. Image Alignment for Multiple Camera High Dynamic Range Microscopy

    OpenAIRE

    Eastwood, Brian S.; Childs, Elisabeth C.

    2012-01-01

    This paper investigates the problem of image alignment for multiple camera high dynamic range (HDR) imaging. HDR imaging combines information from images taken with different exposure settings. Combining information from multiple cameras requires an alignment process that is robust to the intensity differences in the images. HDR applications that use a limited number of component images require an alignment technique that is robust to large exposure differences. We evaluate the suitability fo...

  2. Vacuum mechatronic laser alignment system on the Nova laser

    International Nuclear Information System (INIS)

    Holliday, M.; Wong, K.; Shelton, R.

    1991-11-01

    The experiments conducted on NOVA are done to investigate inertially confined laser fusion reactions. To this end, the ten beams of the laser are aligned to within 30mm. The target chamber employs a vacuum mechatronic based reticle/target positioning system to accomplish this. It is a five degree-of-freedom chamber resident system, known as the Alignment Aids Positioner or AAP. The AAP aids in beam and diagnostic alignment by accurately positioning a reticle at target chamber center to with 7mm. The AAP system increases target positioning and alignment flexibility and accuracy through the use of a computer controlled multi degree-of-freedom stage assembly. This device uses microstepping DC stepper motors with encoders to achieve closed loop control in a 10 -6 torr vacuum. The AAP has two positioning regimes to move the alignment reticle and do beam alignment. One is course positioning in the Y-Z plane that moves a high resolution stage assembly to target chamber center. The other regime is high resolution movement in the X,Y,Z and q directions. 5 refs., 9 figs

  3. Ultra-high accuracy optical testing: creating diffraction-limitedshort-wavelength optical systems

    Energy Technology Data Exchange (ETDEWEB)

    Goldberg, Kenneth A.; Naulleau, Patrick P.; Rekawa, Senajith B.; Denham, Paul E.; Liddle, J. Alexander; Gullikson, Eric M.; Jackson, KeithH.; Anderson, Erik H.; Taylor, John S.; Sommargren, Gary E.; Chapman,Henry N.; Phillion, Donald W.; Johnson, Michael; Barty, Anton; Soufli,Regina; Spiller, Eberhard A.; Walton, Christopher C.; Bajt, Sasa

    2005-08-03

    Since 1993, research in the fabrication of extreme ultraviolet (EUV) optical imaging systems, conducted at Lawrence Berkeley National Laboratory (LBNL) and Lawrence Livermore National Laboratory (LLNL), has produced the highest resolution optical systems ever made. We have pioneered the development of ultra-high-accuracy optical testing and alignment methods, working at extreme ultraviolet wavelengths, and pushing wavefront-measuring interferometry into the 2-20-nm wavelength range (60-600 eV). These coherent measurement techniques, including lateral shearing interferometry and phase-shifting point-diffraction interferometry (PS/PDI) have achieved RMS wavefront measurement accuracies of 0.5-1-{angstrom} and better for primary aberration terms, enabling the creation of diffraction-limited EUV optics. The measurement accuracy is established using careful null-testing procedures, and has been verified repeatedly through high-resolution imaging. We believe these methods are broadly applicable to the advancement of short-wavelength optical systems including space telescopes, microscope objectives, projection lenses, synchrotron beamline optics, diffractive and holographic optics, and more. Measurements have been performed on a tunable undulator beamline at LBNL's Advanced Light Source (ALS), optimized for high coherent flux; although many of these techniques should be adaptable to alternative ultraviolet, EUV, and soft x-ray light sources. To date, we have measured nine prototype all-reflective EUV optical systems with NA values between 0.08 and 0.30 (f/6.25 to f/1.67). These projection-imaging lenses were created for the semiconductor industry's advanced research in EUV photolithography, a technology slated for introduction in 2009-13. This paper reviews the methods used and our program's accomplishments to date.

  4. 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.

  5. 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.

  6. Ultra-high accuracy optical testing: creating diffraction-limited short-wavelength optical systems

    International Nuclear Information System (INIS)

    Goldberg, Kenneth A.; Naulleau, Patrick P.; Rekawa, Senajith B.; Denham, Paul E.; Liddle, J. Alexander; Gullikson, Eric M.; Jackson, KeithH.; Anderson, Erik H.; Taylor, John S.; Sommargren, Gary E.; Chapman, Henry N.; Phillion, Donald W.; Johnson, Michael; Barty, Anton; Soufli, Regina; Spiller, Eberhard A.; Walton, Christopher C.; Bajt, Sasa

    2005-01-01

    Since 1993, research in the fabrication of extreme ultraviolet (EUV) optical imaging systems, conducted at Lawrence Berkeley National Laboratory (LBNL) and Lawrence Livermore National Laboratory (LLNL), has produced the highest resolution optical systems ever made. We have pioneered the development of ultra-high-accuracy optical testing and alignment methods, working at extreme ultraviolet wavelengths, and pushing wavefront-measuring interferometry into the 2-20-nm wavelength range (60-600 eV). These coherent measurement techniques, including lateral shearing interferometry and phase-shifting point-diffraction interferometry (PS/PDI) have achieved RMS wavefront measurement accuracies of 0.5-1-(angstrom) and better for primary aberration terms, enabling the creation of diffraction-limited EUV optics. The measurement accuracy is established using careful null-testing procedures, and has been verified repeatedly through high-resolution imaging. We believe these methods are broadly applicable to the advancement of short-wavelength optical systems including space telescopes, microscope objectives, projection lenses, synchrotron beamline optics, diffractive and holographic optics, and more. Measurements have been performed on a tunable undulator beamline at LBNL's Advanced Light Source (ALS), optimized for high coherent flux; although many of these techniques should be adaptable to alternative ultraviolet, EUV, and soft x-ray light sources. To date, we have measured nine prototype all-reflective EUV optical systems with NA values between 0.08 and 0.30 (f/6.25 to f/1.67). These projection-imaging lenses were created for the semiconductor industry's advanced research in EUV photolithography, a technology slated for introduction in 2009-13. This paper reviews the methods used and our program's accomplishments to date

  7. 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.

  8. Strategy for alignment of electron beam trajectory in LEReC cooling section

    Energy Technology Data Exchange (ETDEWEB)

    Seletskiy, S. [Brookhaven National Lab. (BNL), Upton, NY (United States); Blaskiewicz, M. [Brookhaven National Lab. (BNL), Upton, NY (United States); Fedotov, A. [Brookhaven National Lab. (BNL), Upton, NY (United States); Kayran, D. [Brookhaven National Lab. (BNL), Upton, NY (United States); Kewisch, J. [Brookhaven National Lab. (BNL), Upton, NY (United States); Michnoff, R. [Brookhaven National Lab. (BNL), Upton, NY (United States); Pinayev, I. [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2016-09-23

    We considered the steps required to align the electron beam trajectory through the LEReC cooling section. We devised a detailed procedure for the beam-based alignment of the cooling section solenoids. We showed that it is critical to have an individual control of each CS solenoid current. Finally, we modeled the alignment procedure and showed that with two BPM fitting the solenoid shift can be measured with 40 um accuracy and the solenoid inclination can be measured with 30 urad accuracy. These accuracies are well within the tolerances of the cooling section solenoid alignment.

  9. Detecting the limits of regulatory element conservation anddivergence estimation using pairwise and multiple alignments

    Energy Technology Data Exchange (ETDEWEB)

    Pollard, Daniel A.; Moses, Alan M.; Iyer, Venky N.; Eisen,Michael B.

    2006-08-14

    Background: Molecular evolutionary studies of noncodingsequences rely on multiple alignments. Yet how multiple alignmentaccuracy varies across sequence types, tree topologies, divergences andtools, and further how this variation impacts specific inferences,remains unclear. Results: Here we develop a molecular evolutionsimulation platform, CisEvolver, with models of background noncoding andtranscription factor binding site evolution, and use simulated alignmentsto systematically examine multiple alignment accuracy and its impact ontwo key molecular evolutionary inferences: transcription factor bindingsite conservation and divergence estimation. We find that the accuracy ofmultiple alignments is determined almost exclusively by the pairwisedivergence distance of the two most diverged species and that additionalspecies have a negligible influence on alignment accuracy. Conservedtranscription factor binding sites align better than surroundingnoncoding DNA yet are often found to be misaligned at relatively shortdivergence distances, such that studies of binding site gain and losscould easily be confounded by alignment error. Divergence estimates frommultiple alignments tend to be overestimated at short divergencedistances but reach a tool specific divergence at which they cease toincrease, leading to underestimation at long divergences. Our moststriking finding was that overall alignment accuracy, binding sitealignment accuracy and divergence estimation accuracy vary greatly acrossbranches in a tree and are most accurate for terminal branches connectingsister taxa and least accurate for internal branches connectingsub-alignments. Conclusions: Our results suggest that variation inalignment accuracy can lead to errors in molecular evolutionaryinferences that could be construed as biological variation. Thesefindings have implications for which species to choose for analyses, whatkind of errors would be expected for a given set of species and howmultiple alignment tools and

  10. Evaluation of microRNA alignment techniques

    Science.gov (United States)

    Kaspi, Antony; El-Osta, Assam

    2016-01-01

    Genomic alignment of small RNA (smRNA) sequences such as microRNAs poses considerable challenges due to their short length (∼21 nucleotides [nt]) as well as the large size and complexity of plant and animal genomes. While several tools have been developed for high-throughput mapping of longer mRNA-seq reads (>30 nt), there are few that are specifically designed for mapping of smRNA reads including microRNAs. The accuracy of these mappers has not been systematically determined in the case of smRNA-seq. In addition, it is unknown whether these aligners accurately map smRNA reads containing sequence errors and polymorphisms. By using simulated read sets, we determine the alignment sensitivity and accuracy of 16 short-read mappers and quantify their robustness to mismatches, indels, and nontemplated nucleotide additions. These were explored in the context of a plant genome (Oryza sativa, ∼500 Mbp) and a mammalian genome (Homo sapiens, ∼3.1 Gbp). Analysis of simulated and real smRNA-seq data demonstrates that mapper selection impacts differential expression results and interpretation. These results will inform on best practice for smRNA mapping and enable more accurate smRNA detection and quantification of expression and RNA editing. PMID:27284164

  11. Preparation and Characterization of Highly Aligned Carbon Nanotubes/Polyacrylonitrile Composite Nanofibers

    Directory of Open Access Journals (Sweden)

    Yanhua Song

    2017-01-01

    Full Text Available In the electrospinning process, a modified parallel electrode method (MPEM, conducted by placing a positively charged ring between the needle and the parallel electrode collector, was used to fabricate highly aligned carbon nanotubes/polyacrylonitrile (CNTs/PAN composite nanofibers. Characterizations of the samples—such as morphology, the degree of alignment, and mechanical and conductive properties—were investigated by a combination of scanning electron microscopy (SEM, transmission electron microscopy (TEM, universal testing machine, high-resistance meter, and other methods. The results showed the MPEM could improve the alignment and uniformity of electrospun CNTs/PAN composite nanofibers, and enhance their mechanical and conductive properties. This meant the successful preparation of highly aligned CNT-reinforced PAN nanofibers with enhanced physical properties, suggesting their potential application in appliances and communication areas.

  12. High performance electronics for alignment regulation on the CLIC 30GHz modules

    International Nuclear Information System (INIS)

    Carrica, D.; Coosemans, W.; Pittin, R.

    1999-01-01

    CERN is studying a linear collider (CLIC) to obtain electron-positron collisions with centre-of-mass energies in the TeV range. To demonstrate the feasibility of CLIC, a test facility (CTF2) is being constructed. CTF2 consists of 4 identical modules, each 1.4 m long module consists of 2 linac with a girder and a doublet or a triplet quadrupole. Girders are elements that support mechanically the cavities of the accelerator while the main objective of the quadrupole is to focus particle beams. The alignment system has 2 principal utilities. The first is to pre-align the elements to make the beam pass through the aperture and produce signals in beam position monitors. In respect to these signals the girders and the quadrupoles are moved for making the definitive alignment. The second utility is to maintain the elements in this position. The alignment control system of CTF2 must regulate the position of the girders and quadrupoles with a precision < 10 μm. In fact an accuracy of 1 μ has been obtained on CTF2. Thanks to its flexibility and its simplicity, the system is expected to adapt easily to CLIC even if it means to control modules that involve up to a maximum of 384 motors and 896 sensors

  13. Reliability of image-free navigation to monitor lower-limb alignment.

    Science.gov (United States)

    Pearle, Andrew D; Goleski, Patrick; Musahl, Volker; Kendoff, Daniel

    2009-02-01

    Proper alignment of the mechanical axis of the lower limb is the principal goal of a high tibial osteotomy. A well-accepted and relevant technical specification is the coronal plane lower-limb alignment. Target values for coronal plane alignment after high tibial osteotomy include 2 degrees of overcorrection, while tolerances for this specification have been established as 2 degrees to 4 degrees. However, the role of axial plane and sagittal plane realignment after high tibial osteotomy is poorly understood; consequently, targets and tolerance for this technical specification remain undefined. This article reviews the literature concerning the reliability and precision of navigation in monitoring the clinically relevant specification of lower-limb alignment in high tibial osteotomy. We conclude that image-free navigation registration may be clinically useful for intraoperative monitoring of the coronal plane only. Only fair and poor results for the axial and sagittal planes can be obtained by image-free navigation systems. In the future, combined image-based data, such as those from radiographs, magnetic resonance imaging, and gait analysis, may be used to help to improve the accuracy and reproducibility of quantitative intraoperative monitoring of lower-limb alignment.

  14. Alignment of the eight beams Octal 82 laser

    International Nuclear Information System (INIS)

    Josse, Michel.

    1982-10-01

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

  15. Alignment of the TFTR bumper limiter

    International Nuclear Information System (INIS)

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

    1989-01-01

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

  16. Alignment of the ATLAS central muon spectrometer

    CERN Document Server

    Chevallier, F

    2008-01-01

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

  17. 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.

  18. Capillary self-alignment of mesoscopic foil components for sensor-systems-in-foil

    International Nuclear Information System (INIS)

    Arutinov, Gari; Smits, Edsger C P; Van Heck, Gert; Van den Brand, Jeroen; Schoo, Herman F M; Mastrangeli, Massimo; Dietzel, Andreas

    2012-01-01

    This paper reports on the effective use of capillary self-alignment for low-cost and time-efficient assembly of heterogeneous foil components into a smart electronic identification label. Particularly, we demonstrate the accurate (better than 50 µm) alignment of cm-sized functional foil dies. We investigated the role played by the assembly liquid, by the size and the weight of assembling dies and by their initial offsets in the self-alignment performance. It was shown that there is a definite range of initial offsets allowing dies to align with high accuracy and within approximately the same time window, irrespective of their initial offset. (paper)

  19. Improving mass measurement accuracy in mass spectrometry based proteomics by combining open source tools for chromatographic alignment and internal calibration.

    Science.gov (United States)

    Palmblad, Magnus; van der Burgt, Yuri E M; Dalebout, Hans; Derks, Rico J E; Schoenmaker, Bart; Deelder, André M

    2009-05-02

    Accurate mass determination enhances peptide identification in mass spectrometry based proteomics. We here describe the combination of two previously published open source software tools to improve mass measurement accuracy in Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS). The first program, msalign, aligns one MS/MS dataset with one FTICRMS dataset. The second software, recal2, uses peptides identified from the MS/MS data for automated internal calibration of the FTICR spectra, resulting in sub-ppm mass measurement errors.

  20. Accuracy of Binary Black Hole waveforms for Advanced LIGO searches

    Science.gov (United States)

    Kumar, Prayush; Barkett, Kevin; Bhagwat, Swetha; Chu, Tony; Fong, Heather; Brown, Duncan; Pfeiffer, Harald; Scheel, Mark; Szilagyi, Bela

    2015-04-01

    Coalescing binaries of compact objects are flagship sources for the first direct detection of gravitational waves with LIGO-Virgo observatories. Matched-filtering based detection searches aimed at binaries of black holes will use aligned spin waveforms as filters, and their efficiency hinges on the accuracy of the underlying waveform models. A number of gravitational waveform models are available in literature, e.g. the Effective-One-Body, Phenomenological, and traditional post-Newtonian ones. While Numerical Relativity (NR) simulations provide for the most accurate modeling of gravitational radiation from compact binaries, their computational cost limits their application in large scale searches. In this talk we assess the accuracy of waveform models in two regions of parameter space, which have only been explored cursorily in the past: the high mass-ratio regime as well as the comparable mass-ratio + high spin regime.s Using the SpEC code, six q = 7 simulations with aligned-spins and lasting 60 orbits, and tens of q ∈ [1,3] simulations with high black hole spins were performed. We use them to study the accuracy and intrinsic parameter biases of different waveform families, and assess their viability for Advanced LIGO searches.

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

    Science.gov (United States)

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

    2015-09-22

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

  2. Alignment of the CMS tracker with LHC and cosmic ray data

    CERN Document Server

    Chatrchyan, Serguei; Sirunyan, Albert M; Tumasyan, Armen; Adam, Wolfgang; Bergauer, Thomas; Dragicevic, Marko; Erö, Janos; Fabjan, Christian; Friedl, Markus; Fruehwirth, Rudolf; Ghete, Vasile Mihai; Hartl, Christian; Hörmann, Natascha; Hrubec, Josef; Jeitler, Manfred; Kiesenhofer, Wolfgang; Knünz, Valentin; Krammer, Manfred; Krätschmer, Ilse; Liko, Dietrich; Mikulec, Ivan; Rabady, Dinyar; Rahbaran, Babak; Rohringer, Herbert; Schöfbeck, Robert; Strauss, Josef; Taurok, Anton; Treberer-Treberspurg, Wolfgang; Waltenberger, Wolfgang; Wulz, Claudia-Elisabeth; Mossolov, Vladimir; Shumeiko, Nikolai; Suarez Gonzalez, Juan; Alderweireldt, Sara; Bansal, Monika; Bansal, Sunil; Beaumont, Willem; Cornelis, Tom; De Wolf, Eddi A; Janssen, Xavier; Knutsson, Albert; Luyckx, Sten; Mucibello, Luca; Ochesanu, Silvia; Roland, Benoit; Rougny, Romain; Van Haevermaet, Hans; Van Mechelen, Pierre; Van Remortel, Nick; Van Spilbeeck, Alex; Blekman, Freya; Blyweert, Stijn; D'Hondt, Jorgen; Devroede, Olivier; Heracleous, Natalie; Kalogeropoulos, Alexis; Keaveney, James; Kim, Tae Jeong; Lowette, Steven; Maes, Michael; Olbrechts, Annik; Python, Quentin; Strom, Derek; Tavernier, Stefaan; Van Doninck, Walter; Van Lancker, Luc; Van Mulders, Petra; Van Onsem, Gerrit Patrick; Villella, Ilaria; Caillol, Cécile; Clerbaux, Barbara; De Lentdecker, Gilles; Favart, Laurent; Gay, Arnaud; Léonard, Alexandre; Marage, Pierre Edouard; Mohammadi, Abdollah; Perniè, Luca; Reis, Thomas; Seva, Tomislav; Thomas, Laurent; Vander Velde, Catherine; Vanlaer, Pascal; Wang, Jian; Adler, Volker; Beernaert, Kelly; Benucci, Leonardo; Cimmino, Anna; Costantini, Silvia; Dildick, Sven; Garcia, Guillaume; Klein, Benjamin; Lellouch, Jérémie; Mccartin, Joseph; Ocampo Rios, Alberto Andres; Ryckbosch, Dirk; Salva Diblen, Sinem; Sigamani, Michael; Strobbe, Nadja; Thyssen, Filip; Tytgat, Michael; Walsh, Sinead; Yazgan, Efe; Zaganidis, Nicolas; Basegmez, Suzan; Beluffi, Camille; Bruno, Giacomo; Castello, Roberto; Caudron, Adrien; Ceard, Ludivine; Da Silveira, Gustavo Gil; De Callatay, Bernard; Delaere, Christophe; Du Pree, Tristan; Favart, Denis; Forthomme, Laurent; Giammanco, Andrea; Hollar, Jonathan; Jez, Pavel; Komm, Matthias; Lemaitre, Vincent; Liao, Junhui; Michotte, Daniel; Militaru, Otilia; Nuttens, Claude; Pagano, Davide; Pin, Arnaud; Piotrzkowski, Krzysztof; Popov, Andrey; Quertenmont, Loic; Selvaggi, Michele; Vidal Marono, Miguel; Vizan Garcia, Jesus Manuel; Beliy, Nikita; Caebergs, Thierry; Daubie, Evelyne; Hammad, Gregory Habib; Alves, Gilvan; Correa Martins Junior, Marcos; Dos Reis Martins, Thiago; Pol, Maria Elena; Henrique Gomes E Souza, Moacyr; Aldá Júnior, Walter Luiz; Carvalho, Wagner; Chinellato, Jose; Custódio, Analu; Melo Da Costa, Eliza; De Jesus Damiao, Dilson; De Oliveira Martins, Carley; Fonseca De Souza, Sandro; Malbouisson, Helena; Malek, Magdalena; Matos Figueiredo, Diego; Mundim, Luiz; Nogima, Helio; Prado Da Silva, Wanda Lucia; Santaolalla, Javier; Santoro, Alberto; Sznajder, Andre; Tonelli Manganote, Edmilson José; Vilela Pereira, Antonio; Bernardes, Cesar Augusto; De Almeida Dias, Flavia; Tomei, Thiago; De Moraes Gregores, Eduardo; Mercadante, Pedro G; Novaes, Sergio F; Padula, Sandra; Genchev, Vladimir; Iaydjiev, Plamen; Marinov, Andrey; Piperov, Stefan; Rodozov, Mircho; Sultanov, Georgi; Vutova, Mariana; Dimitrov, Anton; Glushkov, Ivan; Hadjiiska, Roumyana; Kozhuharov, Venelin; Litov, Leander; Pavlov, Borislav; Petkov, Peicho; Bian, Jian-Guo; Chen, Guo-Ming; Chen, He-Sheng; Chen, Mingshui; Du, Ran; Jiang, Chun-Hua; Liang, Dong; Liang, Song; Meng, Xiangwei; Plestina, Roko; Tao, Junquan; Wang, Xianyou; Wang, Zheng; Asawatangtrakuldee, Chayanit; Ban, Yong; Guo, Yifei; Li, Qiang; Li, Wenbo; Liu, Shuai; Mao, Yajun; Qian, Si-Jin; Wang, Dayong; Zhang, Linlin; Zou, Wei; Avila, Carlos; Carrillo Montoya, Camilo Andres; Chaparro Sierra, Luisa Fernanda; Florez, Carlos; Gomez, Juan Pablo; Gomez Moreno, Bernardo; Sanabria, Juan Carlos; Godinovic, Nikola; Lelas, Damir; Polic, Dunja; Puljak, Ivica; Antunovic, Zeljko; Kovac, Marko; Brigljevic, Vuko; Kadija, Kreso; Luetic, Jelena; Mekterovic, Darko; Morovic, Srecko; Sudic, Lucija; Attikis, Alexandros; Mavromanolakis, Georgios; Mousa, Jehad; Nicolaou, Charalambos; Ptochos, Fotios; Razis, Panos A; Finger, Miroslav; Finger Jr, Michael; Abdelalim, Ahmed Ali; Assran, Yasser; Elgammal, Sherif; Ellithi Kamel, Ali; Mahmoud, Mohammed; Radi, Amr; Kadastik, Mario; Müntel, Mait; Murumaa, Marion; Raidal, Martti; Rebane, Liis; Tiko, Andres; Eerola, Paula; Fedi, Giacomo; Voutilainen, Mikko; Härkönen, Jaakko; Karimäki, Veikko; Kinnunen, Ritva; Kortelainen, Matti J; Lampén, Tapio; Lassila-Perini, Kati; Lehti, Sami; Lindén, Tomas; Luukka, Panja-Riina; Mäenpää, Teppo; Peltola, Timo; Tuominen, Eija; Tuominiemi, Jorma; Tuovinen, Esa; Wendland, Lauri; Tuuva, Tuure; Besancon, Marc; Couderc, Fabrice; Dejardin, Marc; Denegri, Daniel; Fabbro, Bernard; Faure, Jean-Louis; Ferri, Federico; Ganjour, Serguei; Givernaud, Alain; Gras, Philippe; Hamel de Monchenault, Gautier; Jarry, Patrick; Locci, Elizabeth; Malcles, Julie; Nayak, Aruna; Rander, John; Rosowsky, André; Titov, Maksym; Baffioni, Stephanie; Beaudette, Florian; Busson, Philippe; Charlot, Claude; Daci, Nadir; Dahms, Torsten; Dalchenko, Mykhailo; Dobrzynski, Ludwik; Florent, Alice; Granier de Cassagnac, Raphael; Miné, Philippe; Mironov, Camelia; Naranjo, Ivo Nicolas; Nguyen, Matthew; Ochando, Christophe; Paganini, Pascal; Sabes, David; Salerno, Roberto; Sauvan, Jean-baptiste; Sirois, Yves; Veelken, Christian; Yilmaz, Yetkin; Zabi, Alexandre; Agram, Jean-Laurent; Andrea, Jeremy; Bloch, Daniel; Bonnin, Christian; Brom, Jean-Marie; Chabert, Eric Christian; Charles, Laurent; Collard, Caroline; Conte, Eric; Drouhin, Frédéric; Fontaine, Jean-Charles; Gelé, Denis; Goerlach, Ulrich; Goetzmann, Christophe; Gross, Laurent; Juillot, Pierre; Le Bihan, Anne-Catherine; Van Hove, Pierre; Gadrat, Sébastien; Baulieu, Guillaume; Beauceron, Stephanie; Beaupere, Nicolas; Boudoul, Gaelle; Brochet, Sébastien; Chasserat, Julien; Chierici, Roberto; Contardo, Didier; Depasse, Pierre; El Mamouni, Houmani; Fan, Jiawei; Fay, Jean; Gascon, Susan; Gouzevitch, Maxime; Ille, Bernard; Kurca, Tibor; Lethuillier, Morgan; Lumb, Nicholas; Mathez, Hervé; Mirabito, Laurent; Perries, Stephane; Ruiz Alvarez, José David; Sgandurra, Louis; Sordini, Viola; Vander Donckt, Muriel; Verdier, Patrice; Viret, Sébastien; Xiao, Hong; Zoccarato, Yannick; Tsamalaidze, Zviad; Autermann, Christian; Beranek, Sarah; Bontenackels, Michael; Calpas, Betty; Edelhoff, Matthias; Esser, Hans; Feld, Lutz; Hindrichs, Otto; Karpinski, Waclaw; Klein, Katja; Kukulies, Christoph; Lipinski, Martin; Ostapchuk, Andrey; Perieanu, Adrian; Pierschel, Gerhard; Preuten, Marius; Raupach, Frank; Sammet, Jan; Schael, Stefan; Schulte, Jan-Frederik; Schwering, Georg; Sprenger, Daniel; Verlage, Tobias; Weber, Hendrik; Wittmer, Bruno; Wlochal, Michael; Zhukov, Valery; Ata, Metin; Caudron, Julien; Dietz-Laursonn, Erik; Duchardt, Deborah; Erdmann, Martin; Fischer, Robert; Güth, Andreas; Hebbeker, Thomas; Heidemann, Carsten; Hoepfner, Kerstin; Klingebiel, Dennis; Knutzen, Simon; Kreuzer, Peter; Merschmeyer, Markus; Meyer, Arnd; Olschewski, Mark; Padeken, Klaas; Papacz, Paul; Reithler, Hans; Schmitz, Stefan Antonius; Sonnenschein, Lars; Teyssier, Daniel; Thüer, Sebastian; Weber, Martin; Cherepanov, Vladimir; Erdogan, Yusuf; Flügge, Günter; Geenen, Heiko; Geisler, Matthias; Haj Ahmad, Wael; Hoehle, Felix; Kargoll, Bastian; Kress, Thomas; Kuessel, Yvonne; Lingemann, Joschka; Nowack, Andreas; Nugent, Ian Michael; Perchalla, Lars; Pistone, Claudia; Pooth, Oliver; Stahl, Achim; Asin, Ivan; Bartosik, Nazar; Behr, Joerg; Behrenhoff, Wolf; Behrens, Ulf; Bell, Alan James; Bergholz, Matthias; Bethani, Agni; Borras, Kerstin; Burgmeier, Armin; Cakir, Altan; Calligaris, Luigi; Campbell, Alan; Choudhury, Somnath; Costanza, Francesco; Diez Pardos, Carmen; Dolinska, Ganna; Dooling, Samantha; Dorland, Tyler; Eckerlin, Guenter; Eckstein, Doris; Eichhorn, Thomas; Flucke, Gero; Geiser, Achim; Grebenyuk, Anastasia; Gunnellini, Paolo; Habib, Shiraz; Hampe, Jan; Hansen, Karsten; Hauk, Johannes; Hellwig, Gregor; Hempel, Maria; Horton, Dean; Jung, Hannes; Kasemann, Matthias; Katsas, Panagiotis; Kieseler, Jan; Kleinwort, Claus; Korol, Ievgen; Krämer, Mira; Krücker, Dirk; Lange, Wolfgang; Leonard, Jessica; Lipka, Katerina; Lohmann, Wolfgang; Lutz, Benjamin; Mankel, Rainer; Marfin, Ihar; Maser, Holger; Melzer-Pellmann, Isabell-Alissandra; Meyer, Andreas Bernhard; Mnich, Joachim; Muhl, Carsten; Mussgiller, Andreas; Naumann-Emme, Sebastian; Novgorodova, Olga; Nowak, Friederike; Perrey, Hanno; Petrukhin, Alexey; Pitzl, Daniel; Placakyte, Ringaile; Raspereza, Alexei; Ribeiro Cipriano, Pedro M; Riedl, Caroline; Ron, Elias; Sahin, Mehmet Özgür; Salfeld-Nebgen, Jakob; Saxena, Pooja; Schmidt, Ringo; Schoerner-Sadenius, Thomas; Schröder, Matthias; Spannagel, Simon; Stein, Matthias; Vargas Trevino, Andrea Del Rocio; Walsh, Roberval; Wissing, Christoph; Zuber, Adam; Aldaya Martin, Maria; Berger, Lutz Olaf; Biskop, Heike; Blobel, Volker; Buhmann, Peter; Centis Vignali, Matteo; Enderle, Holger; Erfle, Joachim; Frensche, Benno; Garutti, Erika; Goebel, Kristin; Görner, Martin; Gosselink, Martijn; Haller, Johannes; Hoffmann, Malte; Höing, Rebekka Sophie; Junkes, Alexandra; Kirschenmann, Henning; Klanner, Robert; Kogler, Roman; Lange, Jörn; Lapsien, Tobias; Lenz, Teresa; Maettig, Stefan; Marchesini, Ivan; Matysek, Michael; Ott, Jochen; Peiffer, Thomas; Pietsch, Niklas; Pöhlsen, Thomas; Rathjens, Denis; Sander, Christian; Schettler, Hannes; Schleper, Peter; Schlieckau, Eike; Schmidt, Alexander; Seidel, Markus; Sibille, Jennifer; Sola, Valentina; Stadie, Hartmut; Steinbrück, Georg; Troendle, Daniel; Usai, Emanuele; Vanelderen, Lukas; Barth, Christian; Barvich, Tobias; Baus, Colin; Berger, Joram; Boegelspacher, Felix; Böser, Christian; Butz, Erik; Chwalek, Thorsten; Colombo, Fabio; De Boer, Wim; Descroix, Alexis; Dierlamm, Alexander; Eber, Robert; Feindt, Michael; Guthoff, Moritz; Hartmann, Frank; Hauth, Thomas; Heindl, Stefan Michael; Held, Hauke; Hoffmann, Karl-Heinz; Husemann, Ulrich; Katkov, Igor; Kornmayer, Andreas; Kuznetsova, Ekaterina; Lobelle Pardo, Patricia; Martschei, Daniel; Mozer, Matthias Ulrich; Müller, Thomas; Niegel, Martin; Nürnberg, Andreas; Oberst, Oliver; Printz, Martin; Quast, Gunter; Rabbertz, Klaus; Ratnikov, Fedor; Röcker, Steffen; Schilling, Frank-Peter; Schott, Gregory; Simonis, Hans-Jürgen; Steck, Pia; Stober, Fred-Markus Helmut; Ulrich, Ralf; Wagner-Kuhr, Jeannine; Wayand, Stefan; Weiler, Thomas; Wolf, Roger; Zeise, Manuel; Anagnostou, Georgios; Daskalakis, Georgios; Geralis, Theodoros; Kesisoglou, Stilianos; Kyriakis, Aristotelis; Loukas, Demetrios; Markou, Athanasios; Markou, Christos; Ntomari, Eleni; Psallidas, Andreas; Topsis-Giotis, Iasonas; Gouskos, Loukas; Panagiotou, Apostolos; Saoulidou, Niki; Stiliaris, Efstathios; Aslanoglou, Xenofon; Evangelou, Ioannis; Flouris, Giannis; Foudas, Costas; Jones, John; Kokkas, Panagiotis; Manthos, Nikolaos; Papadopoulos, Ioannis; Paradas, Evangelos; Bencze, Gyorgy; Hajdu, Csaba; Hidas, Pàl; Horvath, Dezso; Sikler, Ferenc; Veszpremi, Viktor; Vesztergombi, Gyorgy; Zsigmond, Anna Julia; Beni, Noemi; Czellar, Sandor; Molnar, Jozsef; Palinkas, Jozsef; Szillasi, Zoltan; Karancsi, János; Raics, Peter; Trocsanyi, Zoltan Laszlo; Ujvari, Balazs; Swain, Sanjay Kumar; Beri, Suman Bala; Bhatnagar, Vipin; Dhingra, Nitish; Gupta, Ruchi; Kaur, Manjit; Mehta, Manuk Zubin; Mittal, Monika; Nishu, Nishu; Sharma, Archana; Singh, Jasbir; Kumar, Ashok; Kumar, Arun; Ahuja, Sudha; Bhardwaj, Ashutosh; Choudhary, Brajesh C; Kumar, Ajay; Malhotra, Shivali; Naimuddin, Md; Ranjan, Kirti; Sharma, Varun; Shivpuri, Ram Krishen; Banerjee, Sunanda; Bhattacharya, Satyaki; Chatterjee, Kalyanmoy; Dutta, Suchandra; Gomber, Bhawna; Jain, Sandhya; Jain, Shilpi; Khurana, Raman; Modak, Atanu; Mukherjee, Swagata; Roy, Debarati; Sarkar, Subir; Sharan, Manoj; Singh, Anil; Abdulsalam, Abdulla; Dutta, Dipanwita; Kailas, Swaminathan; Kumar, Vineet; Mohanty, Ajit Kumar; Pant, Lalit Mohan; Shukla, Prashant; Topkar, Anita; Aziz, Tariq; Chatterjee, Rajdeep Mohan; Ganguly, Sanmay; Ghosh, Saranya; Guchait, Monoranjan; Gurtu, Atul; Kole, Gouranga; Kumar, Sanjeev; Maity, Manas; Majumder, Gobinda; Mazumdar, Kajari; Mohanty, Gagan Bihari; Parida, Bibhuti; Sudhakar, Katta; Wickramage, Nadeesha; Banerjee, Sudeshna; Dugad, Shashikant; Arfaei, Hessamaddin; Bakhshiansohi, Hamed; Behnamian, Hadi; Etesami, Seyed Mohsen; Fahim, Ali; Jafari, Abideh; Khakzad, Mohsen; Mohammadi Najafabadi, Mojtaba; Naseri, Mohsen; Paktinat Mehdiabadi, Saeid; Safarzadeh, Batool; Zeinali, Maryam; Grunewald, Martin; Abbrescia, Marcello; Barbone, Lucia; Calabria, Cesare; Cariola, Pasquale; Chhibra, Simranjit Singh; Colaleo, Anna; Creanza, Donato; De Filippis, Nicola; De Palma, Mauro; De Robertis, Giuseppe; Fiore, Luigi; Franco, Michele; Iaselli, Giuseppe; Loddo, Flavio; Maggi, Giorgio; Maggi, Marcello; Marangelli, Bartolomeo; My, Salvatore; Nuzzo, Salvatore; Pacifico, Nicola; Pompili, Alexis; Pugliese, Gabriella; Radogna, Raffaella; Sala, Giuliano; Selvaggi, Giovanna; Silvestris, Lucia; Singh, Gurpreet; Venditti, Rosamaria; Verwilligen, Piet; Zito, Giuseppe; Abbiendi, Giovanni; Benvenuti, Alberto; Bonacorsi, Daniele; Braibant-Giacomelli, Sylvie; Brigliadori, Luca; Campanini, Renato; Capiluppi, Paolo; Castro, Andrea; Cavallo, Francesca Romana; Codispoti, Giuseppe; Cuffiani, Marco; Dallavalle, Gaetano-Marco; Fabbri, Fabrizio; Fanfani, Alessandra; Fasanella, Daniele; Giacomelli, Paolo; Grandi, Claudio; Guiducci, Luigi; Marcellini, Stefano; Masetti, Gianni; Meneghelli, Marco; Montanari, Alessandro; Navarria, Francesco; Odorici, Fabrizio; Perrotta, Andrea; Primavera, Federica; Rossi, Antonio; Rovelli, Tiziano; Siroli, Gian Piero; Tosi, Nicolò; Travaglini, Riccardo; Albergo, Sebastiano; Cappello, Gigi; Chiorboli, Massimiliano; Costa, Salvatore; Giordano, Ferdinando; Potenza, Renato; Saizu, Mirela Angela; Scinta, Manuel; Tricomi, Alessia; Tuve, Cristina; Barbagli, Giuseppe; Brianzi, Mirko; Ciaranfi, Roberto; Ciulli, Vitaliano; Civinini, Carlo; D'Alessandro, Raffaello; Focardi, Ettore; Gallo, Elisabetta; Gonzi, Sandro; Gori, Valentina; Lenzi, Piergiulio; Meschini, Marco; Paoletti, Simone; Scarlini, Enrico; Sguazzoni, Giacomo; Tropiano, Antonio; Benussi, Luigi; Bianco, Stefano; Fabbri, Franco; Piccolo, Davide; Fabbricatore, Pasquale; Ferretti, Roberta; Ferro, Fabrizio; Lo Vetere, Maurizio; Musenich, Riccardo; Robutti, Enrico; Tosi, Silvano; Benaglia, Andrea; D'Angelo, Pasqualino; Dinardo, Mauro Emanuele; Fiorendi, Sara; Gennai, Simone; Gerosa, Raffaele; Ghezzi, Alessio; Govoni, Pietro; Lucchini, Marco Toliman; Malvezzi, Sandra; Manzoni, Riccardo Andrea; Martelli, Arabella; Marzocchi, Badder; Menasce, Dario; Moroni, Luigi; Paganoni, Marco; Pedrini, Daniele; Ragazzi, Stefano; Redaelli, Nicola; Tabarelli de Fatis, Tommaso; Buontempo, Salvatore; Cavallo, Nicola; Di Guida, Salvatore; Fabozzi, Francesco; Iorio, Alberto Orso Maria; Lista, Luca; Meola, Sabino; Merola, Mario; Paolucci, Pierluigi; Azzi, Patrizia; Bacchetta, Nicola; Biasotto, Massimo; Bisello, Dario; Branca, Antonio; Carlin, Roberto; Checchia, Paolo; Dall'Osso, Martino; Dorigo, Tommaso; Fanzago, Federica; Galanti, Mario; Gasparini, Fabrizio; Gasparini, Ugo; Giubilato, Piero; Gozzelino, Andrea; Kanishchev, Konstantin; Lacaprara, Stefano; Lazzizzera, Ignazio; Margoni, Martino; Meneguzzo, Anna Teresa; Pazzini, Jacopo; Pozzobon, Nicola; Ronchese, Paolo; Sgaravatto, Massimo; Simonetto, Franco; Torassa, Ezio; Tosi, Mia; Zotto, Pierluigi; Zucchetta, Alberto; Zumerle, Gianni; Gabusi, Michele; Gaioni, Luigi; Manazza, Alessia; Manghisoni, Massimo; Ratti, Lodovico; Ratti, Sergio P; Re, Valerio; Riccardi, Cristina; Traversi, Gianluca; Vitulo, Paolo; Zucca, Stefano; Biasini, Maurizio; Bilei, Gian Mario; Bissi, Lucia; Checcucci, Bruno; Ciangottini, Diego; Conti, Elia; Fanò, Livio; Lariccia, Paolo; Magalotti, Daniel; Mantovani, Giancarlo; Menichelli, Mauro; Passeri, Daniele; Placidi, Pisana; Romeo, Francesco; Saha, Anirban; Salvatore, Michele; Santocchia, Attilio; Servoli, Leonello; Spiezia, Aniello; Androsov, Konstantin; Arezzini, Silvia; Azzurri, Paolo; Bagliesi, Giuseppe; Basti, Andrea; Bernardini, Jacopo; Boccali, Tommaso; Bosi, Filippo; Broccolo, Giuseppe; Calzolari, Federico; Castaldi, Rino; Ciampa, Alberto; Ciocci, Maria Agnese; Dell'Orso, Roberto; Fiori, Francesco; Foà, Lorenzo; Giassi, Alessandro; Grippo, Maria Teresa; Kraan, Aafke; Ligabue, Franco; Lomtadze, Teimuraz; Magazzu, Guido; Martini, Luca; Mazzoni, Enrico; Messineo, Alberto; Moggi, Andrea; Moon, Chang-Seong; Palla, Fabrizio; Raffaelli, Fabrizio; Rizzi, Andrea; Savoy-Navarro, Aurore; Serban, Alin Titus; Spagnolo, Paolo; Squillacioti, Paola; Tenchini, Roberto; Tonelli, Guido; Venturi, Andrea; Verdini, Piero Giorgio; Vernieri, Caterina; Barone, Luciano; Cavallari, Francesca; Del Re, Daniele; Diemoz, Marcella; Grassi, Marco; Jorda, Clara; Longo, Egidio; Margaroli, Fabrizio; Meridiani, Paolo; Micheli, Francesco; Nourbakhsh, Shervin; Organtini, Giovanni; Paramatti, Riccardo; Rahatlou, Shahram; Rovelli, Chiara; Soffi, Livia; Traczyk, Piotr; Amapane, Nicola; Arcidiacono, Roberta; Argiro, Stefano; Arneodo, Michele; Bellan, Riccardo; Biino, Cristina; Cartiglia, Nicolo; Casasso, Stefano; Costa, Marco; Degano, Alessandro; Demaria, Natale; Mariotti, Chiara; Maselli, Silvia; Migliore, Ernesto; Monaco, Vincenzo; Monteil, Ennio; Musich, Marco; Obertino, Maria Margherita; Ortona, Giacomo; Pacher, Luca; Pastrone, Nadia; Pelliccioni, Mario; Potenza, Alberto; Rivetti, Angelo; Romero, Alessandra; Ruspa, Marta; Sacchi, Roberto; Solano, Ada; Staiano, Amedeo; Tamponi, Umberto; Trapani, Pier Paolo; Belforte, Stefano; Candelise, Vieri; Casarsa, Massimo; Cossutti, Fabio; Della Ricca, Giuseppe; Gobbo, Benigno; La Licata, Chiara; Marone, Matteo; Montanino, Damiana; Penzo, Aldo; Schizzi, Andrea; Umer, Tomo; Zanetti, Anna; Chang, Sunghyun; Kim, Tae Yeon; Nam, Soon-Kwon; Kim, Dong Hee; Kim, Gui Nyun; Kim, Ji Eun; Kim, Min Suk; Kong, Dae Jung; Lee, Sangeun; Oh, Young Do; Park, Hyangkyu; Son, Dong-Chul; Kim, Jae Yool; Kim, Zero Jaeho; Song, Sanghyeon; Choi, Suyong; Gyun, Dooyeon; Hong, Byung-Sik; Jo, Mihee; Kim, Hyunchul; Kim, Yongsun; Lee, Kyong Sei; Park, Sung Keun; Roh, Youn; Choi, Minkyoo; Kim, Ji Hyun; Park, Chawon; Park, Inkyu; Park, Sangnam; Ryu, Geonmo; Choi, Young-Il; Choi, Young Kyu; Goh, Junghwan; Kwon, Eunhyang; Lee, Byounghoon; Lee, Jongseok; Seo, Hyunkwan; Yu, Intae; Juodagalvis, Andrius; Komaragiri, Jyothsna Rani; Castilla-Valdez, Heriberto; De La Cruz-Burelo, Eduard; Heredia-de La Cruz, Ivan; Lopez-Fernandez, Ricardo; Martínez-Ortega, Jorge; Sánchez Hernández, Alberto; Villasenor-Cendejas, Luis Manuel; Carrillo Moreno, Salvador; Vazquez Valencia, Fabiola; Salazar Ibarguen, Humberto Antonio; Casimiro Linares, Edgar; Morelos Pineda, Antonio; Krofcheck, David; Butler, Philip H; Doesburg, Robert; Reucroft, Steve; Ahmad, Muhammad; Asghar, Muhammad Irfan; Butt, Jamila; Hoorani, Hafeez R; Khan, Wajid Ali; Khurshid, Taimoor; Qazi, Shamona; Shah, Mehar Ali; Shoaib, Muhammad; Bialkowska, Helena; Bluj, Michal; Boimska, Bożena; Frueboes, Tomasz; Górski, Maciej; Kazana, Malgorzata; Nawrocki, Krzysztof; Romanowska-Rybinska, Katarzyna; Szleper, Michal; Wrochna, Grzegorz; Zalewski, Piotr; Brona, Grzegorz; Bunkowski, Karol; Cwiok, Mikolaj; Dominik, Wojciech; Doroba, Krzysztof; Kalinowski, Artur; Konecki, Marcin; Krolikowski, Jan; Misiura, Maciej; Wolszczak, Weronika; Bargassa, Pedrame; Beirão Da Cruz E Silva, Cristóvão; Faccioli, Pietro; Ferreira Parracho, Pedro Guilherme; Gallinaro, Michele; Nguyen, Federico; Rodrigues Antunes, Joao; Seixas, Joao; Varela, Joao; Vischia, Pietro; Bunin, Pavel; Gavrilenko, Mikhail; Golutvin, Igor; Gorbunov, Ilya; Kamenev, Alexey; Karjavin, Vladimir; Konoplyanikov, Viktor; Kozlov, Guennady; Lanev, Alexander; Malakhov, Alexander; Matveev, Viktor; Moisenz, Petr; Palichik, Vladimir; Perelygin, Victor; Shmatov, Sergey; Skatchkov, Nikolai; Smirnov, Vitaly; Zarubin, Anatoli; Golovtsov, Victor; Ivanov, Yury; Kim, Victor; Levchenko, Petr; Murzin, Victor; Oreshkin, Vadim; Smirnov, Igor; Sulimov, Valentin; Uvarov, Lev; Vavilov, Sergey; Vorobyev, Alexey; Vorobyev, Andrey; Andreev, Yuri; Dermenev, Alexander; Gninenko, Sergei; Golubev, Nikolai; Kirsanov, Mikhail; Krasnikov, Nikolai; Pashenkov, Anatoli; Tlisov, Danila; Toropin, Alexander; Epshteyn, Vladimir; Gavrilov, Vladimir; Lychkovskaya, Natalia; Popov, Vladimir; Safronov, Grigory; Semenov, Sergey; Spiridonov, Alexander; Stolin, Viatcheslav; Vlasov, Evgueni; Zhokin, Alexander; Andreev, Vladimir; Azarkin, Maksim; Dremin, Igor; Kirakosyan, Martin; Leonidov, Andrey; Mesyats, Gennady; Rusakov, Sergey V; Vinogradov, Alexey; Belyaev, Andrey; Boos, Edouard; Dubinin, Mikhail; Dudko, Lev; Ershov, Alexander; Gribushin, Andrey; Kaminskiy, Alexandre; Klyukhin, Vyacheslav; Kodolova, Olga; Lokhtin, Igor; Obraztsov, Stepan; Petrushanko, Sergey; Savrin, Viktor; Azhgirey, Igor; Bayshev, Igor; Bitioukov, Sergei; Kachanov, Vassili; Kalinin, Alexey; Konstantinov, Dmitri; Krychkine, Victor; Petrov, Vladimir; Ryutin, Roman; Sobol, Andrei; Tourtchanovitch, Leonid; Troshin, Sergey; Tyurin, Nikolay; Uzunian, Andrey; Volkov, Alexey; Adzic, Petar; Djordjevic, Milos; Ekmedzic, Marko; Milosevic, Jovan; Aguilar-Benitez, Manuel; Alcaraz Maestre, Juan; Battilana, Carlo; Calvo, Enrique; Cerrada, Marcos; Chamizo Llatas, Maria; Colino, Nicanor; De La Cruz, Begona; Delgado Peris, Antonio; Domínguez Vázquez, Daniel; Fernandez Bedoya, Cristina; Fernández Ramos, Juan Pablo; Ferrando, Antonio; Flix, Jose; Fouz, Maria Cruz; Garcia-Abia, Pablo; Gonzalez Lopez, Oscar; Goy Lopez, Silvia; Hernandez, Jose M; Josa, Maria Isabel; Merino, Gonzalo; Navarro De Martino, Eduardo; Puerta Pelayo, Jesus; Quintario Olmeda, Adrián; Redondo, Ignacio; Romero, Luciano; Senghi Soares, Mara; Willmott, Carlos; Albajar, Carmen; de Trocóniz, Jorge F; Missiroli, Marino; Brun, Hugues; Cuevas, Javier; Fernandez Menendez, Javier; Folgueras, Santiago; Gonzalez Caballero, Isidro; Lloret Iglesias, Lara; Brochero Cifuentes, Javier Andres; Cabrillo, Iban Jose; Calderon, Alicia; Duarte Campderros, Jordi; Fernandez, Marcos; Gomez, Gervasio; Gonzalez Sanchez, Javier; Graziano, Alberto; Jaramillo Echeverria, Richard William; Lopez Virto, Amparo; Marco, Jesus; Marco, Rafael; Martinez Rivero, Celso; Matorras, Francisco; Moya, David; Munoz Sanchez, Francisca Javiela; Piedra Gomez, Jonatan; Rodrigo, Teresa; Rodríguez-Marrero, Ana Yaiza; Ruiz-Jimeno, Alberto; Scodellaro, Luca; Vila, Ivan; Vilar Cortabitarte, Rocio; Abbaneo, Duccio; Ahmed, Imtiaz; Albert, Eric; Auffray, Etiennette; Auzinger, Georg; Bachtis, Michail; Baillon, Paul; Ball, Austin; Barney, David; Bendavid, Joshua; Benhabib, Lamia; Benitez, Jose F; Bernet, Colin; Berruti, Gaia Maria; Bianchi, Giovanni; Blanchot, Georges; Bloch, Philippe; Bocci, Andrea; Bonato, Alessio; Bondu, Olivier; Botta, Cristina; Breuker, Horst; Camporesi, Tiziano; Ceresa, Davide; Cerminara, Gianluca; Christiansen, Jorgen; Christiansen, Tim; Chávez Niemelä, Aleksis Osku; Coarasa Perez, Jose Antonio; Colafranceschi, Stefano; D'Alfonso, Mariarosaria; D'Auria, Andrea; D'Enterria, David; Dabrowski, Anne; Daguin, Jerome; David Tinoco Mendes, Andre; De Guio, Federico; De Roeck, Albert; De Visscher, Simon; Detraz, Stephane; Deyrail, Dominique; Dobson, Marc; Dupont-Sagorin, Niels; Elliott-Peisert, Anna; Eugster, Jürg; Faccio, Federico; Felici, Daniele; Frank, Norbert; Franzoni, Giovanni; Funk, Wolfgang; Giffels, Manuel; Gigi, Dominique; Gill, Karl; Giordano, Domenico; Girone, Maria; Giunta, Marina; Glege, Frank; Gomez-Reino Garrido, Robert; Gowdy, Stephen; Guida, Roberto; Hammer, Josef; Hansen, Magnus; Harris, Philip; Honma, Alan; Innocente, Vincenzo; Janot, Patrick; Kaplon, Jan; Karavakis, Edward; Katopodis, Theodoros; Kottelat, Luc-Joseph; Kousouris, Konstantinos; Kovács, Márk István; Krajczar, Krisztian; Krzempek, Lukasz; Lecoq, Paul; Lourenco, Carlos; Magini, Nicolo; Malgeri, Luca; Mannelli, Marcello; Marchioro, Alessandro; Marconi, Sara; Marques Pinho Noite, João; Masetti, Lorenzo; Meijers, Frans; Mersi, Stefano; Meschi, Emilio; Michelis, Stefano; Moll, Michael; Moortgat, Filip; Mulders, Martijn; Musella, Pasquale; Onnela, Antti; Orsini, Luciano; Pakulski, Tymon; Palencia Cortezon, Enrique; Pavis, Steven; Perez, Emmanuelle; Pernot, Jean-Francois; Perrozzi, Luca; Petagna, Paolo; Petrilli, Achille; Petrucciani, Giovanni; Pfeiffer, Andreas; Pierini, Maurizio; Pimiä, Martti; Piparo, Danilo; Plagge, Michael; Postema, Hans; Racz, Attila; Reece, William; Rolandi, Gigi; Rovere, Marco; Rzonca, Marcin; Sakulin, Hannes; Santanastasio, Francesco; Schäfer, Christoph; Schwick, Christoph; Sekmen, Sezen; Sharma, Archana; Siegrist, Patrice; Silva, Pedro; Simon, Michal; Sphicas, Paraskevas; Spiga, Daniele; Steggemann, Jan; Stieger, Benjamin; Stoye, Markus; Szwarc, Tomasz; Tropea, Paola; Troska, Jan; Tsirou, Andromachi; Vasey, François; Veres, Gabor Istvan; Verlaat, Bart; Vichoudis, Paschalis; Vlimant, Jean-Roch; Wöhri, Hermine Katharina; Zeuner, Wolfram Dietrich; Zwalinski, Lukasz; Bertl, Willi; Deiters, Konrad; Erdmann, Wolfram; Horisberger, Roland; Ingram, Quentin; Kaestli, Hans-Christian; König, Stefan; Kotlinski, Danek; Langenegger, Urs; Meier, Beat; Renker, Dieter; Rohe, Tilman; Streuli, Silvan; Bachmair, Felix; Bäni, Lukas; Becker, Robert; Bianchini, Lorenzo; Bortignon, Pierluigi; Buchmann, Marco-Andrea; Casal, Bruno; Chanon, Nicolas; Da Silva Di Calafiori, Diogo Raphael; Deisher, Amanda; Dissertori, Günther; Dittmar, Michael; Djambazov, Lubomir; Donegà, Mauro; Dünser, Marc; Eller, Philipp; Grab, Christoph; Hits, Dmitry; Horisberger, Urs; Hoss, Jan; Lustermann, Werner; Mangano, Boris; Marini, Andrea Carlo; Martinez Ruiz del Arbol, Pablo; Masciovecchio, Mario; Meister, Daniel; Mohr, Niklas; Nägeli, Christoph; Nef, Pascal; Nessi-Tedaldi, Francesca; Pandolfi, Francesco; Pape, Luc; Pauss, Felicitas; Peruzzi, Marco; Quittnat, Milena; Ronga, Frederic Jean; Röser, Ulf; Rossini, Marco; Starodumov, Andrei; Takahashi, Maiko; Tauscher, Ludwig; Theofilatos, Konstantinos; Treille, Daniel; von Gunten, Hans Peter; Wallny, Rainer; Weber, Hannsjoerg Artur; Amsler, Claude; Bösiger, Kurt; Chiochia, Vincenzo; De Cosa, Annapaola; Favaro, Carlotta; Hinzmann, Andreas; Hreus, Tomas; Ivova Rikova, Mirena; Kilminster, Benjamin; Lange, Clemens; Maier, Reto; Millan Mejias, Barbara; Ngadiuba, Jennifer; Robmann, Peter; Snoek, Hella; Taroni, Silvia; Verzetti, Mauro; Yang, Yong; Cardaci, Marco; Chen, Kuan-Hsin; Ferro, Cristina; Kuo, Chia-Ming; Li, Syue-Wei; Lin, Willis; Lu, Yun-Ju; Volpe, Roberta; Yu, Shin-Shan; Bartalini, Paolo; Chang, Paoti; Chang, You-Hao; Chang, Yu-Wei; Chao, Yuan; Chen, Kai-Feng; Chen, Po-Hsun; Dietz, Charles; Grundler, Ulysses; Hou, George Wei-Shu; Hsiung, Yee; Kao, Kai-Yi; Lei, Yeong-Jyi; Liu, Yueh-Feng; Lu, Rong-Shyang; Majumder, Devdatta; Petrakou, Eleni; Shi, Xin; Shiu, Jing-Ge; Tzeng, Yeng-Ming; Wang, Minzu; Wilken, Rachel; Asavapibhop, Burin; Suwonjandee, Narumon; Adiguzel, Aytul; Bakirci, Mustafa Numan; Cerci, Salim; Dozen, Candan; Dumanoglu, Isa; Eskut, Eda; Girgis, Semiray; Gokbulut, Gul; Gurpinar, Emine; Hos, Ilknur; Kangal, Evrim Ersin; Kayis Topaksu, Aysel; Onengut, Gulsen; Ozdemir, Kadri; Ozturk, Sertac; Polatoz, Ayse; Sogut, Kenan; Sunar Cerci, Deniz; Tali, Bayram; Topakli, Huseyin; Vergili, Mehmet; Akin, Ilina Vasileva; Aliev, Takhmasib; Bilin, Bugra; Bilmis, Selcuk; Deniz, Muhammed; Gamsizkan, Halil; Guler, Ali Murat; Karapinar, Guler; Ocalan, Kadir; Ozpineci, Altug; Serin, Meltem; Sever, Ramazan; Surat, Ugur Emrah; Yalvac, Metin; Zeyrek, Mehmet; Gülmez, Erhan; Isildak, Bora; Kaya, Mithat; Kaya, Ozlem; Ozkorucuklu, Suat; Bahtiyar, Hüseyin; Barlas, Esra; Cankocak, Kerem; Günaydin, Yusuf Oguzhan; Vardarlı, Fuat Ilkehan; Yücel, Mete; Levchuk, Leonid; Sorokin, Pavel; Brooke, James John; Clement, Emyr; Cussans, David; Flacher, Henning; Frazier, Robert; Goldstein, Joel; Grimes, Mark; Heath, Greg P; Heath, Helen F; Jacob, Jeson; Kreczko, Lukasz; Lucas, Chris; Meng, Zhaoxia; Newbold, Dave M; Paramesvaran, Sudarshan; Poll, Anthony; Senkin, Sergey; Smith, Vincent J; Williams, Thomas; Bell, Ken W; Belyaev, Alexander; Brew, Christopher; Brown, Robert M; Cockerill, David JA; Coughlan, John A; Harder, Kristian; Harper, Sam; Ilic, Jelena; Olaiya, Emmanuel; Petyt, David; Shepherd-Themistocleous, Claire; Thea, Alessandro; Tomalin, Ian R; Womersley, William John; Worm, Steven; Baber, Mark; Bainbridge, Robert; Buchmuller, Oliver; Burton, Darren; Colling, David; Cripps, Nicholas; Cutajar, Michael; Dauncey, Paul; Davies, Gavin; Della Negra, Michel; Ferguson, William; Fulcher, Jonathan; Futyan, David; Gilbert, Andrew; Guneratne Bryer, Arlo; Hall, Geoffrey; Hatherell, Zoe; Hays, Jonathan; Iles, Gregory; Jarvis, Martyn; Karapostoli, Georgia; Kenzie, Matthew; Lane, Rebecca; Lucas, Robyn; Lyons, Louis; Magnan, Anne-Marie; Marrouche, Jad; Mathias, Bryn; Nandi, Robin; Nash, Jordan; Nikitenko, Alexander; Pela, Joao; Pesaresi, Mark; Petridis, Konstantinos; Pioppi, Michele; Raymond, David Mark; Rogerson, Samuel; Rose, Andrew; Seez, Christopher; Sharp, Peter; Sparrow, Alex; Tapper, Alexander; Vazquez Acosta, Monica; Virdee, Tejinder; Wakefield, Stuart; Wardle, Nicholas; Cole, Joanne; Hobson, Peter R; Khan, Akram; Kyberd, Paul; Leggat, Duncan; Leslie, Dawn; Martin, William; Reid, Ivan; Symonds, Philip; Teodorescu, Liliana; Turner, Mark; Dittmann, Jay; Hatakeyama, Kenichi; Kasmi, Azeddine; Liu, Hongxuan; Scarborough, Tara; Charaf, Otman; Cooper, Seth; Henderson, Conor; Rumerio, Paolo; Avetisyan, Aram; Bose, Tulika; Fantasia, Cory; Heister, Arno; Lawson, Philip; Lazic, Dragoslav; Rohlf, James; Sperka, David; St John, Jason; Sulak, Lawrence; Alimena, Juliette; Bhattacharya, Saptaparna; Christopher, Grant; Cutts, David; Demiragli, Zeynep; Ferapontov, Alexey; Garabedian, Alex; Heintz, Ulrich; Jabeen, Shabnam; Kukartsev, Gennadiy; Laird, Edward; Landsberg, Greg; Luk, Michael; Narain, Meenakshi; Segala, Michael; Sinthuprasith, Tutanon; Speer, Thomas; Swanson, Joshua; Breedon, Richard; Breto, Guillermo; Calderon De La Barca Sanchez, Manuel; Chauhan, Sushil; Chertok, Maxwell; Conway, John; Conway, Rylan; Cox, Peter Timothy; Erbacher, Robin; Flores, Chad; Gardner, Michael; Ko, Winston; Kopecky, Alexandra; Lander, Richard; Miceli, Tia; Pellett, Dave; Pilot, Justin; Ricci-Tam, Francesca; Rutherford, Britney; Searle, Matthew; Shalhout, Shalhout; Smith, John; Squires, Michael; Thomson, John; Tripathi, Mani; Wilbur, Scott; Yohay, Rachel; Andreev, Valeri; Cline, David; Cousins, Robert; Erhan, Samim; Everaerts, Pieter; Farrell, Chris; Felcini, Marta; Hauser, Jay; Ignatenko, Mikhail; Jarvis, Chad; Rakness, Gregory; Schlein, Peter; Takasugi, Eric; Valuev, Vyacheslav; Weber, Matthias; Babb, John; Burt, Kira; Clare, Robert; Ellison, John Anthony; Gary, J William; Hanson, Gail; Heilman, Jesse; Jandir, Pawandeep; Lacroix, Florent; Liu, Hongliang; Long, Owen Rosser; Luthra, Arun; Malberti, Martina; Nguyen, Harold; Olmedo Negrete, Manuel; Shrinivas, Amithabh; Sturdy, Jared; Sumowidagdo, Suharyo; Wimpenny, Stephen; Andrews, Warren; Branson, James G; Cerati, Giuseppe Benedetto; Cittolin, Sergio; D'Agnolo, Raffaele Tito; Evans, David; Holzner, André; Kelley, Ryan; Kovalskyi, Dmytro; Lebourgeois, Matthew; Letts, James; Macneill, Ian; Padhi, Sanjay; Palmer, Christopher; Pieri, Marco; Sani, Matteo; Sharma, Vivek; Simon, Sean; Sudano, Elizabeth; Tadel, Matevz; Tu, Yanjun; Vartak, Adish; Wasserbaech, Steven; Würthwein, Frank; Yagil, Avraham; Yoo, Jaehyeok; Barge, Derek; Campagnari, Claudio; Danielson, Thomas; Flowers, Kristen; Geffert, Paul; George, Christopher; Golf, Frank; Incandela, Joe; Justus, Christopher; Kyre, Susanne; Magaña Villalba, Ricardo; Mccoll, Nickolas; Mullin, Sam Daniel; Pavlunin, Viktor; Richman, Jeffrey; Rossin, Roberto; Stuart, David; To, Wing; West, Christopher; White, Dean; Apresyan, Artur; Bornheim, Adolf; Bunn, Julian; Chen, Yi; Di Marco, Emanuele; Duarte, Javier; Kcira, Dorian; Mott, Alexander; Newman, Harvey B; Pena, Cristian; Rogan, Christopher; Spiropulu, Maria; Timciuc, Vladlen; Wilkinson, Richard; Xie, Si; Zhu, Ren-Yuan; Azzolini, Virginia; Calamba, Aristotle; Carroll, Ryan; Ferguson, Thomas; Iiyama, Yutaro; Jang, Dong Wook; Paulini, Manfred; Russ, James; Vogel, Helmut; Vorobiev, Igor; Cumalat, John Perry; Drell, Brian Robert; Ford, William T; Gaz, Alessandro; Luiggi Lopez, Eduardo; Nauenberg, Uriel; Smith, James; Stenson, Kevin; Ulmer, Keith; Wagner, Stephen Robert; Alexander, James; Chatterjee, Avishek; Eggert, Nicholas; Gibbons, Lawrence Kent; Hopkins, Walter; Khukhunaishvili, Aleko; Kreis, Benjamin; Mirman, Nathan; Nicolas Kaufman, Gala; Patterson, Juliet Ritchie; Ryd, Anders; Salvati, Emmanuele; Sun, Werner; Teo, Wee Don; Thom, Julia; Thompson, Joshua; Tucker, Jordan; Weng, Yao; Winstrom, Lucas; Wittich, Peter; Winn, Dave; Abdullin, Salavat; Albrow, Michael; Anderson, Jacob; Apollinari, Giorgio; Bauerdick, Lothar AT; Beretvas, Andrew; Berryhill, Jeffrey; Bhat, Pushpalatha C; Burkett, Kevin; Butler, Joel Nathan; Chetluru, Vasundhara; Cheung, Harry; Chlebana, Frank; Chramowicz, John; Cihangir, Selcuk; Cooper, William; Deptuch, Grzegorz; Derylo, Greg; Elvira, Victor Daniel; Fisk, Ian; Freeman, Jim; Gao, Yanyan; Gingu, V Cristinel; Gottschalk, Erik; Gray, Lindsey; Green, Dan; Grünendahl, Stefan; Gutsche, Oliver; Hare, Daryl; Harris, Robert M; Hirschauer, James; Hoff, Jim R; Hooberman, Benjamin; Howell, Joseph; Hrycyk, Michael; Jindariani, Sergo; Johnson, Marvin; Joshi, Umesh; Kaadze, Ketino; Klima, Boaz; Kwan, Simon; Lei, Chi Meng; Linacre, Jacob; Lincoln, Don; Lipton, Ron; Liu, Tiehui; Los, Serguei; Lykken, Joseph; Maeshima, Kaori; Marraffino, John Michael; Martinez Outschoorn, Verena Ingrid; Maruyama, Sho; Mason, David; Matulik, Michael S; McBride, Patricia; Mishra, Kalanand; Mrenna, Stephen; Musienko, Yuri; Nahn, Steve; Newman-Holmes, Catherine; O'Dell, Vivian; Prokofyev, Oleg; Prosser, Alan; Ratnikova, Natalia; Rivera, Ryan; Sexton-Kennedy, Elizabeth; Sharma, Seema; Spalding, William J; Spiegel, Leonard; Taylor, Lucas; Tkaczyk, Slawek; Tran, Nhan Viet; Trimpl, Marcel; Uplegger, Lorenzo; Vaandering, Eric Wayne; Vidal, Richard; Voirin, Erik; Whitbeck, Andrew; Whitmore, Juliana; Wu, Weimin; Yang, Fan; Yun, Jae Chul; Acosta, Darin; Avery, Paul; Bourilkov, Dimitri; Cheng, Tongguang; Das, Souvik; De Gruttola, Michele; Di Giovanni, Gian Piero; Dobur, Didar; Field, Richard D; Fisher, Matthew; Fu, Yu; Furic, Ivan-Kresimir; Hugon, Justin; Kim, Bockjoo; Konigsberg, Jacobo; Korytov, Andrey; Kropivnitskaya, Anna; Kypreos, Theodore; Low, Jia Fu; Matchev, Konstantin; Milenovic, Predrag; Mitselmakher, Guenakh; Muniz, Lana; Rinkevicius, Aurelijus; Shchutska, Lesya; Skhirtladze, Nikoloz; Snowball, Matthew; Yelton, John; Zakaria, Mohammed; Gaultney, Vanessa; Hewamanage, Samantha; Linn, Stephan; Markowitz, Pete; Martinez, German; Rodriguez, Jorge Luis; Adams, Todd; Askew, Andrew; Bochenek, Joseph; Chen, Jie; Diamond, Brendan; Haas, Jeff; Hagopian, Sharon; Hagopian, Vasken; Johnson, Kurtis F; Prosper, Harrison; Veeraraghavan, Venkatesh; Weinberg, Marc; Baarmand, Marc M; Dorney, Brian; Hohlmann, Marcus; Kalakhety, Himali; Yumiceva, Francisco; Adams, Mark Raymond; Apanasevich, Leonard; Bazterra, Victor Eduardo; Betts, Russell Richard; Bucinskaite, Inga; Cavanaugh, Richard; Evdokimov, Olga; Gauthier, Lucie; Gerber, Cecilia Elena; Hofman, David Jonathan; Kapustka, Brian; Khalatyan, Samvel; Kurt, Pelin; Moon, Dong Ho; O'Brien, Christine; Sandoval Gonzalez, Irving Daniel; Silkworth, Christopher; Turner, Paul; Varelas, Nikos; Akgun, Ugur; Albayrak, Elif Asli; Bilki, Burak; Clarida, Warren; Dilsiz, Kamuran; Duru, Firdevs; Haytmyradov, Maksat; Merlo, Jean-Pierre; Mermerkaya, Hamit; Mestvirishvili, Alexi; Moeller, Anthony; Nachtman, Jane; Ogul, Hasan; Onel, Yasar; Ozok, Ferhat; Sen, Sercan; Tan, Ping; Tiras, Emrah; Wetzel, James; Yetkin, Taylan; Yi, Kai; Anderson, Ian; Barnett, Bruce Arnold; Blumenfeld, Barry; Bolognesi, Sara; Fehling, David; Gritsan, Andrei; Maksimovic, Petar; Martin, Christopher; Nash, Kevin; Osherson, Marc; Swartz, Morris; Xiao, Meng; Baringer, Philip; Bean, Alice; Benelli, Gabriele; Gray, Julia; Kenny III, Raymond Patrick; Murray, Michael; Noonan, Daniel; Sanders, Stephen; Sekaric, Jadranka; Stringer, Robert; Tinti, Gemma; Wang, Quan; Wood, Jeffrey Scott; Barfuss, Anne-Fleur; Chakaberia, Irakli; Ivanov, Andrew; Khalil, Sadia; Makouski, Mikhail; Maravin, Yurii; Saini, Lovedeep Kaur; Shrestha, Shruti; Svintradze, Irakli; Taylor, Russell; Toda, Sachiko; Gronberg, Jeffrey; Lange, David; Rebassoo, Finn; Wright, Douglas; Baden, Drew; Calvert, Brian; Eno, Sarah Catherine; Gomez, Jaime; Hadley, Nicholas John; Kellogg, Richard G; Kolberg, Ted; Lu, Ying; Marionneau, Matthieu; Mignerey, Alice; Pedro, Kevin; Skuja, Andris; Temple, Jeffrey; Tonjes, Marguerite; Tonwar, Suresh C; Apyan, Aram; Barbieri, Richard; Bauer, Gerry; Busza, Wit; Cali, Ivan Amos; Chan, Matthew; Di Matteo, Leonardo; Dutta, Valentina; Gomez Ceballos, Guillelmo; Goncharov, Maxim; Gulhan, Doga; Klute, Markus; Lai, Yue Shi; Lee, Yen-Jie; Levin, Andrew; Luckey, Paul David; Ma, Teng; Paus, Christoph; Ralph, Duncan; Roland, Christof; Roland, Gunther; Stephans, George; Stöckli, Fabian; Sumorok, Konstanty; Velicanu, Dragos; Veverka, Jan; Wyslouch, Bolek; Yang, Mingming; Yoon, Sungho; Zanetti, Marco; Zhukova, Victoria; Dahmes, Bryan; De Benedetti, Abraham; Gude, Alexander; Kao, Shih-Chuan; Klapoetke, Kevin; Kubota, Yuichi; Mans, Jeremy; Pastika, Nathaniel; Rusack, Roger; Singovsky, Alexander; Tambe, Norbert; Turkewitz, Jared; Acosta, John Gabriel; Cremaldi, Lucien Marcus; Kroeger, Rob; Oliveros, Sandra; Perera, Lalith; Rahmat, Rahmat; Sanders, David A; Summers, Don; Avdeeva, Ekaterina; Bloom, Kenneth; Bose, Suvadeep; Claes, Daniel R; Dominguez, Aaron; Fangmeier, Caleb; Gonzalez Suarez, Rebeca; Keller, Jason; Knowlton, Dan; Kravchenko, Ilya; Lazo-Flores, Jose; Malik, Sudhir; Meier, Frank; Monroy, Jose; Snow, Gregory R; Dolen, James; George, Jimin; Godshalk, Andrew; Iashvili, Ia; Jain, Supriya; Kaisen, Josh; Kharchilava, Avto; Kumar, Ashish; Rappoccio, Salvatore; Alverson, George; Barberis, Emanuela; Baumgartel, Darin; Chasco, Matthew; Haley, Joseph; Massironi, Andrea; Nash, David; Orimoto, Toyoko; Trocino, Daniele; Wood, Darien; Zhang, Jinzhong; Anastassov, Anton; Hahn, Kristan Allan; Kubik, Andrew; Lusito, Letizia; Mucia, Nicholas; Odell, Nathaniel; Pollack, Brian; Pozdnyakov, Andrey; Schmitt, Michael Henry; Sevova, Stanislava; Stoynev, Stoyan; Sung, Kevin; Trovato, Marco; Velasco, Mayda; Won, Steven; Berry, Douglas; Brinkerhoff, Andrew; Chan, Kwok Ming; Drozdetskiy, Alexey; Hildreth, Michael; Jessop, Colin; Karmgard, Daniel John; Kellams, Nathan; Kolb, Jeff; Lannon, Kevin; Luo, Wuming; Lynch, Sean; Marinelli, Nancy; Morse, David Michael; Pearson, Tessa; Planer, Michael; Ruchti, Randy; Slaunwhite, Jason; Valls, Nil; Wayne, Mitchell; Wolf, Matthias; Woodard, Anna; Antonelli, Louis; Bylsma, Ben; Durkin, Lloyd Stanley; Flowers, Sean; Hill, Christopher; Hughes, Richard; Kotov, Khristian; Ling, Ta-Yung; Puigh, Darren; Rodenburg, Marissa; Smith, Geoffrey; Vuosalo, Carl; Winer, Brian L; Wolfe, Homer; Wulsin, Howard Wells; Berry, Edmund; Elmer, Peter; Halyo, Valerie; Hebda, Philip; Hegeman, Jeroen; Hunt, Adam; Jindal, Pratima; Koay, Sue Ann; Lujan, Paul; Marlow, Daniel; Medvedeva, Tatiana; Mooney, Michael; Olsen, James; Piroué, Pierre; Quan, Xiaohang; Raval, Amita; Saka, Halil; Stickland, David; Tully, Christopher; Werner, Jeremy Scott; Zenz, Seth Conrad; Zuranski, Andrzej; Brownson, Eric; Lopez, Angel; Mendez, Hector; Ramirez Vargas, Juan Eduardo; Alagoz, Enver; Arndt, Kirk; Benedetti, Daniele; Bolla, Gino; Bortoletto, Daniela; Bubna, Mayur; Cervantes, Mayra; De Mattia, Marco; Everett, Adam; Hu, Zhen; Jha, Manoj; Jones, Matthew; Jung, Kurt; Kress, Matthew; Leonardo, Nuno; Lopes Pegna, David; Maroussov, Vassili; Merkel, Petra; Miller, David Harry; Neumeister, Norbert; Radburn-Smith, Benjamin Charles; Shipsey, Ian; Silvers, David; Svyatkovskiy, Alexey; Wang, Fuqiang; Xie, Wei; Xu, Lingshan; Yoo, Hwi Dong; Zablocki, Jakub; Zheng, Yu; Parashar, Neeti; Stupak, John; Adair, Antony; Akgun, Bora; Ecklund, Karl Matthew; Geurts, Frank JM; Li, Wei; Michlin, Benjamin; Padley, Brian Paul; Redjimi, Radia; Roberts, Jay; Zabel, James; Betchart, Burton; Bodek, Arie; Covarelli, Roberto; de Barbaro, Pawel; Demina, Regina; Eshaq, Yossof; Ferbel, Thomas; Garcia-Bellido, Aran; Goldenzweig, Pablo; Han, Jiyeon; Harel, Amnon; Miner, Daniel Carl; Petrillo, Gianluca; Vishnevskiy, Dmitry; Zielinski, Marek; Bhatti, Anwar; Ciesielski, Robert; Demortier, Luc; Goulianos, Konstantin; Lungu, Gheorghe; Malik, Sarah; Mesropian, Christina; Arora, Sanjay; Barker, Anthony; Bartz, Ed; Chou, John Paul; Contreras-Campana, Christian; Contreras-Campana, Emmanuel; Duggan, Daniel; Ferencek, Dinko; Gershtein, Yuri; Gray, Richard; Halkiadakis, Eva; Hidas, Dean; Lath, Amitabh; Panwalkar, Shruti; Park, Michael; Patel, Rishi; Rekovic, Vladimir; Robles, Jorge; Salur, Sevil; Schnetzer, Steve; Seitz, Claudia; Somalwar, Sunil; Stone, Robert; Thomas, Scott; Thomassen, Peter; Walker, Matthew; Rose, Keith; Spanier, Stefan; Yang, Zong-Chang; York, Andrew; Bouhali, Othmane; Eusebi, Ricardo; Flanagan, Will; Gilmore, Jason; Kamon, Teruki; Khotilovich, Vadim; Krutelyov, Vyacheslav; Montalvo, Roy; Osipenkov, Ilya; Pakhotin, Yuriy; Perloff, Alexx; Roe, Jeffrey; Safonov, Alexei; Sakuma, Tai; Suarez, Indara; Tatarinov, Aysen; Toback, David; Akchurin, Nural; Cowden, Christopher; Damgov, Jordan; Dragoiu, Cosmin; Dudero, Phillip Russell; Faulkner, James; Kovitanggoon, Kittikul; Kunori, Shuichi; Lee, Sung Won; Libeiro, Terence; Volobouev, Igor; Appelt, Eric; Delannoy, Andrés G; Greene, Senta; Gurrola, Alfredo; Johns, Willard; Maguire, Charles; Mao, Yaxian; Melo, Andrew; Sharma, Monika; Sheldon, Paul; Snook, Benjamin; Tuo, Shengquan; Velkovska, Julia; Arenton, Michael Wayne; Boutle, Sarah; Cox, Bradley; Francis, Brian; Goodell, Joseph; Hirosky, Robert; Ledovskoy, Alexander; Lin, Chuanzhe; Neu, Christopher; Wood, John; Gollapinni, Sowjanya; Harr, Robert; Karchin, Paul Edmund; Kottachchi Kankanamge Don, Chamath; Lamichhane, Pramod; Belknap, Donald; Borrello, Laura; Carlsmith, Duncan; Cepeda, Maria; Dasu, Sridhara; Duric, Senka; Friis, Evan; Grothe, Monika; Hall-Wilton, Richard; Herndon, Matthew; Hervé, Alain; Klabbers, Pamela; Klukas, Jeffrey; Lanaro, Armando; Levine, Aaron; Loveless, Richard; Mohapatra, Ajit; Ojalvo, Isabel; Palmonari, Francesco; Perry, Thomas; Pierro, Giuseppe Antonio; Polese, Giovanni; Ross, Ian; Sakharov, Alexandre; Sarangi, Tapas; Savin, Alexander; Smith, Wesley H

    2014-06-06

    The central component of the CMS detector is the largest silicon tracker ever built. The precise alignment of this complex device is a formidable challenge, and only achievable with a significant extension of the technologies routinely used for tracking detectors in the past. This article describes the full-scale alignment procedure as it is used during LHC operations. Among the specific features of the method are the simultaneous determination of up to 200,000 alignment parameters with tracks, the measurement of individual sensor curvature parameters, the control of systematic misalignment effects, and the implementation of the whole procedure in a multi-processor environment for high execution speed. Overall, the achieved statistical accuracy on the module alignment is found to be significantly better than 10 microns.

  3. A rank-based sequence aligner with applications in phylogenetic analysis.

    Directory of Open Access Journals (Sweden)

    Liviu P Dinu

    Full Text Available Recent tools for aligning short DNA reads have been designed to optimize the trade-off between correctness and speed. This paper introduces a method for assigning a set of short DNA reads to a reference genome, under Local Rank Distance (LRD. The rank-based aligner proposed in this work aims to improve correctness over speed. However, some indexing strategies to speed up the aligner are also investigated. The LRD aligner is improved in terms of speed by storing [Formula: see text]-mer positions in a hash table for each read. Another improvement, that produces an approximate LRD aligner, is to consider only the positions in the reference that are likely to represent a good positional match of the read. The proposed aligner is evaluated and compared to other state of the art alignment tools in several experiments. A set of experiments are conducted to determine the precision and the recall of the proposed aligner, in the presence of contaminated reads. In another set of experiments, the proposed aligner is used to find the order, the family, or the species of a new (or unknown organism, given only a set of short Next-Generation Sequencing DNA reads. The empirical results show that the aligner proposed in this work is highly accurate from a biological point of view. Compared to the other evaluated tools, the LRD aligner has the important advantage of being very accurate even for a very low base coverage. Thus, the LRD aligner can be considered as a good alternative to standard alignment tools, especially when the accuracy of the aligner is of high importance. Source code and UNIX binaries of the aligner are freely available for future development and use at http://lrd.herokuapp.com/aligners. The software is implemented in C++ and Java, being supported on UNIX and MS Windows.

  4. Some Alignment Considerations for the Next Linear Collider

    International Nuclear Information System (INIS)

    Ruland, R

    2004-01-01

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

  5. Percolation modelling for highly aligned polycrystalline superconducting tapes

    Energy Technology Data Exchange (ETDEWEB)

    Rutter, N A; Glowacki, B A; Evetts, J E [Department of Materials Science and Metallurgy, University of Cambridge, Pembroke Street, Cambridge CB2 3QZ (United Kingdom); IRC in Superconductivity, Madingley Road, Cambridge CB3 0HE (United Kingdom)

    2000-11-01

    Surface and bulk texture measurements have been carried out on highly aligned NiFe tapes, suitable for use as coated conductor substrates. Data from small-area electron backscatter diffraction measurements are compared with those from bulk x-ray analysis in the development of a two-dimensional percolation model, and the two are shown to give very similar results. No evidence of grain-to-grain correlation is found. The model is then developed to assess how the properties of a superconducting layer grown epitaxially on buffered tapes will depend on parameters such as sample size, grain size and the extent of grain alignment. (author)

  6. A fast cross-validation method for alignment of electron tomography images based on Beer-Lambert law

    Science.gov (United States)

    Yan, Rui; Edwards, Thomas J.; Pankratz, Logan M.; Kuhn, Richard J.; Lanman, Jason K.; Liu, Jun; Jiang, Wen

    2015-01-01

    In electron tomography, accurate alignment of tilt series is an essential step in attaining high-resolution 3D reconstructions. Nevertheless, quantitative assessment of alignment quality has remained a challenging issue, even though many alignment methods have been reported. Here, we report a fast and accurate method, tomoAlignEval, based on the Beer-Lambert law, for the evaluation of alignment quality. Our method is able to globally estimate the alignment accuracy by measuring the goodness of log-linear relationship of the beam intensity attenuations at different tilt angles. Extensive tests with experimental data demonstrated its robust performance with stained and cryo samples. Our method is not only significantly faster but also more sensitive than measurements of tomogram resolution using Fourier shell correlation method (FSCe/o). From these tests, we also conclude that while current alignment methods are sufficiently accurate for stained samples, inaccurate alignments remain a major limitation for high resolution cryo-electron tomography. PMID:26455556

  7. A fast cross-validation method for alignment of electron tomography images based on Beer-Lambert law.

    Science.gov (United States)

    Yan, Rui; Edwards, Thomas J; Pankratz, Logan M; Kuhn, Richard J; Lanman, Jason K; Liu, Jun; Jiang, Wen

    2015-11-01

    In electron tomography, accurate alignment of tilt series is an essential step in attaining high-resolution 3D reconstructions. Nevertheless, quantitative assessment of alignment quality has remained a challenging issue, even though many alignment methods have been reported. Here, we report a fast and accurate method, tomoAlignEval, based on the Beer-Lambert law, for the evaluation of alignment quality. Our method is able to globally estimate the alignment accuracy by measuring the goodness of log-linear relationship of the beam intensity attenuations at different tilt angles. Extensive tests with experimental data demonstrated its robust performance with stained and cryo samples. Our method is not only significantly faster but also more sensitive than measurements of tomogram resolution using Fourier shell correlation method (FSCe/o). From these tests, we also conclude that while current alignment methods are sufficiently accurate for stained samples, inaccurate alignments remain a major limitation for high resolution cryo-electron tomography. Copyright © 2015 Elsevier Inc. All rights reserved.

  8. Alignment error of mirror modules of advanced telescope for high-energy astrophysics due to wavefront aberrations

    Science.gov (United States)

    Zocchi, Fabio E.

    2017-10-01

    One of the approaches that is being tested for the integration of the mirror modules of the advanced telescope for high-energy astrophysics x-ray mission of the European Space Agency consists in aligning each module on an optical bench operated at an ultraviolet wavelength. The mirror module is illuminated by a plane wave and, in order to overcome diffraction effects, the centroid of the image produced by the module is used as a reference to assess the accuracy of the optical alignment of the mirror module itself. Among other sources of uncertainty, the wave-front error of the plane wave also introduces an error in the position of the centroid, thus affecting the quality of the mirror module alignment. The power spectral density of the position of the point spread function centroid is here derived from the power spectral density of the wave-front error of the plane wave in the framework of the scalar theory of Fourier diffraction. This allows the defining of a specification on the collimator quality used for generating the plane wave starting from the contribution to the error budget allocated for the uncertainty of the centroid position. The theory generally applies whenever Fourier diffraction is a valid approximation, in which case the obtained result is identical to that derived by geometrical optics considerations.

  9. Spatio-temporal alignment of pedobarographic image sequences.

    Science.gov (United States)

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

    2011-07-01

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

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

    International Nuclear Information System (INIS)

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

    1995-02-01

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

  11. 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

  12. Beam based alignment at the KEK accelerator test facility

    International Nuclear Information System (INIS)

    Ross, M.; Nelson, J.; Woodley, M.; Wolski, A.

    2002-01-01

    The KEK Accelerator Test Facility (ATF) damping ring is a prototype low emittance source for the NLC/JLC linear collider. To achieve the goal normalized vertical emittance gey = 20 nm-rad, magnet placement accuracy better than 30 mm must be achieved. Accurate beam-based alignment (BBA) is required. The ATF arc optics uses a FOBO cell with two horizontally focusing quadrupoles, two sextupoles and a horizontally defocusing gradient dipole, all of which must be aligned with BBA. BBA at ATF uses the quadrupole and sextupole trim windings to find the trajectory through the center of each magnet. The results can be interpreted to assess the accuracy of the mechanical alignment and the beam position monitor offsets

  13. Automated alignment of optical components for high-power diode lasers

    Science.gov (United States)

    Brecher, C.; Pyschny, N.; Haag, S.; Guerrero Lule, V.

    2012-03-01

    Despite major progress in developing brilliant laser sources a huge potential for cost reductions can be found in simpler setups and automated assembly processes, especially for large volume applications. In this presentation, a concept for flexible automation in optics assembly is presented which is based on standard micro assembly systems with relatively large workspace and modular micromanipulators to enhance the system with additional degrees of freedom and a very high motion resolution. The core component is a compact flexure-based micromanipulator especially designed for the alignment of micro optical components which will be described in detail. The manipulator has been applied in different scenarios to develop and investigate automated alignment processes. This paper focuses on the automated alignment of fast axis collimation (FAC) lenses which is a crucial step during the production of diode lasers. The handling and positioning system, the measuring arrangement for process feedback during active alignment as well as the alignment strategy will be described. The fine alignment of the FAC lens is performed with the micromanipulator under concurrent analysis of the far and the near field intensity distribution. An optimization of the image processing chains for the alignment of a FAC in front of a diode bar led to cycle times of less than 30 seconds. An outlook on other applications and future work regarding the development of automated assembly processes as well as new ideas for flexible assembly systems with desktop robots will close the talk.

  14. High-precision optical systems with inexpensive hardware: a unified alignment and structural design approach

    Science.gov (United States)

    Winrow, Edward G.; Chavez, Victor H.

    2011-09-01

    High-precision opto-mechanical structures have historically been plagued by high costs for both hardware and the associated alignment and assembly process. This problem is especially true for space applications where only a few production units are produced. A methodology for optical alignment and optical structure design is presented which shifts the mechanism of maintaining precision from tightly toleranced, machined flight hardware to reusable, modular tooling. Using the proposed methodology, optical alignment error sources are reduced by the direct alignment of optics through their surface retroreflections (pips) as seen through a theodolite. Optical alignment adjustments are actualized through motorized, sub-micron precision actuators in 5 degrees of freedom. Optical structure hardware costs are reduced through the use of simple shapes (tubes, plates) and repeated components. This approach produces significantly cheaper hardware and more efficient assembly without sacrificing alignment precision or optical structure stability. The design, alignment plan and assembly of a 4" aperture, carbon fiber composite, Schmidt-Cassegrain concept telescope is presented.

  15. A three axis turntable's online initial state measurement method based on the high-accuracy laser gyro SINS

    Science.gov (United States)

    Gao, Chunfeng; Wei, Guo; Wang, Qi; Xiong, Zhenyu; Wang, Qun; Long, Xingwu

    2016-10-01

    As an indispensable equipment in inertial technology tests, the three-axis turntable is widely used in the calibration of various types inertial navigation systems (INS). In order to ensure the calibration accuracy of INS, we need to accurately measure the initial state of the turntable. However, the traditional measuring method needs a lot of exterior equipment (such as level instrument, north seeker, autocollimator, etc.), and the test processing is complex, low efficiency. Therefore, it is relatively difficult for the inertial measurement equipment manufacturers to realize the self-inspection of the turntable. Owing to the high precision attitude information provided by the laser gyro strapdown inertial navigation system (SINS) after fine alignment, we can use it as the attitude reference of initial state measurement of three-axis turntable. For the principle that the fixed rotation vector increment is not affected by measuring point, we use the laser gyro INS and the encoder of the turntable to provide the attitudes of turntable mounting plat. Through this way, the high accuracy measurement of perpendicularity error and initial attitude of the three-axis turntable has been achieved.

  16. 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.

  17. Vertically aligned BCN nanotubes with high capacitance.

    Science.gov (United States)

    Iyyamperumal, Eswaramoorthi; Wang, Shuangyin; Dai, Liming

    2012-06-26

    Using a chemical vapor deposition method, we have synthesized vertically aligned BCN nanotubes (VA-BCNs) on a Ni-Fe-coated SiO(2)/Si substrate from a melamine diborate precursor. The effects of pyrolysis conditions on the morphology and thermal property of grown nanotubes, as well as the nanostructure and composition of an individual BCN nanotube, were systematically studied. It was found that nitrogen atoms are bonded to carbons in both graphitic and pyridinic forms and that the resultant VA-BCNs grown at 1000 °C show the highest specific capacitance (321.0 F/g) with an excellent rate capability and high durability with respect to nonaligned BCN (167.3 F/g) and undoped multiwalled carbon nanotubes (117.3 F/g) due to synergetic effects arising from the combined co-doping of B and N in CNTs and the well-aligned nanotube structure.

  18. High Accuracy Transistor Compact Model Calibrations

    Energy Technology Data Exchange (ETDEWEB)

    Hembree, Charles E. [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Mar, Alan [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Robertson, Perry J. [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States)

    2015-09-01

    Typically, transistors are modeled by the application of calibrated nominal and range models. These models consists of differing parameter values that describe the location and the upper and lower limits of a distribution of some transistor characteristic such as current capacity. Correspond- ingly, when using this approach, high degrees of accuracy of the transistor models are not expected since the set of models is a surrogate for a statistical description of the devices. The use of these types of models describes expected performances considering the extremes of process or transistor deviations. In contrast, circuits that have very stringent accuracy requirements require modeling techniques with higher accuracy. Since these accurate models have low error in transistor descriptions, these models can be used to describe part to part variations as well as an accurate description of a single circuit instance. Thus, models that meet these stipulations also enable the calculation of quantifi- cation of margins with respect to a functional threshold and uncertainties in these margins. Given this need, new model high accuracy calibration techniques for bipolar junction transis- tors have been developed and are described in this report.

  19. Evaluation of a patient specific femoral alignment guide for hip resurfacing.

    Science.gov (United States)

    Olsen, Michael; Naudie, Douglas D; Edwards, Max R; Sellan, Michael E; McCalden, Richard W; Schemitsch, Emil H

    2014-03-01

    A novel alternative to conventional instrumentation for femoral component insertion in hip resurfacing is a patient specific, computed tomography based femoral alignment guide. A benchside study using cadaveric femora was performed comparing a custom alignment guide to conventional instrumentation and computer navigation. A clinical series of twenty-five hip resurfacings utilizing a custom alignment guide was conducted by three surgeons experienced in hip resurfacing. Using cadaveric femora, the custom guide was comparable to conventional instrumentation with computer navigation proving superior to both. Clinical femoral component alignment accuracy was 3.7° and measured within ± 5° of plan in 20 of 24 cases. Patient specific femoral alignment guides provide a satisfactory level of accuracy and may be a better alternative to conventional instrumentation for initial femoral guidewire placement in hip resurfacing. Crown Copyright © 2014. All rights reserved.

  20. Precise rotational alignment of x-ray transmission diffraction gratings

    International Nuclear Information System (INIS)

    Hill, S.L.

    1988-01-01

    Gold transmission diffraction gratings used for x-ray spectroscopy must sometimes be rotationally aligned to the axis of a diagnostic instrument to within sub-milliradian accuracy. We have fabricated transmission diffraction gratings with high line-densities (grating period of 200 and 300 nm) using uv holographic and x-ray lithography. Since the submicron features of the gratings are not optically visible, precision alignment is time consuming and difficult to verify in situ. We have developed a technique to write an optically visible alignment pattern onto these gratings using a scanning electron microscope (SEM). At high magnification (15000 X) several submicron lines of the grating are observable in the SEM, making it possible to write an alignment pattern parallel to the grating lines in an electron-beam-sensitive coating that overlays the grating. We create an alignment pattern by following a 1-cm-long grating line using the SEM's joystick-controlled translation stage. By following the same grating line we are assured the traveled direction of the SEM electron beam is parallel to the grating to better than 10 μradian. The electron-beam-exposed line-width can be large (5 to 15 μm wide) depending on the SEM magnification, and is therefore optically visible. The exposed pattern is eventually made a permanent feature of the grating by ion beam etching or gold electroplating. The pattern can be used to accurately align the grating to the axis of a diagnostic instrument. More importantly, the alignment of the grating can be quickly verified in situ

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

    Science.gov (United States)

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

    2017-12-21

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

  2. High Throughput Preparation of Aligned Nanofibers Using an Improved Bubble-Electrospinning

    Directory of Open Access Journals (Sweden)

    Liang Yu

    2017-11-01

    Full Text Available An improved bubble-electrospinning, consisting of a cone shaped air nozzle, a copper solution reservoir connected directly to the power generator, and a high speed rotating copper wire drum as a collector, was presented successfully to obtain high throughput preparation of aligned nanofibers. The influences of drum rotation speed on morphology and properties of obtained nanofibers were explored and researched. The results showed that the alignment degree, diameter distribution, and properties of nanofibers were improved with the increase of the drum rotation speed.

  3. Linear accelerator section alignment in a vacuum chamber

    International Nuclear Information System (INIS)

    Vengrov, R.M.; Vinogradskij, N.N.; Danil'tsev, E.N.; Iosseliani, D.D.; Kosyak, V.S.; Porubaj, N.I.; Ugarov, S.B.

    1989-01-01

    Alignment technique for multisectional accelerating structures, that may be used in designing new accelerators for experimental and applied purposes, is described. The accuracy of the alignment of four-chamber resonator sections directly in an accelerator vacuum volume without its depressurization is not less than 100 μm. 8 refs.; 5 figs.; 5 tabs

  4. Multiple network alignment on quantum computers

    Science.gov (United States)

    Daskin, Anmer; Grama, Ananth; Kais, Sabre

    2014-12-01

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

  5. Shapes and alignments at high spin in some rare-earth nuclei

    International Nuclear Information System (INIS)

    Deleplanque, M.A.; Diamond, R.M.; Stephens, F.S.; Macchiavelli, A.O.; Doessing, T.; Draper, J.E.; Dines, E.L.

    1985-01-01

    The structure of nuclei at high spins is dominated by an interplay between deformation and alignment effects. Cranking models predict various shapes but at the highest spins, there is a tendency towards large triaxial deformations and sometimes towards very large prolate deformations (superdeformations). Directly involved in the shape changes are aligned orbitals which come down to the Fermi level as the nucleus rotates more rapidly. At a certain frequency, they become populated and cause large alignments. The mechanism of these changes has been explored by looking at a series of rare earth quasirotational nuclei from Dy to W in the transition region around N = 90 neutrons. The continuum spectra, corrected for incomplete population (feeding) of the high spins, are directly proportional to dynamic effective moments of inertia which describe how much spin is generated at each rotational frequency

  6. Unscented Kalman filter for SINS alignment

    Institute of Scientific and Technical Information of China (English)

    Zhou Zhanxin; Gao Yanan; Chen Jiabin

    2007-01-01

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

  7. 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.

  8. Alignment of CT images of skull dysmorphology using anatomy-based perpendicular axes

    International Nuclear Information System (INIS)

    Yoo, Sun K; Kim, Yong O; Kim, Hee-Joung; Kim, Nam H; Jang, Young Beom; Kim, Kee-Deog; Lee, Hye-Yeon

    2003-01-01

    Rigid body registration of 3D CT scans, based on manual identification of homologous landmarks, is useful for the visual analysis of skull dysmorphology. In this paper, a robust and simple alignment method was proposed to allow for the comparison of skull morphologies, within and between individuals with craniofacial anomalies, based on 3D CT scans, and the minimum number of anatomical landmarks, under rigidity and uniqueness constraints. Three perpendicular axes, extracted from anatomical landmarks, define the absolute coordinate system, through a rigid body transformation, to align multiple CT images for different patients and acquisition times. The accuracy of the alignment method depends on the accuracy of the localized landmarks and target points. The numerical simulation generalizes the accuracy requirements of the alignment method. Experiments using a human dried skull specimen, and ten sets of skull CT images (the pre- and post-operative CT scans of four plagiocephaly, and one fibrous dysplasia patients), demonstrated the feasibility of the technique in clinical practice

  9. Measuring Parameters of Massive Black Hole Binaries with Partially Aligned Spins

    Science.gov (United States)

    Lang, Ryan N.; Hughes, Scott A.; Cornish, Neil J.

    2011-01-01

    The future space-based gravitational wave detector LISA will be able to measure parameters of coalescing massive black hole binaries, often to extremely high accuracy. Previous work has demonstrated that the black hole spins can have a strong impact on the accuracy of parameter measurement. Relativistic spin-induced precession modulates the waveform in a manner which can break degeneracies between parameters, in principle significantly improving how well they are measured. Recent studies have indicated, however, that spin precession may be weak for an important subset of astrophysical binary black holes: those in which the spins are aligned due to interactions with gas. In this paper, we examine how well a binary's parameters can be measured when its spins are partially aligned and compare results using waveforms that include higher post-Newtonian harmonics to those that are truncated at leading quadrupole order. We find that the weakened precession can substantially degrade parameter estimation, particularly for the "extrinsic" parameters sky position and distance. Absent higher harmonics, LISA typically localizes the sky position of a nearly aligned binary about an order of magnitude less accurately than one for which the spin orientations are random. Our knowledge of a source's sky position will thus be worst for the gas-rich systems which are most likely to produce electromagnetic counterparts. Fortunately, higher harmonics of the waveform can make up for this degradation. By including harmonics beyond the quadrupole in our waveform model, we find that the accuracy with which most of the binary's parameters are measured can be substantially improved. In some cases, the improvement is such that they are measured almost as well as when the binary spins are randomly aligned.

  10. High-frequency self-aligned graphene transistors with transferred gate stacks

    Science.gov (United States)

    Cheng, Rui; Bai, Jingwei; Liao, Lei; Zhou, Hailong; Chen, Yu; Liu, Lixin; Lin, Yung-Chen; Jiang, Shan; Huang, Yu; Duan, Xiangfeng

    2012-01-01

    Graphene has attracted enormous attention for radio-frequency transistor applications because of its exceptional high carrier mobility, high carrier saturation velocity, and large critical current density. Herein we report a new approach for the scalable fabrication of high-performance graphene transistors with transferred gate stacks. Specifically, arrays of gate stacks are first patterned on a sacrificial substrate, and then transferred onto arbitrary substrates with graphene on top. A self-aligned process, enabled by the unique structure of the transferred gate stacks, is then used to position precisely the source and drain electrodes with minimized access resistance or parasitic capacitance. This process has therefore enabled scalable fabrication of self-aligned graphene transistors with unprecedented performance including a record-high cutoff frequency up to 427 GHz. Our study defines a unique pathway to large-scale fabrication of high-performance graphene transistors, and holds significant potential for future application of graphene-based devices in ultra–high-frequency circuits. PMID:22753503

  11. High-accuracy 3-D modeling of cultural heritage: the digitizing of Donatello's "Maddalena".

    Science.gov (United States)

    Guidi, Gabriele; Beraldin, J Angelo; Atzeni, Carlo

    2004-03-01

    Three-dimensional digital modeling of Heritage works of art through optical scanners, has been demonstrated in recent years with results of exceptional interest. However, the routine application of three-dimensional (3-D) modeling to Heritage conservation still requires the systematic investigation of a number of technical problems. In this paper, the acquisition process of the 3-D digital model of the Maddalena by Donatello, a wooden statue representing one of the major masterpieces of the Italian Renaissance which was swept away by the Florence flood of 1966 and successively restored, is described. The paper reports all the steps of the acquisition procedure, from the project planning to the solution of the various problems due to range camera calibration and to material non optically cooperative. Since the scientific focus is centered on the 3-D model overall dimensional accuracy, a methodology for its quality control is described. Such control has demonstrated how, in some situations, the ICP-based alignment can lead to incorrect results. To circumvent this difficulty we propose an alignment technique based on the fusion of ICP with close-range digital photogrammetry and a non-invasive procedure in order to generate a final accurate model. In the end detailed results are presented, demonstrating the improvement of the final model, and how the proposed sensor fusion ensure a pre-specified level of accuracy.

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

    Science.gov (United States)

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

    2018-03-01

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

  13. 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

  14. Design and Test of Object Aligning Grippers for Industrial Applications

    DEFF Research Database (Denmark)

    Ellekilde, Lars-Peter; Petersen, Henrik Gordon

    2006-01-01

    In this paper we will present a new concept for gripping objects in industrial applications. We assume that a priori, the object pose is only known with a relative low accuracy. Despite this, our method can lead to high accuracy gripping suitable for e.g. industrial assembly. Our concept...... is to augment a simple parallel gripper by mounting a set of object speci?c jaws. Given the right shapes these jaws enable the gripper to automatically align the object, and thereby compensate for errors in the original object pose estimation. We will introduce a couple of automatic and semi-automatic design...

  15. High-precision correlative fluorescence and electron cryo microscopy using two independent alignment markers

    International Nuclear Information System (INIS)

    Schellenberger, Pascale; Kaufmann, Rainer; Siebert, C. Alistair; Hagen, Christoph; Wodrich, Harald; Grünewald, Kay

    2014-01-01

    Correlative light and electron microscopy (CLEM) is an emerging technique which combines functional information provided by fluorescence microscopy (FM) with the high-resolution structural information of electron microscopy (EM). So far, correlative cryo microscopy of frozen-hydrated samples has not reached better than micrometre range accuracy. Here, a method is presented that enables the correlation between fluorescently tagged proteins and electron cryo tomography (cryoET) data with nanometre range precision. Specifically, thin areas of vitrified whole cells are examined by correlative fluorescence cryo microscopy (cryoFM) and cryoET. Novel aspects of the presented cryoCLEM workflow not only include the implementation of two independent electron dense fluorescent markers to improve the precision of the alignment, but also the ability of obtaining an estimate of the correlation accuracy for each individual object of interest. The correlative workflow from plunge-freezing to cryoET is detailed step-by-step for the example of locating fluorescence-labelled adenovirus particles trafficking inside a cell. - Highlights: • Vitrified mammalian cell were imaged by fluorescence and electron cryo microscopy. • TetraSpeck fluorescence markers were added to correct shifts between cryo fluorescence channels. • FluoSpheres fiducials were used as reference points to assign new coordinates to cryoEM images. • Adenovirus particles were localised with an average correlation precision of 63 nm

  16. High-precision correlative fluorescence and electron cryo microscopy using two independent alignment markers

    Energy Technology Data Exchange (ETDEWEB)

    Schellenberger, Pascale [Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Kaufmann, Rainer [Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU (United Kingdom); Siebert, C. Alistair; Hagen, Christoph [Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Wodrich, Harald [Microbiologie Fondamentale et Pathogénicité, MFP CNRS UMR 5234, University of Bordeaux SEGALEN, 146 rue Leo Seignat, 33076 Bordeaux (France); Grünewald, Kay, E-mail: kay@strubi.ox.ac.uk [Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom)

    2014-08-01

    Correlative light and electron microscopy (CLEM) is an emerging technique which combines functional information provided by fluorescence microscopy (FM) with the high-resolution structural information of electron microscopy (EM). So far, correlative cryo microscopy of frozen-hydrated samples has not reached better than micrometre range accuracy. Here, a method is presented that enables the correlation between fluorescently tagged proteins and electron cryo tomography (cryoET) data with nanometre range precision. Specifically, thin areas of vitrified whole cells are examined by correlative fluorescence cryo microscopy (cryoFM) and cryoET. Novel aspects of the presented cryoCLEM workflow not only include the implementation of two independent electron dense fluorescent markers to improve the precision of the alignment, but also the ability of obtaining an estimate of the correlation accuracy for each individual object of interest. The correlative workflow from plunge-freezing to cryoET is detailed step-by-step for the example of locating fluorescence-labelled adenovirus particles trafficking inside a cell. - Highlights: • Vitrified mammalian cell were imaged by fluorescence and electron cryo microscopy. • TetraSpeck fluorescence markers were added to correct shifts between cryo fluorescence channels. • FluoSpheres fiducials were used as reference points to assign new coordinates to cryoEM images. • Adenovirus particles were localised with an average correlation precision of 63 nm.

  17. The use of low density high accuracy (LDHA) data for correction of high density low accuracy (HDLA) point cloud

    Science.gov (United States)

    Rak, Michal Bartosz; Wozniak, Adam; Mayer, J. R. R.

    2016-06-01

    Coordinate measuring techniques rely on computer processing of coordinate values of points gathered from physical surfaces using contact or non-contact methods. Contact measurements are characterized by low density and high accuracy. On the other hand optical methods gather high density data of the whole object in a short time but with accuracy at least one order of magnitude lower than for contact measurements. Thus the drawback of contact methods is low density of data, while for non-contact methods it is low accuracy. In this paper a method for fusion of data from two measurements of fundamentally different nature: high density low accuracy (HDLA) and low density high accuracy (LDHA) is presented to overcome the limitations of both measuring methods. In the proposed method the concept of virtual markers is used to find a representation of pairs of corresponding characteristic points in both sets of data. In each pair the coordinates of the point from contact measurements is treated as a reference for the corresponding point from non-contact measurement. Transformation enabling displacement of characteristic points from optical measurement to their match from contact measurements is determined and applied to the whole point cloud. The efficiency of the proposed algorithm was evaluated by comparison with data from a coordinate measuring machine (CMM). Three surfaces were used for this evaluation: plane, turbine blade and engine cover. For the planar surface the achieved improvement was of around 200 μm. Similar results were obtained for the turbine blade but for the engine cover the improvement was smaller. For both freeform surfaces the improvement was higher for raw data than for data after creation of mesh of triangles.

  18. Survey and alignment of the Fermilab recycler antiproton storage ring

    International Nuclear Information System (INIS)

    Arics, Babatunde O.O.

    1999-01-01

    In June of 1999 Fermilab commissioned a newly constructed antiproton storage ring, the 'Recycler Ring', in the Main Injector tunnel directly above the Main Injector beamline. The Recycler Ring is a fixed 8 GeV kinetic energy storage ring and is constructed of strontium ferrite permanent magnets. The 3319.4-meter-circumference Recycler Ring consists of 344 gradient magnets and 100 quadrupoles all of which are permanent magnets. This paper discusses the methods employed to survey and align these permanent magnets within the Recycler Ring with the specified accuracy. The Laser Tracker was the major instrument used for the final magnet alignment. The magnets were aligned along the Recycler Ring with a relative accuracy of ±0.25 mm. (author)

  19. 25m2 target-aligned heliostat with closed-loop control

    CSIR Research Space (South Africa)

    Roos, TH

    2007-09-01

    Full Text Available system making use of a solar tracker has been developed and tested on a 1.252m target-aligned miniheliostat. A tracking accuracy of 3.3 milliradians was obtained. A good focal spot has been obtained with the 252m target-aligned research heliostat....

  20. High yield growth of patterned vertically aligned carbon nanotubes using inkjet-printed catalyst.

    Science.gov (United States)

    Beard, James D; Stringer, Jonathan; Ghita, Oana R; Smith, Patrick J

    2013-10-09

    This study reports on the fabrication of vertically aligned carbon nanotubes localized at specific sites on a growth substrate by deposition of a nanoparticle suspension using inkjet printing. Carbon nanotubes were grown with high yield as vertically aligned forests to a length of approximately 400 μm. The use of inkjet printing for catalyst fabrication considerably improves the production rate of vertically aligned patterned nanotube forests compared with conventional patterning techniques, for example, electron beam lithography or photolithography.

  1. 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.

  2. Diagnostic accuracy of high-definition CT coronary angiography in high-risk patients

    International Nuclear Information System (INIS)

    Iyengar, S.S.; Morgan-Hughes, G.; Ukoumunne, O.; Clayton, B.; Davies, E.J.; Nikolaou, V.; Hyde, C.J.; Shore, A.C.; Roobottom, C.A.

    2016-01-01

    Aim: To assess the diagnostic accuracy of computed tomography coronary angiography (CTCA) using a combination of high-definition CT (HD-CTCA) and high level of reader experience, with invasive coronary angiography (ICA) as the reference standard, in high-risk patients for the investigation of coronary artery disease (CAD). Materials and methods: Three hundred high-risk patients underwent HD-CTCA and ICA. Independent experts evaluated the images for the presence of significant CAD, defined primarily as the presence of moderate (≥50%) stenosis and secondarily as the presence of severe (≥70%) stenosis in at least one coronary segment, in a blinded fashion. HD-CTCA was compared to ICA as the reference standard. Results: No patients were excluded. Two hundred and six patients (69%) had moderate and 178 (59%) had severe stenosis in at least one vessel at ICA. The sensitivity, specificity, positive predictive value, and negative predictive value were 97.1%, 97.9%, 99% and 93.9% for moderate stenosis, and 98.9%, 93.4%, 95.7% and 98.3%, for severe stenosis, on a per-patient basis. Conclusion: The combination of HD-CTCA and experienced readers applied to a high-risk population, results in high diagnostic accuracy comparable to ICA. Modern generation CT systems in experienced hands might be considered for an expanded role. - Highlights: • Diagnostic accuracy of High-Definition CT Angiography (HD-CTCA) has been assessed. • Invasive Coronary angiography (ICA) is the reference standard. • Diagnostic accuracy of HD-CTCA is comparable to ICA. • Diagnostic accuracy is not affected by coronary calcium or stents. • HD-CTCA provides a non-invasive alternative in high-risk patients.

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

    Science.gov (United States)

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

    2013-11-26

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

  4. Self-aligned photolithography for the fabrication of fully transparent high-voltage devices

    Science.gov (United States)

    Zhang, Yonghui; Mei, Zengxia; Huo, Wenxing; Wang, Tao; Liang, Huili; Du, Xiaolong

    2018-05-01

    High-voltage devices, working in the range of hundreds of volts, are indispensable elements in the driving or readout circuits for various kinds of displays, integrated microelectromechanical systems and x-ray imaging sensors. However, the device performances are found hardly uniform or repeatable due to the misalignment issue, which are extremely common for offset drain high-voltage devices. To resolve this issue, this article reports a set of self-aligned photolithography technology for the fabrication of high-voltage devices. High-performance fully-transparent high-voltage thin film transistors, diodes and logic inverters are successfully fabricated with this technology. Unlike other self-aligned routes, opaque masks are introduced on the backside of the transparent substrate to facilitate proximity exposure method. The photolithography process is simulated and analyzed with technology computer aided design simulation to explain the working principle of the proximity exposure method. The substrate thickness is found to be vital for the implementation of this technology based on both simulation and experimental results. The electrical performance of high-voltage devices is dependent on the offset length, which can be delicately modulated by changing the exposure dose. The presented self-aligned photolithography technology is proved to be feasible in high-voltage circuits, demonstrating its huge potential in practical industrial applications.

  5. 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.

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

    Science.gov (United States)

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

    2017-08-01

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

  7. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez

    2011-01-01

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

  8. 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.

  9. Accuracy of Topcon CM-1000 videokeratoscope on spherical test surfaces.

    Science.gov (United States)

    Pérez-Yern, E; Fimia-Gil, A; Mateos, F; Carretero, L

    1997-01-01

    Many videokeratoscopes use mathematical formulas to calculate corneal radii; calculations depend on slope, curvature, coordinate position, or focal properties of the surface. Accuracy of each type of videokeratoscope must be evaluated. A controversy exists about whether axial or tangential methods best provide a precise description of corneal shape; therefore results with the Topcon CM-1000 using both methods were evaluated. Measurements were done on black polymethylmethacrylate (PMMA) spherical calibrated surfaces. Lenses were first aligned and measured and then misaligned in different directions and measured. Results for each position were compared with the zero or alignment position. Accuracy of the CM-1000 was high even under extreme misalignment conditions. Tolerance to misalignment was high (about 300 mm). Misalignment-induced variations in the output results were small (usually less than 0.05 mm). However, important variations (more than 1.00 diopter [D]) were found for the lowest measured radius (6 mm). In some cases, small differences between axial and tangential radii for the same point could be found. With the exception of extremely low radii of curvature, the CM-1000 was accurate for measuring spherical surfaces. Further investigation remains to be done on aspheric surfaces and in clinical practice.

  10. SU-F-I-59: Quality Assurance Phantom for PET/CT Alignment and Attenuation Correction

    International Nuclear Information System (INIS)

    Lin, T; Hamacher, K

    2016-01-01

    Purpose: This study utilizes a commercial PET/CT phantom to investigate two specific properties of a PET/CT system: the alignment accuracy of PET images with those from CT used for attenuation correction and the accuracy of this correction in PET images. Methods: A commercial PET/CT phantom consisting of three aluminum rods, two long central cylinders containing uniform activity, and attenuating materials such as air, water, bone and iodine contrast was scanned using a standard PET/CT protocol. Images reconstructed with 2 mm slice thickness and a 512 by 512 matrix were obtained. The center of each aluminum rod in the PET and CT images was compared to evaluate alignment accuracy. ROIs were drawn on transaxial images of the central rods at each section of attenuating material to determine the corrected activity (in BQML). BQML values were graphed as a function of slice number to provide a visual representation of the attenuation-correction throughout the whole phantom. Results: Alignment accuracy is high between the PET and CT images. The maximum deviation between the two in the axial plane is less than 1.5 mm, which is less than the width of a single pixel. BQML values measured along different sections of the large central rods are similar among the different attenuating materials except iodine contrast. Deviation of BQML values in the air and bone sections from the water section is less than 1%. Conclusion: Accurate alignment of PET and CT images is critical to ensure proper calculation and application of CT-based attenuation correction. This study presents a simple and quick method to evaluate the two with a single acquisition. As the phantom also includes spheres of increasing diameter, this could serve as a straightforward means to annually evaluate the status of a modern PET/CT system.

  11. SU-F-I-59: Quality Assurance Phantom for PET/CT Alignment and Attenuation Correction

    Energy Technology Data Exchange (ETDEWEB)

    Lin, T; Hamacher, K [Columbia University Medical Center, New York, NY (United States)

    2016-06-15

    Purpose: This study utilizes a commercial PET/CT phantom to investigate two specific properties of a PET/CT system: the alignment accuracy of PET images with those from CT used for attenuation correction and the accuracy of this correction in PET images. Methods: A commercial PET/CT phantom consisting of three aluminum rods, two long central cylinders containing uniform activity, and attenuating materials such as air, water, bone and iodine contrast was scanned using a standard PET/CT protocol. Images reconstructed with 2 mm slice thickness and a 512 by 512 matrix were obtained. The center of each aluminum rod in the PET and CT images was compared to evaluate alignment accuracy. ROIs were drawn on transaxial images of the central rods at each section of attenuating material to determine the corrected activity (in BQML). BQML values were graphed as a function of slice number to provide a visual representation of the attenuation-correction throughout the whole phantom. Results: Alignment accuracy is high between the PET and CT images. The maximum deviation between the two in the axial plane is less than 1.5 mm, which is less than the width of a single pixel. BQML values measured along different sections of the large central rods are similar among the different attenuating materials except iodine contrast. Deviation of BQML values in the air and bone sections from the water section is less than 1%. Conclusion: Accurate alignment of PET and CT images is critical to ensure proper calculation and application of CT-based attenuation correction. This study presents a simple and quick method to evaluate the two with a single acquisition. As the phantom also includes spheres of increasing diameter, this could serve as a straightforward means to annually evaluate the status of a modern PET/CT system.

  12. 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).

  13. Aligned Carbon Nanotubes for High-Performance Films and Composites

    Science.gov (United States)

    Zhang, Liwen

    Carbon nanotubes (CNTs) with extraordinary properties and thus many potential applications have been predicted to be the best reinforcements for the next-generation multifunctional composite materials. Difficulties exist in transferring the most use of the unprecedented properties of individual CNTs to macroscopic forms of CNT assemblies. Therefore, this thesis focuses on two main goals: 1) discussing the issues that influence the performance of bulk CNT products, and 2) fabricating high-performance dry CNT films and composite films with an understanding of the fundamental structure-property relationship in these materials. Dry CNT films were fabricated by a winding process using CNT arrays with heights of 230 mum, 300 im and 360 mum. The structures of the as-produced films, as well as their mechanical and electrical properties were examined in order to find out the effects of different CNT lengths. It was found that the shorter CNTs synthesized by shorter time in the CVD furnace exhibited less structural defects and amorphous carbon, resulting in more compact packing and better nanotube alignment when made into dry films, thus, having better mechanical and electrical performance. A novel microcombing approach was developed to mitigate the CNT waviness and alignment in the dry films, and ultrahigh mechanical properties and exceptional electrical performance were obtained. This method utilized a pair of sharp surgical blades with microsized features at the blade edges as micro-combs to, for the first time, disentangle and straighten the wavy CNTs in the dry-drawn CNT sheet at single-layer level. The as-combed CNT sheet exhibited high level of nanotube alignment and straightness, reduced structural defects, and enhanced nanotube packing density. The dry CNT films produced by microcombing had a very high Young's modulus of 172 GPa, excellent tensile strength of 3.2 GPa, and unprecedented electrical conductivity of 1.8x10 5 S/m, which were records for CNT films or

  14. Strategy and validation of fiducialisation for the pre-alignment of CLIC components

    CERN Document Server

    Griffet, S; Kemppinen, J; Mainaud Durand, H; Rude, V; Sterbini, G

    2012-01-01

    The feasibility of the high energy e+ e- linear collider CLIC (Compact Linear Collider) is very dependent on the ability to accurately pre-align its components. There are two 20 km long Main Linacs which meet in an interaction point (IP). The Main Linacs are composed of thousands of 2 m long modules. One of the challenges is to meet very tight alignment tolerances at the level of CLIC module: for example, the magnetic centre of a Drive Beam Quad needs to be aligned within 20 µm rms with respect to a straight line. Such accuracies cannot be achieved using usual measurement devices. Thus it is necessary to work in close collaboration with the metrology lab. To test and improve many critical points, including alignment, a CLIC mock-up is being assembled at CERN. This paper describes the application of the strategy of fiducialisation for the pre-alignment of CLIC mock-up components. It also deals with the first results obtained by performing measurements using a CMM (Coordinate Measuring Machine) to ensure the f...

  15. Systematic Calibration for Ultra-High Accuracy Inertial Measurement Units

    Directory of Open Access Journals (Sweden)

    Qingzhong Cai

    2016-06-01

    Full Text Available An inertial navigation system (INS has been widely used in challenging GPS environments. With the rapid development of modern physics, an atomic gyroscope will come into use in the near future with a predicted accuracy of 5 × 10−6°/h or better. However, existing calibration methods and devices can not satisfy the accuracy requirements of future ultra-high accuracy inertial sensors. In this paper, an improved calibration model is established by introducing gyro g-sensitivity errors, accelerometer cross-coupling errors and lever arm errors. A systematic calibration method is proposed based on a 51-state Kalman filter and smoother. Simulation results show that the proposed calibration method can realize the estimation of all the parameters using a common dual-axis turntable. Laboratory and sailing tests prove that the position accuracy in a five-day inertial navigation can be improved about 8% by the proposed calibration method. The accuracy can be improved at least 20% when the position accuracy of the atomic gyro INS can reach a level of 0.1 nautical miles/5 d. Compared with the existing calibration methods, the proposed method, with more error sources and high order small error parameters calibrated for ultra-high accuracy inertial measurement units (IMUs using common turntables, has a great application potential in future atomic gyro INSs.

  16. 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...

  17. Study and Development of a Laser Based Alignment System

    CERN Multimedia

    Stern, G

    2014-01-01

    CLIC (Compact Linear Collider) has tight requirements regarding pre-alignment of beam related components: 10 µm accuracy over a sliding window of 200 m along the 20 km of linac. To perform such an alignment, a new system is proposed combining laser beam as straight line reference and camera/shutter assemblies as sensors. The poster describes the alignment system and shows results regarding laser pointing stability with respect to time, shutter type, distance and environment. These results give a frame for future building and calibrating of sensors.

  18. SU-E-J-138: An IGRT QA Device for Measuring with Tenths-Millimeter Accuracy KV and MV Isocenter Congruence, Couch Travel and Laser Alignment of Accelerators Used for SRS and SBRT

    Energy Technology Data Exchange (ETDEWEB)

    Brezovich, I; Popple, R; Duan, J; Huang, M; Benhabib, S; Shen, S; Cardan, R; Wu, X [University of Alabama Birmingham, Birmingham, AL (United States)

    2014-06-01

    Purpose: To develop a practical device having sufficient accuracy for daily QA tests of accelerators used for SRS and SBRT. Methods: The UAB (Universal Alignment Ball) consists of a 6.35 mm (1/4 inch) diameter tungsten sphere located concentrically within a 25.4 mm (1 inch) diameter acrylic plastic (PMMA) sphere. The spheres are embedded in polystyrene foam, which, in turn, is surrounded by a cylindrical PMMA shell. The UAB is placed on the couch and aligned with wall lasers according to marks that have known positions in relation to the center of the spheres. Using planar and cone beam images the couch is shifted till the surface of the PMMA sphere matches Eclipse-generated circular contours. Anterior and lateral MV images taken with small MLC openings allow measurement of distance between kV and MV isocenter, laser and MLC alignment. Measurements were taken over a one-month period. Results: Artifacts from the tungsten sphere were confined within the PMMA sphere and did not affect cone beam localization of the sphere boundary, allowing 0.1 mm precise alignment with a computer-generated circle centered at kV isocenter. In tests extending over a one-month period, the distance between kV and MV isocenters along the vertical, longitudinal and lateral directions was 0.125 +/−0.06, 0.19 +/−0.08, and 0.02 +/−0.08 mm, respectively. Laser misalignment along these directions was 0.34 +/- 0.15, 0.74 +/−0.29, and 0.49 +/−0.22 mm. Automated couch shifts moved the spheres to within 0.1 mm of the selected position. The center of a 1cmx1cm MLC-defined field remained within +/−0.2 mm of the tungsten sphere center as the gantry was rotated. Conclusion: The UAB is practical for daily end-to-end QA tests of accelerator alignment. It provides tenths-mm accuracy for measuring agreement of kV and MV isocenters, couch motions, gantry flex and laser alignment.

  19. 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°.

  20. Accurate Alignment of Plasma Channels Based on Laser Centroid Oscillations

    International Nuclear Information System (INIS)

    Gonsalves, Anthony; Nakamura, Kei; Lin, Chen; Osterhoff, Jens; Shiraishi, Satomi; Schroeder, Carl; Geddes, Cameron; Toth, Csaba; Esarey, Eric; Leemans, Wim

    2011-01-01

    A technique has been developed to accurately align a laser beam through a plasma channel by minimizing the shift in laser centroid and angle at the channel outptut. If only the shift in centroid or angle is measured, then accurate alignment is provided by minimizing laser centroid motion at the channel exit as the channel properties are scanned. The improvement in alignment accuracy provided by this technique is important for minimizing electron beam pointing errors in laser plasma accelerators.

  1. Centroid stabilization for laser alignment to corner cubes: designing a matched filter

    Energy Technology Data Exchange (ETDEWEB)

    Awwal, Abdul A. S.; Bliss, Erlan; Brunton, Gordon; Kamm, Victoria Miller; Leach, Richard R.; Lowe-Webb, Roger; Roberts, Randy; Wilhelmsen, Karl

    2016-11-08

    Automation of image-based alignment of National Ignition Facility high energy laser beams is providing the capability of executing multiple target shots per day. One important alignment is beam centration through the second and third harmonic generating crystals in the final optics assembly (FOA), which employs two retroreflecting corner cubes as centering references for each beam. Beam-to-beam variations and systematic beam changes over time in the FOA corner cube images can lead to a reduction in accuracy as well as increased convergence durations for the template-based position detector. A systematic approach is described that maintains FOA corner cube templates and guarantees stable position estimation.

  2. Partial alignment and measurement of residual dipolar couplings of proteins under high hydrostatic pressure

    Energy Technology Data Exchange (ETDEWEB)

    Fu, Yinan; Wand, A. Joshua, E-mail: wand@mail.med.upenn.edu [University of Pennsylvania, Department of Biochemistry and Biophysics, Johnson Research Foundation (United States)

    2013-08-15

    High-pressure NMR spectroscopy has emerged as a complementary approach for investigating various structural and thermodynamic properties of macromolecules. Noticeably absent from the array of experimental restraints that have been employed to characterize protein structures at high hydrostatic pressure is the residual dipolar coupling, which requires the partial alignment of the macromolecule of interest. Here we examine five alignment media that are commonly used at ambient pressure for this purpose. We find that the spontaneous alignment of Pf1 phage, d(GpG) and a C12E5/n-hexnanol mixture in a magnetic field is preserved under high hydrostatic pressure. However, DMPC/DHPC bicelles and collagen gel are found to be unsuitable. Evidence is presented to demonstrate that pressure-induced structural changes can be identified using the residual dipolar coupling.

  3. Measurements of magnetic field alignment

    International Nuclear Information System (INIS)

    Kuchnir, M.; Schmidt, E.E.

    1987-01-01

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

  4. Enhanced spatio-temporal alignment of plantar pressure image sequences using B-splines.

    Science.gov (United States)

    Oliveira, Francisco P M; Tavares, João Manuel R S

    2013-03-01

    This article presents an enhanced methodology to align plantar pressure image sequences simultaneously in time and space. The temporal alignment of the sequences is accomplished using B-splines in the time modeling, and the spatial alignment can be attained using several geometric transformation models. The methodology was tested on a dataset of 156 real plantar pressure image sequences (3 sequences for each foot of the 26 subjects) that was acquired using a common commercial plate during barefoot walking. In the alignment of image sequences that were synthetically deformed both in time and space, an outstanding accuracy was achieved with the cubic B-splines. This accuracy was significantly better (p align real image sequences with unknown transformation involved, the alignment based on cubic B-splines also achieved superior results than our previous methodology (p alignment on the dynamic center of pressure (COP) displacement was also assessed by computing the intraclass correlation coefficients (ICC) before and after the temporal alignment of the three image sequence trials of each foot of the associated subject at six time instants. The results showed that, generally, the ICCs related to the medio-lateral COP displacement were greater when the sequences were temporally aligned than the ICCs of the original sequences. Based on the experimental findings, one can conclude that the cubic B-splines are a remarkable solution for the temporal alignment of plantar pressure image sequences. These findings also show that the temporal alignment can increase the consistency of the COP displacement on related acquired plantar pressure image sequences.

  5. Improving scanner wafer alignment performance by target optimization

    Science.gov (United States)

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

    2016-03-01

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

  6. Improving Accuracy for Image Fusion in Abdominal Ultrasonography

    Directory of Open Access Journals (Sweden)

    Caroline Ewertsen

    2012-08-01

    Full Text Available Image fusion involving real-time ultrasound (US is a technique where previously recorded computed tomography (CT or magnetic resonance images (MRI are reformatted in a projection to fit the real-time US images after an initial co-registration. The co-registration aligns the images by means of common planes or points. We evaluated the accuracy of the alignment when varying parameters as patient position, respiratory phase and distance from the co-registration points/planes. We performed a total of 80 co-registrations and obtained the highest accuracy when the respiratory phase for the co-registration procedure was the same as when the CT or MRI was obtained. Furthermore, choosing co-registration points/planes close to the area of interest also improved the accuracy. With all settings optimized a mean error of 3.2 mm was obtained. We conclude that image fusion involving real-time US is an accurate method for abdominal examinations and that the accuracy is influenced by various adjustable factors that should be kept in mind.

  7. 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.

  8. High anisotropy of flow-aligned bicellar membrane systems

    KAUST Repository

    Kogan, Maxim; Nordé n, Bengt; Beke-Somfai, Tamá s

    2013-01-01

    In recent years, multi-lipid bicellar systems have emerged as promising membrane models. The fast orientational diffusion and magnetic alignability made these systems very attractive for NMR investigations. However, their alignment was so far

  9. 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.

  10. 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.

  11. Fabrication Process Changes for Performance Improvement of a RF MEMS Resonator: Conformable Contact Lithography, Moire Alignment, and Chlorine Dry Etching

    National Research Council Canada - National Science Library

    Sakai, Mark

    2005-01-01

    .... A CCL process utilizing moire alignment marks is described. An automated moire-based alignment system using Labview software is presented which demonstrates sub-100 nm alignment accuracy for a single alignment mark...

  12. Measuring and aligning accelerator components to the nanometre scale

    CERN Document Server

    Catalán Lasheras, N; Modena, M

    2014-01-01

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

  13. Ultra-high density aligned Carbon-nanotube with controled nano-morphology for supercapacitors

    Science.gov (United States)

    Ghaffari, Mehdi; Zhao, Ran; Liu, Yang; Zhou, Yue; Cheng, Jiping; Guzman de Villoria, Roberto; Wardle, B. L.; Zhang, Q. M.

    2012-02-01

    Recent advances in fabricating controlled-morphology vertically aligned carbon nanotubes (VA-CNTs) with ultrahigh volume fractioncreate unique opportunities for developing unconventional supercapacitors with ultra-high energy density, power density, and long charge/discharge cycle life.Continuous paths through inter-VA-CNT channels allow fast ion transport, and high electrical conduction of the aligned CNTs in the composite electrodes lead to fast discharge speed. We investigate the charge-discharge characteristics of VA-CNTs with >20 vol% of CNT and ionic liquids as electrolytes. By employing both the electric and electromechanical spectroscopes, as well as nanostructured materials characterization, the ion transport and storage behaviors in porous electrodes are studied. The results suggest pathways for optimizing the electrode morphology in supercapacitorsusing ultra-high volume fraction VA-CNTs to further enhance performance.

  14. 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.

  15. 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.

  16. Survey and alignment data analysis for the ALS storage ring

    International Nuclear Information System (INIS)

    Keller, R.

    1993-05-01

    The survey and alignment effort for the Advanced Light Source (ALS) accelerator complex has been described elsewhere. Data analysis for this task comprises the creation of ideal data, comparison of measured coordinates with ideal ones, and computation of alignment values, taking into account the effects caused by finite observation accuracy. A novel approach has been taken, using personal computer spreadsheets rather than more conventional programming methods. This approach was induced by the necessities to create and frequently refine the analysis procedures while measurements were already underway, and further by hardware constraints that limited the use of an available surveying code. A major benefit consists in the ability to identify and deal with discrepancies that occasionally arise when different techniques are used to observe the same object, in a timely and efficient manner. As a result of the performed survey and alignment work, the ALS lattice magnets have been positioned with accuracies well exceeding the original specifications

  17. High anisotropy of flow-aligned bicellar membrane systems

    KAUST Repository

    Kogan, Maxim

    2013-10-01

    In recent years, multi-lipid bicellar systems have emerged as promising membrane models. The fast orientational diffusion and magnetic alignability made these systems very attractive for NMR investigations. However, their alignment was so far achieved with a strong magnetic field, which limited their use with other methods that require macroscopic orientation. Recently, it was shown that bicelles could be aligned also by shear flow in a Couette flow cell, making it applicable to structural and biophysical studies by polarized light spectroscopy. Considering the sensitivity of this lipid system to small variations in composition and physicochemical parameters, efficient use of such a flow-cell method with coupled techniques will critically depend on the detailed understanding of how the lipid systems behave under flow conditions. In the present study we have characterized the flow alignment behavior of the commonly used dimyristoyl phosphatidylcholine/dicaproyl phosphatidylcholine (DMPC/DHPC) bicelle system, for various temperatures, lipid compositions, and lipid concentrations. We conclude that at optimal flow conditions the selected bicellar systems can produce the most efficient flow alignment out of any lipid systems used so far. The highest degree of orientation of DMPC/DHPC samples is noticed in a narrow temperature interval, at a practical temperature around 25 C, most likely in the phase transition region characterized by maximum sample viscosity. The change of macroscopic orientation factor as function of the above conditions is now described in detail. The increase in macroscopic alignment observed for bicelles will most likely allow recording of higher resolution spectra on membrane systems, which provide deeper structural insight and analysis into properties of biomolecules interacting with solution phase lipid membranes. © 2013 Elsevier Ireland Ltd.

  18. Effect of magnetic quadrupole lens alignment on a nuclear microprobe resolution

    International Nuclear Information System (INIS)

    Kolinko, S.V.; Ponomarev, A.G.

    2016-01-01

    The paper reports the research trends in developing probe-forming systems with high demagnification and analysis factors that limit a nuclear microprobe resolution. Parasitic aberrations caused by tilts and offsets of magnetic quadrupoles are studied in terms of their effect on probe parameters on a target. The most common arrangements of probe-forming systems such as a triplet and “Russian quadruplet” with separated geometry are considered. The accuracy prerequisites for the positioning of the quadrupoles are defined, and practical guidelines for alignment of probe-forming systems with high demagnification factors are suggested.

  19. Large-area aligned growth of single-crystalline organic nanowire arrays for high-performance photodetectors

    International Nuclear Information System (INIS)

    Wu Yiming; Zhang Xiujuan; Pan Huanhuan; Zhang Xiwei; Zhang Yuping; Zhang Xiaozhen; Jie Jiansheng

    2013-01-01

    Due to their extraordinary properties, single-crystalline organic nanowires (NWs) are important building blocks for future low-cost and efficient nano-optoelectronic devices. However, it remains a critical challenge to assemble organic NWs rationally in an orientation-, dimensionality- and location-controlled manner. Herein, we demonstrate a feasible method for aligned growth of single-crystalline copper phthalocyanine (CuPc) NW arrays with high density, large-area uniformity and perfect crossed alignment by using Au film as a template. The growth process was investigated in detail. The Au film was found to have a critical function in the aligned growth of NWs, but may only serve as the active site for NW nucleation because of the large surface energy, as well as direct the subsequent aligned growth. The as-prepared NWs were then transferred to construct single NW-based photoconductive devices, which demonstrated excellent photoresponse properties with robust stability and reproducibility; the device showed a high switching ratio of ∼180, a fast response speed of ∼100 ms and could stand continuous operation up to 2 h. Importantly, this strategy can be extended to other organic molecules for their synthesis of NW arrays, revealing great potential for use in the construction of large-scale high-performance functional nano-optoelectronic devices. (paper)

  20. The alignment of the ATLAS Inner Detector in Run 2

    CERN Document Server

    Ripellino, Giulia; The ATLAS collaboration

    2016-01-01

    The ATLAS reconstruction of charged particle trajectories relies on the Inner Detector tracking system. The accuracy of the reconstruction is limited by the finite resolution of the detector elements and the knowledge about their positions. A precise alignment of the detector is therefore essential. In this poster we present the strategy and the status of the Inner Detector alignment in ATLAS during the LHC Run 2.

  1. 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.

  2. High performance transistors via aligned polyfluorene-sorted carbon nanotubes

    Science.gov (United States)

    Brady, Gerald J.; Joo, Yongho; Singha Roy, Susmit; Gopalan, Padma; Arnold, Michael S.

    2014-02-01

    We evaluate the performance of exceptionally electronic-type sorted, semiconducting, aligned single-walled carbon nanotubes (s-SWCNTs) in field effect transistors (FETs). High on-conductance and high on/off conductance modulation are simultaneously achieved at channel lengths which are both shorter and longer than individual s-SWCNTs. The s-SWCNTs are isolated from heterogeneous mixtures using a polyfluorene-derivative as a selective agent and aligned on substrates via dose-controlled, floating evaporative self-assembly at densities of ˜50 s-SWCNTs μm-1. At a channel length of 9 μm the s-SWCNTs percolate to span the FET channel, and the on/off ratio and charge transport mobility are 2.2 × 107 and 46 cm2 V-1 s-1, respectively. At a channel length of 400 nm, a large fraction of the s-SWCNTs directly span the channel, and the on-conductance per width is 61 μS μm-1 and the on/off ratio is 4 × 105. These results are considerably better than previous solution-processed FETs, which have suffered from poor on/off ratio due to spurious metallic nanotubes that bridge the channel. 4071 individual and small bundles of s-SWCNTs are tested in 400 nm channel length FETs, and all show semiconducting behavior, demonstrating the high fidelity of polyfluorenes as selective agents and the promise of assembling s-SWCNTs from solution to create high performance semiconductor electronic devices.

  3. Alignment of the stanford linear collider Arcs

    International Nuclear Information System (INIS)

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

    1987-01-01

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

  4. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez and Y. Pakhotin

    2012-01-01

      A new track-based alignment for the DT chambers is ready for deployment: an offline tag has already been produced which will become part of the 52X Global Tag. This alignment was validated within the muon alignment group both at low and high momentum using a W/Z skim sample. It shows an improved mass resolution for pairs of stand-alone muons, improved curvature resolution at high momentum, and improved DT segment extrapolation residuals. The validation workflow for high-momentum muons used to depend solely on the “split cosmics” method, looking at the curvature difference between muon tracks reconstructed in the upper or lower half of CMS. The validation has now been extended to include energetic muons decaying from heavily boosted Zs: the di-muon invariant mass for global and stand-alone muons is reconstructed, and the invariant mass resolution is compared for different alignments. The main areas of development over the next few months will be preparing a new track-based C...

  5. Short-term magnetic field alignment variations of equatorial ionospheric irregularities

    International Nuclear Information System (INIS)

    Johnson, A.L.

    1988-01-01

    The ionospheric irregularities that cause equatorial scintillation are elongated along the north-south magnetic field lines. During a 1981 field campaign at Ascension Island, 250-MHz receivers were spaced from 300 m to 1.6 km along the field lines, and the signals received from the Marisat satellite were cross correlated. Data collected during eight nights of fading showed a linear relationship between fading rate and cross correlation. The alignment of the antennas was adjusted to give a zero time lag between the widely spaced receivers with a measurement accuracy of 0.03 s. Since the average irregularity velocity was 125 m/s, this time accuracy translated to an angular measurement accuracy of 0.1 deg. During a 4-hour period of nightly fading, occasional differences in time of arrival were noted that corresponded to a tilt in the north-south alignment of + or - 1 deg. Data from several nights of fading were analyzed, and each night exhibited the same variance in the north-south irregularity alignment. It is postulated that the shift in the measured peak correlation may have been caused by patches of irregularities at different altitudes where the magnetic field lines have a slightly different direction. 13 references

  6. High Thermal Conductivity of Copper Matrix Composite Coatings with Highly-Aligned Graphite Nanoplatelets

    Science.gov (United States)

    Tagliaferri, Vincenzo; Ucciardello, Nadia

    2017-01-01

    Nanocomposite coatings with highly-aligned graphite nanoplatelets in a copper matrix were successfully fabricated by electrodeposition. For the first time, the disposition and thermal conductivity of the nanofiller has been evaluated. The degree of alignment and inclination of the filling materials has been quantitatively evaluated by polarized micro-Raman spectroscopy. The room temperature values of the thermal conductivity were extracted for the graphite nanoplatelets by the dependence of the Raman G-peak frequency on the laser power excitation. Temperature dependency of the G-peak shift has been also measured. Most remarkable is the global thermal conductivity of 640 ± 20 W·m−1·K−1 (+57% of copper) obtained for the composite coating by the flash method. Our experimental results are accounted for by an effective medium approximation (EMA) model that considers the influence of filler geometry, orientation, and thermal conductivity inside a copper matrix. PMID:29068424

  7. 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.

  8. Template synthesis and magnetic properties of highly aligned barium hexaferrite (BaFe12O19) nanofibers

    International Nuclear Information System (INIS)

    Huang, Boneng; Li, Congju; Wang, Jiaona

    2013-01-01

    Using electrospun poly(ethylene terephthalate)/citric acid (PET/CA) microfibers as the template, highly aligned barium hexaferrite (BaFe 12 O 19 ) nanofibers with diameters of ca. 800 nm and lengths up to 2 cm were synthesized by sol–gel precursor coating technique and subsequent high temperature calcination. Structural and morphological investigations revealed that individual BaFe 12 O 19 nanofibers were composed of numerous nanocrystallites stacking alternatively along the nanofiber axis, the average grain size was ca. 225 nm and the single crystallites on each BaFe 12 O 19 nanofibers were of random orientations. The formation mechanism of aligned BaFe 12 O 19 nanofibers was proposed based on experiment. The magnetic measurement revealed that the aligned BaFe 12 O 19 nanofibers exhibited orientation-dependent magnetic behavior with respect to the applied magnetic field. The magnetic anisotropy with the easy magnetizing axis along the length of the nanofibers was due to the shape anisotropy. Such aligned magnetic nanofibers can find relevance in application requiring an orientation-dependent physical response. - Highlights: ► A simple method was used to synthesize the aligned BaFe 12 O 19 nanofibers. ► The aligned BaFe 12 O 19 nanofibers display an obvious orientation-dependent magnetic behavior. ► The method can be readily applied to other aligned one-dimensional inorganic nanomaterials

  9. Research on Horizontal Accuracy Method of High Spatial Resolution Remotely Sensed Orthophoto Image

    Science.gov (United States)

    Xu, Y. M.; Zhang, J. X.; Yu, F.; Dong, S.

    2018-04-01

    At present, in the inspection and acceptance of high spatial resolution remotly sensed orthophoto image, the horizontal accuracy detection is testing and evaluating the accuracy of images, which mostly based on a set of testing points with the same accuracy and reliability. However, it is difficult to get a set of testing points with the same accuracy and reliability in the areas where the field measurement is difficult and the reference data with high accuracy is not enough. So it is difficult to test and evaluate the horizontal accuracy of the orthophoto image. The uncertainty of the horizontal accuracy has become a bottleneck for the application of satellite borne high-resolution remote sensing image and the scope of service expansion. Therefore, this paper proposes a new method to test the horizontal accuracy of orthophoto image. This method using the testing points with different accuracy and reliability. These points' source is high accuracy reference data and field measurement. The new method solves the horizontal accuracy detection of the orthophoto image in the difficult areas and provides the basis for providing reliable orthophoto images to the users.

  10. AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework.

    Directory of Open Access Journals (Sweden)

    Qi Zheng

    2016-10-01

    Full Text Available Accurate mapping of next-generation sequencing (NGS reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present. Here we developed a generalized software toolkit "AlignerBoost", which utilizes a Bayesian-based framework to accurately estimate mapping quality of ambiguously mapped NGS reads. We tested AlignerBoost with both simulated and real DNA-seq and RNA-seq datasets at various thresholds. In most cases, but especially for reads falling within repetitive regions, AlignerBoost dramatically increases the mapping precision of modern NGS aligners without significantly compromising the sensitivity even without mapping quality filters. When using higher mapping quality cutoffs, AlignerBoost achieves a much lower false mapping rate while exhibiting comparable or higher sensitivity compared to the aligner default modes, therefore significantly boosting the detection power of NGS aligners even using extreme thresholds. AlignerBoost is also SNP-aware, and higher quality alignments can be achieved if provided with known SNPs. AlignerBoost's algorithm is computationally efficient, and can process one million alignments within 30 seconds on a typical desktop computer. AlignerBoost is implemented as a uniform Java application and is freely available at https://github.com/Grice-Lab/AlignerBoost.

  11. AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework.

    Science.gov (United States)

    Zheng, Qi; Grice, Elizabeth A

    2016-10-01

    Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present. Here we developed a generalized software toolkit "AlignerBoost", which utilizes a Bayesian-based framework to accurately estimate mapping quality of ambiguously mapped NGS reads. We tested AlignerBoost with both simulated and real DNA-seq and RNA-seq datasets at various thresholds. In most cases, but especially for reads falling within repetitive regions, AlignerBoost dramatically increases the mapping precision of modern NGS aligners without significantly compromising the sensitivity even without mapping quality filters. When using higher mapping quality cutoffs, AlignerBoost achieves a much lower false mapping rate while exhibiting comparable or higher sensitivity compared to the aligner default modes, therefore significantly boosting the detection power of NGS aligners even using extreme thresholds. AlignerBoost is also SNP-aware, and higher quality alignments can be achieved if provided with known SNPs. AlignerBoost's algorithm is computationally efficient, and can process one million alignments within 30 seconds on a typical desktop computer. AlignerBoost is implemented as a uniform Java application and is freely available at https://github.com/Grice-Lab/AlignerBoost.

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

    Science.gov (United States)

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

    2017-09-01

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

  13. High-performance supercapacitors based on vertically aligned carbon nanotubes and nonaqueous electrolytes

    International Nuclear Information System (INIS)

    Kim, Byungwoo; Kim, Woong; Chung, Haegeun

    2012-01-01

    We demonstrate the high performance of supercapacitors fabricated with vertically aligned carbon nanotubes and nonaqueous electrolytes such as ionic liquids and conventional organic electrolytes. Specific capacitance, maximum power and energy density of the supercapacitor measured in ionic liquid were ∼75 F g −1 , ∼987 kW kg −1 and ∼27 W h kg −1 , respectively. The high power performance was consistently indicated by a fast relaxation time constant of 0.2 s. In addition, electrochemical oxidation of the carbon nanotubes improved the specific capacitance (∼158 F g −1 ) and energy density (∼53 W h kg −1 ). Both high power and energy density could be attributed to the fast ion transport realized by the alignment of carbon nanotubes and the wide operational voltage defined by the ionic liquid. The demonstrated carbon-nanotube- and nonaqueous-electrolyte-based supercapacitors show great potential for the development of high-performance energy storage devices. (paper)

  14. High-performance supercapacitors based on vertically aligned carbon nanotubes and nonaqueous electrolytes.

    Science.gov (United States)

    Kim, Byungwoo; Chung, Haegeun; Kim, Woong

    2012-04-20

    We demonstrate the high performance of supercapacitors fabricated with vertically aligned carbon nanotubes and nonaqueous electrolytes such as ionic liquids and conventional organic electrolytes. Specific capacitance, maximum power and energy density of the supercapacitor measured in ionic liquid were ~75 F g(-1), ~987 kW kg(-1) and ~27 W h kg(-1), respectively. The high power performance was consistently indicated by a fast relaxation time constant of 0.2 s. In addition, electrochemical oxidation of the carbon nanotubes improved the specific capacitance (~158 F g(-1)) and energy density (~53 W h kg(-1)). Both high power and energy density could be attributed to the fast ion transport realized by the alignment of carbon nanotubes and the wide operational voltage defined by the ionic liquid. The demonstrated carbon-nanotube- and nonaqueous-electrolyte-based supercapacitors show great potential for the development of high-performance energy storage devices. © 2012 IOP Publishing Ltd

  15. High-performance supercapacitors based on vertically aligned carbon nanotubes and nonaqueous electrolytes

    Science.gov (United States)

    Kim, Byungwoo; Chung, Haegeun; Kim, Woong

    2012-04-01

    We demonstrate the high performance of supercapacitors fabricated with vertically aligned carbon nanotubes and nonaqueous electrolytes such as ionic liquids and conventional organic electrolytes. Specific capacitance, maximum power and energy density of the supercapacitor measured in ionic liquid were ˜75 F g-1, ˜987 kW kg-1 and ˜27 W h kg-1, respectively. The high power performance was consistently indicated by a fast relaxation time constant of 0.2 s. In addition, electrochemical oxidation of the carbon nanotubes improved the specific capacitance (˜158 F g-1) and energy density (˜53 W h kg-1). Both high power and energy density could be attributed to the fast ion transport realized by the alignment of carbon nanotubes and the wide operational voltage defined by the ionic liquid. The demonstrated carbon-nanotube- and nonaqueous-electrolyte-based supercapacitors show great potential for the development of high-performance energy storage devices.

  16. 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.

  17. 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.

  18. High accuracy 3-D laser radar

    DEFF Research Database (Denmark)

    Busck, Jens; Heiselberg, Henning

    2004-01-01

    We have developed a mono-static staring 3-D laser radar based on gated viewing with range accuracy below 1 m at 10 m and 1 cm at 100. We use a high sensitivity, fast, intensified CCD camera, and a Nd:Yag passively Q-switched 32.4 kHz pulsed green laser at 532 nm. The CCD has 752x582 pixels. Camera...

  19. High performance transistors via aligned polyfluorene-sorted carbon nanotubes

    International Nuclear Information System (INIS)

    Brady, Gerald J.; Joo, Yongho; Singha Roy, Susmit; Gopalan, Padma; Arnold, Michael S.

    2014-01-01

    We evaluate the performance of exceptionally electronic-type sorted, semiconducting, aligned single-walled carbon nanotubes (s-SWCNTs) in field effect transistors (FETs). High on-conductance and high on/off conductance modulation are simultaneously achieved at channel lengths which are both shorter and longer than individual s-SWCNTs. The s-SWCNTs are isolated from heterogeneous mixtures using a polyfluorene-derivative as a selective agent and aligned on substrates via dose-controlled, floating evaporative self-assembly at densities of ∼50 s-SWCNTs μm −1 . At a channel length of 9 μm the s-SWCNTs percolate to span the FET channel, and the on/off ratio and charge transport mobility are 2.2 × 10 7 and 46 cm 2  V −1  s −1 , respectively. At a channel length of 400 nm, a large fraction of the s-SWCNTs directly span the channel, and the on-conductance per width is 61 μS μm −1 and the on/off ratio is 4 × 10 5 . These results are considerably better than previous solution-processed FETs, which have suffered from poor on/off ratio due to spurious metallic nanotubes that bridge the channel. 4071 individual and small bundles of s-SWCNTs are tested in 400 nm channel length FETs, and all show semiconducting behavior, demonstrating the high fidelity of polyfluorenes as selective agents and the promise of assembling s-SWCNTs from solution to create high performance semiconductor electronic devices

  20. High performance transistors via aligned polyfluorene-sorted carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Brady, Gerald J.; Joo, Yongho; Singha Roy, Susmit; Gopalan, Padma; Arnold, Michael S., E-mail: msarnold@wisc.edu [Department of Materials Science and Engineering, University of Wisconsin-Madison, 1509 University Avenue, Madison, Wisconsin 53706 (United States)

    2014-02-24

    We evaluate the performance of exceptionally electronic-type sorted, semiconducting, aligned single-walled carbon nanotubes (s-SWCNTs) in field effect transistors (FETs). High on-conductance and high on/off conductance modulation are simultaneously achieved at channel lengths which are both shorter and longer than individual s-SWCNTs. The s-SWCNTs are isolated from heterogeneous mixtures using a polyfluorene-derivative as a selective agent and aligned on substrates via dose-controlled, floating evaporative self-assembly at densities of ∼50 s-SWCNTs μm{sup −1}. At a channel length of 9 μm the s-SWCNTs percolate to span the FET channel, and the on/off ratio and charge transport mobility are 2.2 × 10{sup 7} and 46 cm{sup 2} V{sup −1} s{sup −1}, respectively. At a channel length of 400 nm, a large fraction of the s-SWCNTs directly span the channel, and the on-conductance per width is 61 μS μm{sup −1} and the on/off ratio is 4 × 10{sup 5}. These results are considerably better than previous solution-processed FETs, which have suffered from poor on/off ratio due to spurious metallic nanotubes that bridge the channel. 4071 individual and small bundles of s-SWCNTs are tested in 400 nm channel length FETs, and all show semiconducting behavior, demonstrating the high fidelity of polyfluorenes as selective agents and the promise of assembling s-SWCNTs from solution to create high performance semiconductor electronic devices.

  1. A Robust Highly Aligned DNA Nanowire Array-Enabled Lithography for Graphene Nanoribbon Transistors.

    Science.gov (United States)

    Kang, Seok Hee; Hwang, Wan Sik; Lin, Zhiqun; Kwon, Se Hun; Hong, Suck Won

    2015-12-09

    Because of its excellent charge carrier mobility at the Dirac point, graphene possesses exceptional properties for high-performance devices. Of particular interest is the potential use of graphene nanoribbons or graphene nanomesh for field-effect transistors. Herein, highly aligned DNA nanowire arrays were crafted by flow-assisted self-assembly of a drop of DNA aqueous solution on a flat polymer substrate. Subsequently, they were exploited as "ink" and transfer-printed on chemical vapor deposited (CVD)-grown graphene substrate. The oriented DNA nanowires served as the lithographic resist for selective removal of graphene, forming highly aligned graphene nanoribbons. Intriguingly, these graphene nanoribbons can be readily produced over a large area (i.e., millimeter scale) with a high degree of feature-size controllability and a low level of defects, rendering the fabrication of flexible two terminal devices and field-effect transistors.

  2. High accuracy autonomous navigation using the global positioning system (GPS)

    Science.gov (United States)

    Truong, Son H.; Hart, Roger C.; Shoan, Wendy C.; Wood, Terri; Long, Anne C.; Oza, Dipak H.; Lee, Taesul

    1997-01-01

    The application of global positioning system (GPS) technology to the improvement of the accuracy and economy of spacecraft navigation, is reported. High-accuracy autonomous navigation algorithms are currently being qualified in conjunction with the GPS attitude determination flyer (GADFLY) experiment for the small satellite technology initiative Lewis spacecraft. Preflight performance assessments indicated that these algorithms are able to provide a real time total position accuracy of better than 10 m and a velocity accuracy of better than 0.01 m/s, with selective availability at typical levels. It is expected that the position accuracy will be increased to 2 m if corrections are provided by the GPS wide area augmentation system.

  3. BinAligner: a heuristic method to align biological networks.

    Science.gov (United States)

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

    2013-01-01

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

  4. Alignment of high-throughput sequencing data inside in-memory databases.

    Science.gov (United States)

    Firnkorn, Daniel; Knaup-Gregori, Petra; Lorenzo Bermejo, Justo; Ganzinger, Matthias

    2014-01-01

    In times of high-throughput DNA sequencing techniques, performance-capable analysis of DNA sequences is of high importance. Computer supported DNA analysis is still an intensive time-consuming task. In this paper we explore the potential of a new In-Memory database technology by using SAP's High Performance Analytic Appliance (HANA). We focus on read alignment as one of the first steps in DNA sequence analysis. In particular, we examined the widely used Burrows-Wheeler Aligner (BWA) and implemented stored procedures in both, HANA and the free database system MySQL, to compare execution time and memory management. To ensure that the results are comparable, MySQL has been running in memory as well, utilizing its integrated memory engine for database table creation. We implemented stored procedures, containing exact and inexact searching of DNA reads within the reference genome GRCh37. Due to technical restrictions in SAP HANA concerning recursion, the inexact matching problem could not be implemented on this platform. Hence, performance analysis between HANA and MySQL was made by comparing the execution time of the exact search procedures. Here, HANA was approximately 27 times faster than MySQL which means, that there is a high potential within the new In-Memory concepts, leading to further developments of DNA analysis procedures in the future.

  5. 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.

  6. LumiCal alignment system - Status report

    CERN Document Server

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

    2015-01-01

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

  7. High accuracy wavelength calibration for a scanning visible spectrometer

    Energy Technology Data Exchange (ETDEWEB)

    Scotti, Filippo; Bell, Ronald E. [Princeton Plasma Physics Laboratory, Princeton, New Jersey 08543 (United States)

    2010-10-15

    Spectroscopic applications for plasma velocity measurements often require wavelength accuracies {<=}0.2 A. An automated calibration, which is stable over time and environmental conditions without the need to recalibrate after each grating movement, was developed for a scanning spectrometer to achieve high wavelength accuracy over the visible spectrum. This method fits all relevant spectrometer parameters using multiple calibration spectra. With a stepping-motor controlled sine drive, an accuracy of {approx}0.25 A has been demonstrated. With the addition of a high resolution (0.075 arc sec) optical encoder on the grating stage, greater precision ({approx}0.005 A) is possible, allowing absolute velocity measurements within {approx}0.3 km/s. This level of precision requires monitoring of atmospheric temperature and pressure and of grating bulk temperature to correct for changes in the refractive index of air and the groove density, respectively.

  8. Switched-capacitor techniques for high-accuracy filter and ADC design

    NARCIS (Netherlands)

    Quinn, P.J.; Roermund, van A.H.M.

    2007-01-01

    Switched capacitor (SC) techniques are well proven to be excellent candidates for implementing critical analogue functions with high accuracy, surpassing other analogue techniques when embedded in mixed-signal CMOS VLSI. Conventional SC circuits are primarily limited in accuracy by a) capacitor

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

    Science.gov (United States)

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

    2015-01-01

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

  10. 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.

  11. Laser interference lithography with highly accurate interferometric alignment

    NARCIS (Netherlands)

    van Soest, Frank J.; van Wolferen, Hendricus A.G.M.; Hoekstra, Hugo; de Ridder, R.M.; Worhoff, Kerstin; Lambeck, Paul

    It is shown experimentally that in laser interference lithography, by using a reference grating, respective grating layers can be positioned with high relative accuracy. A 0.001 degree angular and a few nanometers lateral resolution have been demonstrated.

  12. High-performance field emission device utilizing vertically aligned carbon nanotubes-based pillar architectures

    Science.gov (United States)

    Gupta, Bipin Kumar; Kedawat, Garima; Gangwar, Amit Kumar; Nagpal, Kanika; Kashyap, Pradeep Kumar; Srivastava, Shubhda; Singh, Satbir; Kumar, Pawan; Suryawanshi, Sachin R.; Seo, Deok Min; Tripathi, Prashant; More, Mahendra A.; Srivastava, O. N.; Hahm, Myung Gwan; Late, Dattatray J.

    2018-01-01

    The vertical aligned carbon nanotubes (CNTs)-based pillar architectures were created on laminated silicon oxide/silicon (SiO2/Si) wafer substrate at 775 °C by using water-assisted chemical vapor deposition under low pressure process condition. The lamination was carried out by aluminum (Al, 10.0 nm thickness) as a barrier layer and iron (Fe, 1.5 nm thickness) as a catalyst precursor layer sequentially on a silicon wafer substrate. Scanning electron microscope (SEM) images show that synthesized CNTs are vertically aligned and uniformly distributed with a high density. The CNTs have approximately 2-30 walls with an inner diameter of 3-8 nm. Raman spectrum analysis shows G-band at 1580 cm-1 and D-band at 1340 cm-1. The G-band is higher than D-band, which indicates that CNTs are highly graphitized. The field emission analysis of the CNTs revealed high field emission current density (4mA/cm2 at 1.2V/μm), low turn-on field (0.6 V/μm) and field enhancement factor (6917) with better stability and longer lifetime. Emitter morphology resulting in improved promising field emission performances, which is a crucial factor for the fabrication of pillared shaped vertical aligned CNTs bundles as practical electron sources.

  13. High-performance field emission device utilizing vertically aligned carbon nanotubes-based pillar architectures

    Directory of Open Access Journals (Sweden)

    Bipin Kumar Gupta

    2018-01-01

    Full Text Available The vertical aligned carbon nanotubes (CNTs-based pillar architectures were created on laminated silicon oxide/silicon (SiO2/Si wafer substrate at 775 °C by using water-assisted chemical vapor deposition under low pressure process condition. The lamination was carried out by aluminum (Al, 10.0 nm thickness as a barrier layer and iron (Fe, 1.5 nm thickness as a catalyst precursor layer sequentially on a silicon wafer substrate. Scanning electron microscope (SEM images show that synthesized CNTs are vertically aligned and uniformly distributed with a high density. The CNTs have approximately 2–30 walls with an inner diameter of 3–8 nm. Raman spectrum analysis shows G-band at 1580 cm−1 and D-band at 1340 cm−1. The G-band is higher than D-band, which indicates that CNTs are highly graphitized. The field emission analysis of the CNTs revealed high field emission current density (4mA/cm2 at 1.2V/μm, low turn-on field (0.6 V/μm and field enhancement factor (6917 with better stability and longer lifetime. Emitter morphology resulting in improved promising field emission performances, which is a crucial factor for the fabrication of pillared shaped vertical aligned CNTs bundles as practical electron sources.

  14. Precision crystal alignment for high-resolution electron microscope imaging

    International Nuclear Information System (INIS)

    Wood, G.J.; Beeching, M.J.

    1990-01-01

    One of the more difficult tasks involved in obtaining quality high-resolution electron micrographs is the precise alignment of a specimen into the required zone. The current accepted procedure, which involves changing to diffraction mode and searching for symmetric point diffraction pattern, is insensitive to small amounts of misalignment and at best qualitative. On-line analysis of the fourier space representation of the image, both for determining and correcting crystal tilt, is investigated. 8 refs., 42 figs

  15. High-accuracy mass spectrometry for fundamental studies.

    Science.gov (United States)

    Kluge, H-Jürgen

    2010-01-01

    Mass spectrometry for fundamental studies in metrology and atomic, nuclear and particle physics requires extreme sensitivity and efficiency as well as ultimate resolving power and accuracy. An overview will be given on the global status of high-accuracy mass spectrometry for fundamental physics and metrology. Three quite different examples of modern mass spectrometric experiments in physics are presented: (i) the retardation spectrometer KATRIN at the Forschungszentrum Karlsruhe, employing electrostatic filtering in combination with magnetic-adiabatic collimation-the biggest mass spectrometer for determining the smallest mass, i.e. the mass of the electron anti-neutrino, (ii) the Experimental Cooler-Storage Ring at GSI-a mass spectrometer of medium size, relative to other accelerators, for determining medium-heavy masses and (iii) the Penning trap facility, SHIPTRAP, at GSI-the smallest mass spectrometer for determining the heaviest masses, those of super-heavy elements. Finally, a short view into the future will address the GSI project HITRAP at GSI for fundamental studies with highly-charged ions.

  16. Accuracy Assessment for the Three-Dimensional Coordinates by High-Speed Videogrammetric Measurement

    Directory of Open Access Journals (Sweden)

    Xianglei Liu

    2018-01-01

    Full Text Available High-speed CMOS camera is a new kind of transducer to make the videogrammetric measurement for monitoring the displacement of high-speed shaking table structure. The purpose of this paper is to validate the three-dimensional coordinate accuracy of the shaking table structure acquired from the presented high-speed videogrammetric measuring system. In the paper, all of the key intermediate links are discussed, including the high-speed CMOS videogrammetric measurement system, the layout of the control network, the elliptical target detection, and the accuracy validation of final 3D spatial results. Through the accuracy analysis, the submillimeter accuracy can be made for the final the three-dimensional spatial coordinates which certify that the proposed high-speed videogrammetric technique is a better alternative technique which can replace the traditional transducer technique for monitoring the dynamic response for the shaking table structure.

  17. Survey and alignment of high energy physics accelerators and transport lines

    International Nuclear Information System (INIS)

    Ruland, R.E.

    1992-11-01

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

  18. Relay telescope for high power laser alignment system

    Science.gov (United States)

    Dane, C. Brent; Hackel, Lloyd; Harris, Fritz B.

    2006-09-19

    A laser system includes an optical path having an intracavity relay telescope with a telescope focal point for imaging an output of the gain medium between an image location at or near the gain medium and an image location at or near an output coupler for the laser system. A kinematic mount is provided within a vacuum chamber, and adapted to secure beam baffles near the telescope focal point. An access port on the vacuum chamber is adapted for allowing insertion and removal of the beam baffles. A first baffle formed using an alignment pinhole aperture is used during alignment of the laser system. A second tapered baffle replaces the alignment aperture during operation and acts as a far-field baffle in which off angle beams strike the baffle a grazing angle of incidence, reducing fluence levels at the impact areas.

  19. Low power and high accuracy spike sorting microprocessor with on-line interpolation and re-alignment in 90 nm CMOS process.

    Science.gov (United States)

    Chen, Tung-Chien; Ma, Tsung-Chuan; Chen, Yun-Yu; Chen, Liang-Gee

    2012-01-01

    Accurate spike sorting is an important issue for neuroscientific and neuroprosthetic applications. The sorting of spikes depends on the features extracted from the neural waveforms, and a better sorting performance usually comes with a higher sampling rate (SR). However for the long duration experiments on free-moving subjects, the miniaturized and wireless neural recording ICs are the current trend, and the compromise on sorting accuracy is usually made by a lower SR for the lower power consumption. In this paper, we implement an on-chip spike sorting processor with integrated interpolation hardware in order to improve the performance in terms of power versus accuracy. According to the fabrication results in 90nm process, if the interpolation is appropriately performed during the spike sorting, the system operated at the SR of 12.5 k samples per second (sps) can outperform the one not having interpolation at 25 ksps on both accuracy and power.

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

    Science.gov (United States)

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

    2017-12-01

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

  1. An angle encoder for super-high resolution and super-high accuracy using SelfA

    Science.gov (United States)

    Watanabe, Tsukasa; Kon, Masahito; Nabeshima, Nobuo; Taniguchi, Kayoko

    2014-06-01

    Angular measurement technology at high resolution for applications such as in hard disk drive manufacturing machines, precision measurement equipment and aspherical process machines requires a rotary encoder with high accuracy, high resolution and high response speed. However, a rotary encoder has angular deviation factors during operation due to scale error or installation error. It has been assumed to be impossible to achieve accuracy below 0.1″ in angular measurement or control after the installation onto the rotating axis. Self-calibration (Lu and Trumper 2007 CIRP Ann. 56 499; Kim et al 2011 Proc. MacroScale; Probst 2008 Meas. Sci. Technol. 19 015101; Probst et al Meas. Sci. Technol. 9 1059; Tadashi and Makoto 1993 J. Robot. Mechatronics 5 448; Ralf et al 2006 Meas. Sci. Technol. 17 2811) and cross-calibration (Probst et al 1998 Meas. Sci. Technol. 9 1059; Just et al 2009 Precis. Eng. 33 530; Burnashev 2013 Quantum Electron. 43 130) technologies for a rotary encoder have been actively discussed on the basis of the principle of circular closure. This discussion prompted the development of rotary tables which achieve reliable and high accuracy angular verification. We apply these technologies for the development of a rotary encoder not only to meet the requirement of super-high accuracy but also to meet that of super-high resolution. This paper presents the development of an encoder with 221 = 2097 152 resolutions per rotation (360°), that is, corresponding to a 0.62″ signal period, achieved by the combination of a laser rotary encoder supplied by Magnescale Co., Ltd and a self-calibratable encoder (SelfA) supplied by The National Institute of Advanced Industrial Science & Technology (AIST). In addition, this paper introduces the development of a rotary encoder to guarantee ±0.03″ accuracy at any point of the interpolated signal, with respect to the encoder at the minimum resolution of 233, that is, corresponding to a 0.0015″ signal period after

  2. Fabrication of Single, Vertically Aligned Carbon Nanotubes in 3D Nanoscale Architectures

    Science.gov (United States)

    Kaul, Anupama B.; Megerian, Krikor G.; Von Allmen, Paul A.; Baron, Richard L.

    2010-01-01

    Plasma-enhanced chemical vapor deposition (PECVD) and high-throughput manufacturing techniques for integrating single, aligned carbon nanotubes (CNTs) into novel 3D nanoscale architectures have been developed. First, the PECVD growth technique ensures excellent alignment of the tubes, since the tubes align in the direction of the electric field in the plasma as they are growing. Second, the tubes generated with this technique are all metallic, so their chirality is predetermined, which is important for electronic applications. Third, a wafer-scale manufacturing process was developed that is high-throughput and low-cost, and yet enables the integration of just single, aligned tubes with nanoscale 3D architectures with unprecedented placement accuracy and does not rely on e-beam lithography. Such techniques should lend themselves to the integration of PECVD grown tubes for applications ranging from interconnects, nanoelectromechanical systems (NEMS), sensors, bioprobes, or other 3D electronic devices. Chemically amplified polyhydroxystyrene-resin-based deep UV resists were used in conjunction with excimer laser-based (lambda = 248 nm) step-and-repeat lithography to form Ni catalyst dots = 300 nm in diameter that nucleated single, vertically aligned tubes with high yield using dc PECVD growth. This is the first time such chemically amplified resists have been used, resulting in the nucleation of single, vertically aligned tubes. In addition, novel 3D nanoscale architectures have been created using topdown techniques that integrate single, vertically aligned tubes. These were enabled by implementing techniques that use deep-UV chemically amplified resists for small-feature-size resolution; optical lithography units that allow unprecedented control over layer-to-layer registration; and ICP (inductively coupled plasma) etching techniques that result in near-vertical, high-aspect-ratio, 3D nanoscale architectures, in conjunction with the use of materials that are

  3. 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

  4. Aligning the CMS Muon Endcap Detector with a System of Optical Sensors

    CERN Document Server

    Hohlmann, Marcus; Guragain, Samir; Andreev, Valery; Yang, Xiaofeng; Bellinger, James; Carlsmith, Duncan; Feyzi, Farshid; Loveless, Richard J; Northacker, David; Eartly, David P; Prokofiev, Oleg; Sknar, Vladimir

    2008-01-01

    The positions and orientations of one sixth of 468 large cathode strip chambers in the endcaps of the CMS muon detector are directly monitored by several hundred sensors including 2-D optical sensors with linear CCDs illuminated by cross-hair lasers. Position measurements obtained by photogrammetry and survey under field-off conditions show that chambers in the +Z endcap have been placed on the yoke disks with an average accuracy of $\\approx 1$ mm in all 3 dimensions. We reconstruct absolute Z$_{CMS}$ positions and orientations of chambers at B=0T and B=4T using data from the optical alignment system. The measured position resolution and sensitivity to relative motion is about 60 $\\mu m$. The precision for measuring chamber positions taking into account mechanical tolerances is \\mbox{$\\approx 270 \\mu m$}. Comparing reconstruction of optical alignment data and photogrammetry measurements at B=0T indicates an accuracy of $\\approx$ 680 $\\mu m$ currently achieved with the hardware alignment system. Optical positi...

  5. High precision optical fiber alignment using tube laser bending

    NARCIS (Netherlands)

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

    2016-01-01

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

  6. 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.

  7. On the accuracy of short read mapping

    DEFF Research Database (Denmark)

    Menzel, Karl Peter; Frellsen, Jes; Plass, Mireya

    2013-01-01

    .e., mapping the reads to a reference genome. In this new situation, conventional alignment tools are obsolete, as they cannot handle this huge amount of data in a reasonable amount of time. Thus, new mapping algorithms have been developed, which are fast at the expense of a small decrease in accuracy...

  8. Biodiesel and Integrated STEM: Vertical Alignment of High School Biology/Biochemistry and Chemistry

    Science.gov (United States)

    Burrows, Andrea C.; Breiner, Jonathan M.; Keiner, Jennifer; Behm, Chris

    2014-01-01

    This article explores the vertical alignment of two high school classes, biology and chemistry, around the core concept of biodiesel fuel production. High school teachers and university faculty members investigated biodiesel as it relates to societal impact through a National Science Foundation Research Experience for Teachers. Using an action…

  9. 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.

  10. 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.

  11. The influence of conductivities consistent with field-aligned currents on high-latitude convection patterns

    International Nuclear Information System (INIS)

    Blomberg, L.G.; Marklund, G.T.

    1988-02-01

    The influence on the high-latitude ionospheric convection of conductivities associated with upward field-aligned currents is investigated. Potential patterns are calculated from a given distribution of field-aligned currents and a conductivity model. The resulting patterns are shown to be modified considerably by including a coupling term between the conductivity and the field-aligned current in the conductivity model. The clockwise rotation of the entire potential pattern is reduced when the conductivity enhancement coincides with the regions of upward field-aligned current. Also, the electric field within these regions turns out to be rather insensitive to change in the magnitude of the current. In regions of downward current or when the current-dependent conductivity is excluded there is on the other hand an almost linear relationship between current and electric field. Although the particles producing the conductivity enhancement may not be the same as those carrying the major part of the field-aligned current it is clear from observations that there is a positive correlation between upward current conductivity. Therefore, the simple relationship used in this study is believed to reflect rather well the principal features of the current-conductivity coupling, which is of im- portance to the modelling of ionospheric electrodynamics. (With 26 refs.) (authors)

  12. 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.

  13. Linear Fresnel zone plate based two-state alignment system for 0.25 micron x-ray lithography

    International Nuclear Information System (INIS)

    Chen, G.

    1993-01-01

    X-ray lithography has proven to be a cost effective and promising technique for fabricating Integrated Circuits (ICs) with minimum feature sizes of less than 0.25 μm. Since IC fabrication is a multilevel process, to preserve the functionality of devices, circuit patterns printed at each lithography level must match existing patterns on the wafer with an accuracy of less than 1/3 ∼ 1/5 of the minimum feature size. An alignment system is used to position the mask relative to the wafer so that mask circuit patterns can be printed on the wafer at the designed position. As the minimum printed feature size shrinks, the overlay requirements of a lithography tool become more stringent. A stepper for 0.25 μm feature device fabrication requires an overlay accuracy of 0.075 μm, of which only 0.05 μm (mean + 3σ) is allocated to its alignment system. This thesis presents the development of a linear Fresnel zone late based two-state alignment (TSA) method for a 0.25 μm x-ray lithography tool. The authors first analyze the overlay requirement in a lithography process and the error allocation to the alignment system for a 0.25 μ feature x-ray lithography tool. They then describe the principle of the two-state alignment, its computer simulation and the optimal alignment mark design. They carried out an optical bench test for the one-axes alignment setup and experimentally evaluated the performance of the system. They developed a three-axes TSA system and integrated the system with the ES-3 x-ray beamline to construct the CXrL aligner, an experimental x-ray exposure system in CXrL. They measured the alignment accuracy of the exposure system to be better than 0.035 μm (3σ) on both metal and dielectric alignment mark substrates. They also studied the effect of processing coatings on the alignment signal with different wafer mark substrates. They successfully printed the 0.5 μm gate level patterns for the first NMOS test chip at CXrL

  14. High-performance Supercapacitors Based on Electrochemical-induced Vertical-aligned Carbon Nanotubes and Polyaniline Nanocomposite Electrodes

    Science.gov (United States)

    Wu, Guan; Tan, Pengfeng; Wang, Dongxing; Li, Zhe; Peng, Lu; Hu, Ying; Wang, Caifeng; Zhu, Wei; Chen, Su; Chen, Wei

    2017-03-01

    Supercapacitors, which store electrical energy through reversible ion on the surface of conductive electrodes have gained enormous attention for variously portable energy storage devices. Since the capacitive performance is mainly determined by the structural and electrochemical properties of electrodes, the electrodes become more crucial to higher performance. However, due to the disordered microstructure and low electrochemical activity of electrode for ion tortuous migration and accumulation, the supercapacitors present relatively low capacitance and energy density. Here we report a high-performance supercapacitor based on polyaniline/vertical-aligned carbon nanotubes (PANI/VA-CNTs) nanocomposite electrodes where the vertical-aligned-structure is formed by the electrochemical-induction (0.75 V). The supercapacitor displays large specific capacitance of 403.3 F g-1, which is 6 times higher than disordered CNTs in HClO4 electrolyte. Additionally, the supercapacitor can also present high specific capacitance (314.6 F g-1), excellent cycling stability (90.2% retention after 3000 cycles at 4 A g-1) and high energy density (98.1 Wh kg-1) in EMIBF4 organic electrolyte. The key to high-performance lies in the vertical-aligned-structure providing direct path channel for ion faster diffusion and high electrochemical capacitance of polyaniline for ion more accommodation.

  15. High-performance Supercapacitors Based on Electrochemical-induced Vertical-aligned Carbon Nanotubes and Polyaniline Nanocomposite Electrodes.

    Science.gov (United States)

    Wu, Guan; Tan, Pengfeng; Wang, Dongxing; Li, Zhe; Peng, Lu; Hu, Ying; Wang, Caifeng; Zhu, Wei; Chen, Su; Chen, Wei

    2017-03-08

    Supercapacitors, which store electrical energy through reversible ion on the surface of conductive electrodes have gained enormous attention for variously portable energy storage devices. Since the capacitive performance is mainly determined by the structural and electrochemical properties of electrodes, the electrodes become more crucial to higher performance. However, due to the disordered microstructure and low electrochemical activity of electrode for ion tortuous migration and accumulation, the supercapacitors present relatively low capacitance and energy density. Here we report a high-performance supercapacitor based on polyaniline/vertical-aligned carbon nanotubes (PANI/VA-CNTs) nanocomposite electrodes where the vertical-aligned-structure is formed by the electrochemical-induction (0.75 V). The supercapacitor displays large specific capacitance of 403.3 F g -1 , which is 6 times higher than disordered CNTs in HClO 4 electrolyte. Additionally, the supercapacitor can also present high specific capacitance (314.6 F g -1 ), excellent cycling stability (90.2% retention after 3000 cycles at 4 A g -1 ) and high energy density (98.1 Wh kg -1 ) in EMIBF 4 organic electrolyte. The key to high-performance lies in the vertical-aligned-structure providing direct path channel for ion faster diffusion and high electrochemical capacitance of polyaniline for ion more accommodation.

  16. 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.

  17. 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...

  18. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez

    2011-01-01

    A new set of muon alignment constants was approved in August. The relative position between muon chambers is essentially unchanged, indicating good detector stability. The main changes concern the global positioning of the barrel and of the endcap rings to match the new Tracker geometry. Detailed studies of the differences between track-based and optical alignment of DTs have proven to be a valuable tool for constraining Tracker alignment weak modes, and this information is now being used as part of the alignment procedure. In addition to the “split-cosmic” analysis used to investigate the muon momentum resolution at high momentum, a new procedure based on reconstructing the invariant mass of di-muons from boosted Zs is under development. Both procedures show an improvement in the momentum precision of Global Muons with respect to Tracker-only Muons. Recent developments in track-based alignment include a better treatment of the tails of residual distributions and accounting for correla...

  19. IMU-to-Segment Assignment and Orientation Alignment for the Lower Body Using Deep Learning.

    Science.gov (United States)

    Zimmermann, Tobias; Taetz, Bertram; Bleser, Gabriele

    2018-01-19

    Human body motion analysis based on wearable inertial measurement units (IMUs) receives a lot of attention from both the research community and the and industrial community. This is due to the significant role in, for instance, mobile health systems, sports and human computer interaction. In sensor based activity recognition, one of the major issues for obtaining reliable results is the sensor placement/assignment on the body. For inertial motion capture (joint kinematics estimation) and analysis, the IMU-to-segment (I2S) assignment and alignment are central issues to obtain biomechanical joint angles. Existing approaches for I2S assignment usually rely on hand crafted features and shallow classification approaches (e.g., support vector machines), with no agreement regarding the most suitable features for the assignment task. Moreover, estimating the complete orientation alignment of an IMU relative to the segment it is attached to using a machine learning approach has not been shown in literature so far. This is likely due to the high amount of training data that have to be recorded to suitably represent possible IMU alignment variations. In this work, we propose online approaches for solving the assignment and alignment tasks for an arbitrary amount of IMUs with respect to a biomechanical lower body model using a deep learning architecture and windows of 128 gyroscope and accelerometer data samples. For this, we combine convolutional neural networks (CNNs) for local filter learning with long-short-term memory (LSTM) recurrent networks as well as generalized recurrent units (GRUs) for learning time dynamic features. The assignment task is casted as a classification problem, while the alignment task is casted as a regression problem. In this framework, we demonstrate the feasibility of augmenting a limited amount of real IMU training data with simulated alignment variations and IMU data for improving the recognition/estimation accuracies. With the proposed

  20. IMU-to-Segment Assignment and Orientation Alignment for the Lower Body Using Deep Learning

    Directory of Open Access Journals (Sweden)

    Tobias Zimmermann

    2018-01-01

    Full Text Available Human body motion analysis based on wearable inertial measurement units (IMUs receives a lot of attention from both the research community and the and industrial community. This is due to the significant role in, for instance, mobile health systems, sports and human computer interaction. In sensor based activity recognition, one of the major issues for obtaining reliable results is the sensor placement/assignment on the body. For inertial motion capture (joint kinematics estimation and analysis, the IMU-to-segment (I2S assignment and alignment are central issues to obtain biomechanical joint angles. Existing approaches for I2S assignment usually rely on hand crafted features and shallow classification approaches (e.g., support vector machines, with no agreement regarding the most suitable features for the assignment task. Moreover, estimating the complete orientation alignment of an IMU relative to the segment it is attached to using a machine learning approach has not been shown in literature so far. This is likely due to the high amount of training data that have to be recorded to suitably represent possible IMU alignment variations. In this work, we propose online approaches for solving the assignment and alignment tasks for an arbitrary amount of IMUs with respect to a biomechanical lower body model using a deep learning architecture and windows of 128 gyroscope and accelerometer data samples. For this, we combine convolutional neural networks (CNNs for local filter learning with long-short-term memory (LSTM recurrent networks as well as generalized recurrent units (GRUs for learning time dynamic features. The assignment task is casted as a classification problem, while the alignment task is casted as a regression problem. In this framework, we demonstrate the feasibility of augmenting a limited amount of real IMU training data with simulated alignment variations and IMU data for improving the recognition/estimation accuracies. With the

  1. Overlay accuracy on a flexible web with a roll printing process based on a roll-to-roll system.

    Science.gov (United States)

    Chang, Jaehyuk; Lee, Sunggun; Lee, Ki Beom; Lee, Seungjun; Cho, Young Tae; Seo, Jungwoo; Lee, Sukwon; Jo, Gugrae; Lee, Ki-yong; Kong, Hyang-Shik; Kwon, Sin

    2015-05-01

    For high-quality flexible devices from printing processes based on Roll-to-Roll (R2R) systems, overlay alignment during the patterning of each functional layer poses a major challenge. The reason is because flexible substrates have a relatively low stiffness compared with rigid substrates, and they are easily deformed during web handling in the R2R system. To achieve a high overlay accuracy for a flexible substrate, it is important not only to develop web handling modules (such as web guiding, tension control, winding, and unwinding) and a precise printing tool but also to control the synchronization of each unit in the total system. A R2R web handling system and reverse offset printing process were developed in this work, and an overlay between the 1st and 2nd layers of ±5μm on a 500 mm-wide film was achieved at a σ level of 2.4 and 2.8 (x and y directions, respectively) in a continuous R2R printing process. This paper presents the components and mechanisms used in reverse offset printing based on a R2R system and the printing results including positioning accuracy and overlay alignment accuracy.

  2. An angle encoder for super-high resolution and super-high accuracy using SelfA

    International Nuclear Information System (INIS)

    Watanabe, Tsukasa; Kon, Masahito; Nabeshima, Nobuo; Taniguchi, Kayoko

    2014-01-01

    Angular measurement technology at high resolution for applications such as in hard disk drive manufacturing machines, precision measurement equipment and aspherical process machines requires a rotary encoder with high accuracy, high resolution and high response speed. However, a rotary encoder has angular deviation factors during operation due to scale error or installation error. It has been assumed to be impossible to achieve accuracy below 0.1″ in angular measurement or control after the installation onto the rotating axis. Self-calibration (Lu and Trumper 2007 CIRP Ann. 56 499; Kim et al 2011 Proc. MacroScale; Probst 2008 Meas. Sci. Technol. 19 015101; Probst et al Meas. Sci. Technol. 9 1059; Tadashi and Makoto 1993 J. Robot. Mechatronics 5 448; Ralf et al 2006 Meas. Sci. Technol. 17 2811) and cross-calibration (Probst et al 1998 Meas. Sci. Technol. 9 1059; Just et al 2009 Precis. Eng. 33 530; Burnashev 2013 Quantum Electron. 43 130) technologies for a rotary encoder have been actively discussed on the basis of the principle of circular closure. This discussion prompted the development of rotary tables which achieve reliable and high accuracy angular verification. We apply these technologies for the development of a rotary encoder not only to meet the requirement of super-high accuracy but also to meet that of super-high resolution. This paper presents the development of an encoder with 2 21 = 2097 152 resolutions per rotation (360°), that is, corresponding to a 0.62″ signal period, achieved by the combination of a laser rotary encoder supplied by Magnescale Co., Ltd and a self-calibratable encoder (SelfA) supplied by The National Institute of Advanced Industrial Science and Technology (AIST). In addition, this paper introduces the development of a rotary encoder to guarantee ±0.03″ accuracy at any point of the interpolated signal, with respect to the encoder at the minimum resolution of 2 33 , that is, corresponding to a 0.0015″ signal period

  3. Fast and High Accuracy Wire Scanner

    CERN Document Server

    Koujili, M; Koopman, J; Ramos, D; Sapinski, M; De Freitas, J; Ait Amira, Y; Djerdir, A

    2009-01-01

    Scanning of a high intensity particle beam imposes challenging requirements on a Wire Scanner system. It is expected to reach a scanning speed of 20 m.s-1 with a position accuracy of the order of 1 μm. In addition a timing accuracy better than 1 millisecond is needed. The adopted solution consists of a fork holding a wire rotating by a maximum of 200°. Fork, rotor and angular position sensor are mounted on the same axis and located in a chamber connected to the beam vacuum. The requirements imply the design of a system with extremely low vibration, vacuum compatibility, radiation and temperature tolerance. The adopted solution consists of a rotary brushless synchronous motor with the permanent magnet rotor installed inside of the vacuum chamber and the stator installed outside. The accurate position sensor will be mounted on the rotary shaft inside of the vacuum chamber, has to resist a bake-out temperature of 200°C and ionizing radiation up to a dozen of kGy/year. A digital feedback controller allows maxi...

  4. Fabrication and design of bioactive agent coated, highly-aligned electrospun matrices for nerve tissue engineering: Preparation, characterization and application

    Science.gov (United States)

    Lee, Sang Jin; Heo, Min; Lee, Donghyun; Heo, Dong Nyoung; Lim, Ho-Nam; Kwon, Il Keun

    2017-12-01

    In this study, we designed highly-aligned thermoplastic polycarbonate urethane (PCU) fibrous scaffolds coated with bioactive compounds, such as Poly-L-Lysine (PLL) and Poly-L-Ornithine (PLO), to enhance cellular adhesion and directivity. These products were characterized by scanning electron microscope (SEM) analysis which demonstrated that highly aligned fiber strands were formed without beads when coated onto a mandrel rotating at 1800 rpm. During in vitro cell test, PLO-coated, aligned PCU scaffolds were found to have significantly higher proliferation rates than PLL coated and bare PCU scaffolds. Interestingly, dental pulp stem cells (DPSCs) were observed to stretch along the longitudinal axis parallel to the cell direction on highly aligned scaffolds. These results clearly confirm that our strategy may suggest a useful paradigm by inducing neural tissue repair as a means to remodeling and healing of tissue for restorative procedures in neural tissue engineering.

  5. The effect of instrument alignment on peripheral refraction measurements by automated optometer.

    Science.gov (United States)

    Ehsaei, Asieh; Chisholm, Catharine M; Mallen, Edward A H; Pacey, Ian E

    2011-07-01

    Interest in peripheral refraction measurement has grown in recent years in response to the insight it may provide into myopia development. In light of the likely increase in the clinical use of open-field autorefractors for peripheral refraction measurements, the question of instrument alignment and its impact on the accuracy of refraction measurements is raised. The aim of this study was to investigate the accuracy and precision when an open-field device was moved away from alignment with the corneal reflex towards the pupil margins, and to determine the optimum alignment position for peripheral refraction measurements. Autorefractions were performed on the right eyes of 10 healthy participants using the Shin-Nippon NVision-K 5001 autorefractor. At least five measurements were taken with the subject fixating a distance target in the primary position of gaze, and then four peripheral fixation targets located along the horizontal meridian (10° and 20° eccentricities in the nasal and temporal retina). Measurements were taken at seven alignment positions across the pupil for each fixation angle. Refraction was recorded as the spherical and cylindrical power. The central objective refraction achieved under cycloplegia based on the autorefraction result for the whole sample, ranged between -5.62 D and +1.85 D for the value of sphere, with a maximum astigmatism of -1.00 D. Acceptable alignment position range varied with fixation angle but was -1.0 to +1.0 mm in width across the pupil. Peripheral refraction measurements centred on the entrance pupil were as reliable as those centred on the corneal reflex. Our data suggest that for peripheral refraction measurements, there is a range of acceptable positions and operators can be confident of the validity of results obtained if aligned half way between the pupil centre and corneal reflex. The alignment becomes more critical at greater eccentricities. Ophthalmic & Physiological Optics © 2011 The College of Optometrists.

  6. Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic.

    Science.gov (United States)

    Brown, Peter; Pullan, Wayne; Yang, Yuedong; Zhou, Yaoqi

    2016-02-01

    The three dimensional tertiary structure of a protein at near atomic level resolution provides insight alluding to its function and evolution. As protein structure decides its functionality, similarity in structure usually implies similarity in function. As such, structure alignment techniques are often useful in the classifications of protein function. Given the rapidly growing rate of new, experimentally determined structures being made available from repositories such as the Protein Data Bank, fast and accurate computational structure comparison tools are required. This paper presents SPalignNS, a non-sequential protein structure alignment tool using a novel asymmetrical greedy search technique. The performance of SPalignNS was evaluated against existing sequential and non-sequential structure alignment methods by performing trials with commonly used datasets. These benchmark datasets used to gauge alignment accuracy include (i) 9538 pairwise alignments implied by the HOMSTRAD database of homologous proteins; (ii) a subset of 64 difficult alignments from set (i) that have low structure similarity; (iii) 199 pairwise alignments of proteins with similar structure but different topology; and (iv) a subset of 20 pairwise alignments from the RIPC set. SPalignNS is shown to achieve greater alignment accuracy (lower or comparable root-mean squared distance with increased structure overlap coverage) for all datasets, and the highest agreement with reference alignments from the challenging dataset (iv) above, when compared with both sequentially constrained alignments and other non-sequential alignments. SPalignNS was implemented in C++. The source code, binary executable, and a web server version is freely available at: http://sparks-lab.org yaoqi.zhou@griffith.edu.au. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  7. Requirements for alignment of electron cyclotron current drive for neoclassical tearing mode stabilization in ITER

    International Nuclear Information System (INIS)

    La Haye, R.J.; Ferron, J.R.; Humphreys, D.A.; Luce, T.C.; Petty, C.C.; Prater, R.; Strait, E.J.; Welander, A.S.

    2008-01-01

    ITER will rely on electron cyclotron stabilization of neoclassical tearing mode islands. The large size and low torque applied in ITER imply slow plasma rotation and susceptibility to island locking by the resistive wall; locking is likely to lead to a loss of the high confinement H-mode, a beta collapse and possibly disruption. 'Front' steering of the launcher, with narrower electron cyclotron current drive (ECCD), has resolved the issue in 'remote' steering of the driven current being too broad and relatively ineffective. However, narrower current drive places demands on alignment of the current drive on the rational surface that is being stabilized. DIII-D alignment techniques with and without (preemptive) an island are reviewed. The results are used to check models for the effect of misalignment and are then applied to ITER. Criteria for accuracy of alignment as a function of injected power and for the necessary time response of the controller are presented

  8. Biaxial magnetic grain alignment

    International Nuclear Information System (INIS)

    Staines, M.; Genoud, J.-Y.; Mawdsley, A.; Manojlovic, V.

    2000-01-01

    Full text: We describe a dynamic magnetic grain alignment technique which can be used to produce YBCO thick films with a high degree of biaxial texture. The technique is, however, generally applicable to preparing ceramics or composite materials from granular materials with orthorhombic or lower crystal symmetry and is therefore not restricted to superconducting applications. Because magnetic alignment is a bulk effect, textured substrates are not required, unlike epitaxial coated tape processes such as RABiTS. We have used the technique to produce thick films of Y-247 on untextured silver substrates. After processing to Y-123 the films show a clear enhancement of critical current density relative to identically prepared untextured or uniaxially textured samples. We describe procedures for preparing materials using magnetic biaxial grain alignment with the emphasis on alignment in epoxy, which can give extremely high texture. X-ray rocking curves with FWHM of as little as 1-2 degrees have been measured

  9. An optical sensor for the alignment of the Atlas Muon Spectrometer

    International Nuclear Information System (INIS)

    Barriere, J.-Ch.; Cloue, O.; Duboue, B.; Gautard, V.; Graffin, P.; Guyot, C.; Perrin, P.; Ponsot, P.; Reinert, Y.; Schuller, J.-P.; Schune, Ph.

    2003-01-01

    In the Atlas muon spectrometer (ATLAS Technical Proposal, CERN/LHCC/94-43, 15 December 1994, ATLAS Muon Spectrometer Technical Design Report, CERN/LHCC/97-22, 31 May 1997 and http://atlasinfo.cern.ch:80/Atlas/Welcome.html) the alignment system should control the spatial position of the muon chambers with an accuracy of 30 μm and 200 μrad for a range of ±5 mm and ±10 mrad. The alignment device described in this paper, called Praxial, fulfills these requirements

  10. Numerical Upscaling of Solute Transport in Fractured Porous Media Based on Flow Aligned Blocks

    Science.gov (United States)

    Leube, P.; Nowak, W.; Sanchez-Vila, X.

    2013-12-01

    High-contrast or fractured-porous media (FPM) pose one of the largest unresolved challenges for simulating large hydrogeological systems. The high contrast in advective transport between fast conduits and low-permeability rock matrix, including complex mass transfer processes, leads to the typical complex characteristics of early bulk arrivals and long tailings. Adequate direct representation of FPM requires enormous numerical resolutions. For large scales, e.g. the catchment scale, and when allowing for uncertainty in the fracture network architecture or in matrix properties, computational costs quickly reach an intractable level. In such cases, multi-scale simulation techniques have become useful tools. They allow decreasing the complexity of models by aggregating and transferring their parameters to coarser scales and so drastically reduce the computational costs. However, these advantages come at a loss of detail and accuracy. In this work, we develop and test a new multi-scale or upscaled modeling approach based on block upscaling. The novelty is that individual blocks are defined by and aligned with the local flow coordinates. We choose a multi-rate mass transfer (MRMT) model to represent the remaining sub-block non-Fickian behavior within these blocks on the coarse scale. To make the scale transition simple and to save computational costs, we capture sub-block features by temporal moments (TM) of block-wise particle arrival times to be matched with the MRMT model. By predicting spatial mass distributions of injected tracers in a synthetic test scenario, our coarse-scale solution matches reasonably well with the corresponding fine-scale reference solution. For predicting higher TM-orders (such as arrival time and effective dispersion), the prediction accuracy steadily decreases. This is compensated to some extent by the MRMT model. If the MRMT model becomes too complex, it loses its effect. We also found that prediction accuracy is sensitive to the choice of

  11. Radiation chemistry in high pressure paying attention to molecular motion and alignment

    International Nuclear Information System (INIS)

    Sasuga, Tsuneo

    1978-01-01

    Effects of high pressure or radiation-induced cross-linking of synthetic rubbers and polymerization of methacrylates and acrylonitrile (AN) have been studied paying attention to molecular motion and alignment. The following were revealed from radiation-induced crosslinking reaction, pressure-volume-temperature (P-V-T) measurement and chemical relaxation of polymer crosslinked at high pressure: (1) The rate of crosslinking is increased in compression especially in polymers containing double bonds, due to chain reaction through double bonds. (2) Crosslinking points of the polymer with double bonds crosslinked at high pressure are dispersed as cluster. (3) Crosslinking reaction is intimately related with change of the molecular motion in a polymer under pressure. Van't Hoff plots of methacrylates and AN breaked at a pressure depending on the monomer. The pressure giving the breaks depends on length of methacrylate. P-V curves of the polymer-monomer coexistence system as-polymerized exhibit peculiar behavior at the pressure giving the breaks. AN exhibits complicated polymerization behavior at a pressure changing compressibility of the monomer. From above results etc. it is concluded that monomer molecules are aligned in short range at a pressure corresponding to geometrical structure of the monomer molecules. (auth.)

  12. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    Gervasio Gomez

    2012-01-01

      The new alignment for the DT chambers has been successfully used in physics analysis starting with the 52X Global Tag. The remaining main areas of development over the next few months will be preparing a new track-based CSC alignment and producing realistic APEs (alignment position errors) and MC misalignment scenarios to match the latest muon alignment constants. Work on these items has been delayed from the intended timeline, mostly due to a large involvement of the muon alignment man-power in physics analyses over the first half of this year. As CMS keeps probing higher and higher energies, special attention must be paid to the reconstruction of very-high-energy muons. Recent muon POG reports from mid-June show a φ-dependence in curvature bias in Monte Carlo samples. This bias is observed already at the tracker level, where it is constant with muon pT, while it grows with pT as muon chamber information is added to the tracks. Similar studies show a much smaller effect in data, at le...

  13. 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.

  14. 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

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

    DEFF Research Database (Denmark)

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

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

  16. 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

  17. Transparent silicon strip sensors for the optical alignment of particle detector systems

    International Nuclear Information System (INIS)

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

    1995-05-01

    Modern large-area precision tracking detectors require increasing accuracy for the alignment of their components. A novel multi-point laser alignment system has been developed for such applications. The position of detector components with respect to reference laser beams is monitored by semi-transparent optical position sensors which work on the principle of silicon strip photodiodes. Two types of custom designed transparent strip sensors, based on crystalline and on amorphous silicon as active material, have been studied. The sensors are optimised for the typical diameters of collimated laser beams of 3-5 mm over distances of 10-20 m. They provide very high position resolution, on the order of 1 μm, uniformly over a wide measurement range of several centimeters. The preparation of the sensor surfaces requires special attention in order to achieve high light transmittance and minimum distortion of the traversing laser beams. At selected wavelengths, produced by laser diodes, transmission rates above 90% have been achieved. This allows to position more than 30 sensors along one laser beam. The sensors will be equipped with custom designed integrated readout electronics. (orig.)

  18. High-accuracy measurements of the normal specular reflectance

    International Nuclear Information System (INIS)

    Voarino, Philippe; Piombini, Herve; Sabary, Frederic; Marteau, Daniel; Dubard, Jimmy; Hameury, Jacques; Filtz, Jean Remy

    2008-01-01

    The French Laser Megajoule (LMJ) is designed and constructed by the French Commissariata l'Energie Atomique (CEA). Its amplifying section needs highly reflective multilayer mirrors for the flash lamps. To monitor and improve the coating process, the reflectors have to be characterized to high accuracy. The described spectrophotometer is designed to measure normal specular reflectance with high repeatability by using a small spot size of 100 μm. Results are compared with ellipsometric measurements. The instrument can also perform spatial characterization to detect coating nonuniformity

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

    Science.gov (United States)

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

    2017-10-17

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

  20. Calibration results using highly aberrated images for aligning the JWST instruments to the telescope

    Science.gov (United States)

    Smith, Koby Z.; Acton, D. Scott; Gallagher, Ben B.; Knight, J. Scott; Dean, Bruce H.; Jurling, Alden S.; Zielinski, Thomas P.

    2016-07-01

    The James Webb Space Telescope (JWST) project is an international collaboration led by NASA's Goddard Space Flight Center (GSFC) in Greenbelt, MD. JWST is NASA's flagship observatory that will operate nearly a million miles away from Earth at the L2 Lagrange point. JWST's optical design is a three-mirror anastigmat with four main optical components; 1) the eighteen Primary Mirror Segment Assemblies (PMSA), 2) a single Secondary Mirror Assembly (SMA), 3) an Aft-Optics Subsystem (AOS) consisting of a Tertiary Mirror and Fine Steering Mirror, and 4) an Integrated Science Instrument Module consisting of the various instruments for JWST. JWST's optical system has been designed to accommodate a significant amount of alignment capability and risk with the PMSAs and SMA having rigid body motion available on-orbit just for alignment purposes. However, the Aft-Optics Subsystem (AOS) and Integrated Science Instrument Module (ISIM) are essentially fixed optical subsystems within JWST, and therefore the cryogenic alignment of the AOS to the ISIM is critical to the optical performance and mission success of JWST. In support of this cryogenic alignment of the AOS to ISIM, an array of fiber optic sources, known as the AOS Source Plate Assembly (ASPA), are placed near the intermediate image location of JWST (between the secondary and tertiary mirrors) during thermal vacuum ground-test operations. The AOS produces images of the ASPA fiber optic sources at the JWST focal surface location, where they are captured by the various science instruments. In this manner, the AOS provides an optical yardstick by which the instruments within ISIM can evaluate their relative positions to and the alignment of the AOS to ISIM can be quantified. However, since the ASPA is located at the intermediate image location of the JWST three-mirror anastigmat design, the images of these fiber optic sources produced by the AOS are highly aberrated with approximately 2-3μm RMS wavefront error consisting

  1. Alignment of the Stanford Linear Collider Arcs: Concepts and results

    International Nuclear Information System (INIS)

    Pitthan, R.; Bell, B.; Friedsam, H.; Pietryka, M.; Oren, W.; Ruland, R.

    1987-02-01

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

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

    International Nuclear Information System (INIS)

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

    2011-01-01

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

  3. 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.

  4. A high accuracy land use/cover retrieval system

    Directory of Open Access Journals (Sweden)

    Alaa Hefnawy

    2012-03-01

    Full Text Available The effects of spatial resolution on the accuracy of mapping land use/cover types have received increasing attention as a large number of multi-scale earth observation data become available. Although many methods of semi automated image classification of remotely sensed data have been established for improving the accuracy of land use/cover classification during the past 40 years, most of them were employed in single-resolution image classification, which led to unsatisfactory results. In this paper, we propose a multi-resolution fast adaptive content-based retrieval system of satellite images. Through our proposed system, we apply a Super Resolution technique for the Landsat-TM images to have a high resolution dataset. The human–computer interactive system is based on modified radial basis function for retrieval of satellite database images. We apply the backpropagation supervised artificial neural network classifier for both the multi and single resolution datasets. The results show significant improved land use/cover classification accuracy for the multi-resolution approach compared with those from single-resolution approach.

  5. High accuracy satellite drag model (HASDM)

    Science.gov (United States)

    Storz, Mark F.; Bowman, Bruce R.; Branson, Major James I.; Casali, Stephen J.; Tobiska, W. Kent

    The dominant error source in force models used to predict low-perigee satellite trajectories is atmospheric drag. Errors in operational thermospheric density models cause significant errors in predicted satellite positions, since these models do not account for dynamic changes in atmospheric drag for orbit predictions. The Air Force Space Battlelab's High Accuracy Satellite Drag Model (HASDM) estimates and predicts (out three days) a dynamically varying global density field. HASDM includes the Dynamic Calibration Atmosphere (DCA) algorithm that solves for the phases and amplitudes of the diurnal and semidiurnal variations of thermospheric density near real-time from the observed drag effects on a set of Low Earth Orbit (LEO) calibration satellites. The density correction is expressed as a function of latitude, local solar time and altitude. In HASDM, a time series prediction filter relates the extreme ultraviolet (EUV) energy index E10.7 and the geomagnetic storm index ap, to the DCA density correction parameters. The E10.7 index is generated by the SOLAR2000 model, the first full spectrum model of solar irradiance. The estimated and predicted density fields will be used operationally to significantly improve the accuracy of predicted trajectories for all low-perigee satellites.

  6. Tidal alignment of galaxies

    Energy Technology Data Exchange (ETDEWEB)

    Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš

    2015-08-01

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

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

    Science.gov (United States)

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

    2018-06-01

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

  8. The art of editing RNA structural alignments

    DEFF Research Database (Denmark)

    Andersen, Ebbe Sloth

    2014-01-01

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

  9. Computer navigation experience in hip resurfacing improves femoral component alignment using a conventional jig.

    Science.gov (United States)

    Morison, Zachary; Mehra, Akshay; Olsen, Michael; Donnelly, Michael; Schemitsch, Emil

    2013-11-01

    The use of computer navigation has been shown to improve the accuracy of femoral component placement compared to conventional instrumentation in hip resurfacing. Whether exposure to computer navigation improves accuracy when the procedure is subsequently performed with conventional instrumentation without navigation has not been explored. We examined whether femoral component alignment utilizing a conventional jig improves following experience with the use of imageless computer navigation for hip resurfacing. Between December 2004 and December 2008, 213 consecutive hip resurfacings were performed by a single surgeon. The first 17 (Cohort 1) and the last 9 (Cohort 2) hip resurfacings were performed using a conventional guidewire alignment jig. In 187 cases, the femoral component was implanted using the imageless computer navigation. Cohorts 1 and 2 were compared for femoral component alignment accuracy. All components in Cohort 2 achieved the position determined by the preoperative plan. The mean deviation of the stem-shaft angle (SSA) from the preoperatively planned target position was 2.2° in Cohort 2 and 5.6° in Cohort 1 (P = 0.01). Four implants in Cohort 1 were positioned at least 10° varus compared to the target SSA position and another four were retroverted. Femoral component placement utilizing conventional instrumentation may be more accurate following experience using imageless computer navigation.

  10. Alignment of Escherichia coli K12 DNA sequences to a genomic restriction map.

    Science.gov (United States)

    Rudd, K E; Miller, W; Ostell, J; Benson, D A

    1990-01-25

    We use the extensive published information describing the genome of Escherichia coli and new restriction map alignment software to align DNA sequence, genetic, and physical maps. Restriction map alignment software is used which considers restriction maps as strings analogous to DNA or protein sequences except that two values, enzyme name and DNA base address, are associated with each position on the string. The resulting alignments reveal a nearly linear relationship between the physical and genetic maps of the E. coli chromosome. Physical map comparisons with the 1976, 1980, and 1983 genetic maps demonstrate a better fit with the more recent maps. The results of these alignments are genomic kilobase coordinates, orientation and rank of the alignment that best fits the genetic data. A statistical measure based on extreme value distribution is applied to the alignments. Additional computer analyses allow us to estimate the accuracy of the published E. coli genomic restriction map, simulate rearrangements of the bacterial chromosome, and search for repetitive DNA. The procedures we used are general enough to be applicable to other genome mapping projects.

  11. Pattern optimizing verification of self-align quadruple patterning

    Science.gov (United States)

    Yamato, Masatoshi; Yamada, Kazuki; Oyama, Kenichi; Hara, Arisa; Natori, Sakurako; Yamauchi, Shouhei; Koike, Kyohei; Yaegashi, Hidetami

    2017-03-01

    Lithographic scaling continues to advance by extending the life of 193nm immersion technology, and spacer-type multi-patterning is undeniably the driving force behind this trend. Multi-patterning techniques such as self-aligned double patterning (SADP) and self-aligned quadruple patterning (SAQP) have come to be used in memory devices, and they have also been adopted in logic devices to create constituent patterns in the formation of 1D layout designs. Multi-patterning has consequently become an indispensible technology in the fabrication of all advanced devices. In general, items that must be managed when using multi-patterning include critical dimension uniformity (CDU), line edge roughness (LER), and line width roughness (LWR). Recently, moreover, there has been increasing focus on judging and managing pattern resolution performance from a more detailed perspective and on making a right/wrong judgment from the perspective of edge placement error (EPE). To begin with, pattern resolution performance in spacer-type multi-patterning is affected by the process accuracy of the core (mandrel) pattern. Improving the controllability of CD and LER of the mandrel is most important, and to reduce LER, an appropriate smoothing technique should be carefully selected. In addition, the atomic layer deposition (ALD) technique is generally used to meet the need for high accuracy in forming the spacer film. Advances in scaling are accompanied by stricter requirements in the controllability of fine processing. In this paper, we first describe our efforts in improving controllability by selecting the most appropriate materials for the mandrel pattern and spacer film. Then, based on the materials selected, we present experimental results on a technique for improving etching selectivity.

  12. Quality assurance of CT-PET alignment and image registration for radiation treatment planning

    International Nuclear Information System (INIS)

    Gong, S.J.; O'Keefe, G.J.; Gunawardana, D.H.

    2005-01-01

    A multi-layer point source phantom was first used to calibrate and verify the CT-PET system alignment. A partial whole-body Aldcrson RANDO Man Phantom (head through mid-femur) was externally and internally marked with small metal cannulas filled with 18F-FDG and then scanned with both modalities. Six series of phantom studies with different acquisition settings and scan positions were performed to reveal possible system bias and evaluate the accuracy and reliabilities of Philips Syntegra program in image alignment, coregistration and fusion. The registration error was assessed quantitatively by measuring the root-mean-square distance between the iso-centers of corresponding fiducial marker geometries in reference CT volumes and transformed CT or PET volumes. Results: Experimental data confirms the accuracy of manual, parameter, point and image-based registration using Syntegra is better than 2 mm. Comparisons between blind and cross definition of iso-centers of fiducial marks indicate that the fused CT and PET is superior to visual correlation of CT and PET side-by-side. Conclusion: In this work we demonstrate the QA procedures of Gemini image alignment and registration. Syntegra produces intrinsic and robust multi-modality image registration and fusion with careful user interaction. The registration accuracy is generally better than the spatial resolution of the PET scanner used and this appears to be sufficient for most RTP CT-PET registration procedures

  13. Feasibility study of multipoint based laser alignment system for CLIC

    CERN Document Server

    Stern, G; Mainaud-Durand, H; Piedigrossi, D; Geiger, A

    2012-01-01

    CLIC (Compact LInear Collider) is a study for a future electron-positron collider that would allow physicists to explore a new energy region beyond the capabilities oftoday’s particle accelerators. Alignment is one of the major challenges within the CLIC study in order to achieve the high requirement of a multi-TeV center of mass colliding beam energy range (nominal 3 TeV). To reach this energy in a realistic and cost efficient scenario all accelerator components have to be aligned with an accuracy of 10 μm over a sliding window of 200 m. The demand for a straight line reference is so far based on stretched wires coupled with Wire Positioning Sensors (WPS). These solutions are currently further developed inorder to reduce the drawbacks which are mainly given by their costs and difficult implementation. However, it should be validated through inter-comparison with a solution ideally based on a different physical principle. Therefore, a new metrological approach is proposed using a laser beam as straight lin...

  14. Efficient and robust model-to-image alignment using 3D scale-invariant features.

    Science.gov (United States)

    Toews, Matthew; Wells, William M

    2013-04-01

    This paper presents feature-based alignment (FBA), a general method for efficient and robust model-to-image alignment. Volumetric images, e.g. CT scans of the human body, are modeled probabilistically as a collage of 3D scale-invariant image features within a normalized reference space. Features are incorporated as a latent random variable and marginalized out in computing a maximum a posteriori alignment solution. The model is learned from features extracted in pre-aligned training images, then fit to features extracted from a new image to identify a globally optimal locally linear alignment solution. Novel techniques are presented for determining local feature orientation and efficiently encoding feature intensity in 3D. Experiments involving difficult magnetic resonance (MR) images of the human brain demonstrate FBA achieves alignment accuracy similar to widely-used registration methods, while requiring a fraction of the memory and computation resources and offering a more robust, globally optimal solution. Experiments on CT human body scans demonstrate FBA as an effective system for automatic human body alignment where other alignment methods break down. Copyright © 2012 Elsevier B.V. All rights reserved.

  15. The Poisson alignment reference system implementation at the Advanced Photon Source

    International Nuclear Information System (INIS)

    Feier, I.

    1998-01-01

    The Poisson spot was established using a collimated laser beam from a 3-mW diode laser. It was monitored on a quadrant detector and found to be very sensitive to vibration and air disturbances. Therefore, for future work we strongly recommend a sealed vacuum tube in which the Poisson line may be propagated. A digital single-axis feedback system was employed to generate an straight line reference (SLR) on the X axis. Pointing accuracy was better than 8 ± 2 microns at a distance of 5 m. The digital system was found to be quite slow with a maximum bandwidth of 47 ± 9 Hz. Slow drifts were easily corrected but any vibration over 5 Hz was not. We recommend an analog proportional-integral-derivative (PID) controller for high bandwidth and smooth operation of the kinematic mirror. Although the Poisson alignment system (PAS) at the Advanced Photon Source is still in its infancy, it already shows great promise as a possible alignment system for the low-energy undulator test line (LEUTL). Since components such as wigglers and quadruples will initially be aligned with respect to each other using conventional means and mounted on some kind of rigid rail, the goal would be to align six to ten such rails over a distance of about 30 m. The PAS could be used to align these rails by mounting a sphere at the joint between two rails. These spheres would need to be in a vacuum pipe to eliminate the refractive effects of air. Each sphere would not be attached to either rail but instead to a flange connecting the vacuum pipes of each rail. Thus the whole line would be made up of straight, rigid segments that could be aligned by moving the joints. Each sphere would have its own detector, allowing the operators to actively monitor the position of each joint and therefore the overall alignment of the system

  16. 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

  17. 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.

  18. Mechanical alignment based on beam diagnostics

    International Nuclear Information System (INIS)

    Farvacque, L.; Martin, D.; Nagaoka, R.

    1999-01-01

    This article studies the consequences of misalignment of the different components on the displacement of the beam. 3 types of motion have been investigated: quadrupole vertical displacement, quadrupole tilt and sextupole vertical displacement. For each shift a response matrix has been designed and from this formulation, aligning quadrupoles means inverting this matrix. The strategy for correction depends on the accuracy of the response matrix and on the quality of the beam position measurements. A modelling of the corrections is proposed. (A.C.)

  19. Adaptive sensor-based ultra-high accuracy solar concentrator tracker

    Science.gov (United States)

    Brinkley, Jordyn; Hassanzadeh, Ali

    2017-09-01

    Conventional solar trackers use information of the sun's position, either by direct sensing or by GPS. Our method uses the shading of the receiver. This, coupled with nonimaging optics design allows us to achieve ultra-high concentration. Incorporating a sensor based shadow tracking method with a two stage concentration solar hybrid parabolic trough allows the system to maintain high concentration with acute accuracy.

  20. Coarse Alignment Technology on Moving base for SINS Based on the Improved Quaternion Filter Algorithm.

    Science.gov (United States)

    Zhang, Tao; Zhu, Yongyun; Zhou, Feng; Yan, Yaxiong; Tong, Jinwu

    2017-06-17

    Initial alignment of the strapdown inertial navigation system (SINS) is intended to determine the initial attitude matrix in a short time with certain accuracy. The alignment accuracy of the quaternion filter algorithm is remarkable, but the convergence rate is slow. To solve this problem, this paper proposes an improved quaternion filter algorithm for faster initial alignment based on the error model of the quaternion filter algorithm. The improved quaternion filter algorithm constructs the K matrix based on the principle of optimal quaternion algorithm, and rebuilds the measurement model by containing acceleration and velocity errors to make the convergence rate faster. A doppler velocity log (DVL) provides the reference velocity for the improved quaternion filter alignment algorithm. In order to demonstrate the performance of the improved quaternion filter algorithm in the field, a turntable experiment and a vehicle test are carried out. The results of the experiments show that the convergence rate of the proposed improved quaternion filter is faster than that of the tradition quaternion filter algorithm. In addition, the improved quaternion filter algorithm also demonstrates advantages in terms of correctness, effectiveness, and practicability.

  1. Automated, feature-based image alignment for high-resolution imaging mass spectrometry of large biological samples

    NARCIS (Netherlands)

    Broersen, A.; Liere, van R.; Altelaar, A.F.M.; Heeren, R.M.A.; McDonnell, L.A.

    2008-01-01

    High-resolution imaging mass spectrometry of large biological samples is the goal of several research groups. In mosaic imaging, the most common method, the large sample is divided into a mosaic of small areas that are then analyzed with high resolution. Here we present an automated alignment

  2. Development and Validation of a Multipoint Based Laser Alignment System for CLIC

    CERN Document Server

    Stern, G; Lackner, F; Mainaud-Durand, H; Piedigrossi, D; Sandomierski, J; Sosin, M; Geiger, A; Guillaume, S

    2013-01-01

    Alignment is one of the major challenges within CLIC study, since all accelerator components have to be aligned with accuracy up to 10 μm over sliding windows of 200 m. So far, the straight line reference concept has been based on stretched wires coupled with Wire Positioning Sensors. This concept should be validated through inter-comparison with an alternative solution. This paper proposes an alternative concept where laser beam acts as straight line reference and optical shutters coupled with cameras visualise the beam. The principle was first validated by a series of tests using low-cost components. Yet, in order to further decrease measurement uncertainty in this validation step, a high-precision automatised micrometric table and reference targets have been added to the setup. The paper presents the results obtained with this new equipment, in terms of measurement precision. In addition, the paper gives an overview of first tests done at long distance (up to 53 m), having emphasis on beam divergence

  3. High accuracy digital aging monitor based on PLL-VCO circuit

    International Nuclear Information System (INIS)

    Zhang Yuejun; Jiang Zhidi; Wang Pengjun; Zhang Xuelong

    2015-01-01

    As the manufacturing process is scaled down to the nanoscale, the aging phenomenon significantly affects the reliability and lifetime of integrated circuits. Consequently, the precise measurement of digital CMOS aging is a key aspect of nanoscale aging tolerant circuit design. This paper proposes a high accuracy digital aging monitor using phase-locked loop and voltage-controlled oscillator (PLL-VCO) circuit. The proposed monitor eliminates the circuit self-aging effect for the characteristic of PLL, whose frequency has no relationship with circuit aging phenomenon. The PLL-VCO monitor is implemented in TSMC low power 65 nm CMOS technology, and its area occupies 303.28 × 298.94 μm 2 . After accelerating aging tests, the experimental results show that PLL-VCO monitor improves accuracy about high temperature by 2.4% and high voltage by 18.7%. (semiconductor integrated circuits)

  4. Aligning Responsible Business Practices

    DEFF Research Database (Denmark)

    Weller, Angeli E.

    2017-01-01

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

  5. 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.

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

    Science.gov (United States)

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

    2015-01-01

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

  7. 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

  8. Identifications of the polar cap boundary and the auroral belt in the high-altitude magnetosphere: a model for field-aligned currents

    International Nuclear Information System (INIS)

    Sugiura, M.

    1975-01-01

    By means of the Ogo 5 Goddard Space Flight Center fluxgate magnetometer data the polar cap boundary is identified in the high-altitude magnetosphere by a sudden transition from a dipolar field to a more taillike configuration. It is inferred that there exists a field-aligned-current layer at the polar cap boundary. In the night side magnetosphere the polar cap boundary is identified as the high-latitude boundary of the plasma sheet. The field-aligned current flows downward to the ionosphere on the morning side of the magnetosphere and upward from the ionosphere on the afternoon side. The basic pattern of the magnetic field variations observed during the satellite's traversal of the auroral belt is presented. Currents flow in opposite directions in the two field-aligned-current layers. The current directions in these layers as observed by Ogo 5 in the high-altitude magnetosphere are the same as those observed at low altitudes by the polar-orbiting Triad satellite (Armstrong and Zmuda, 1973). The magnetic field in the region where the lower-latitude field-aligned-current layer is situated is essentially meridional. A model is presented in which two field-aligned-current systems, one at the polar cap boundary and the other on the low-latitude part of the auroral belt, are main []y connected by ionospheric currents flowing across the auroral belt. The existence of field-aligned currents deduced from the Ogo 5 observations is a permanent feature of the magnetosphere. Intensifications of the field-aligned currents and occurrences of multiple pairs of field-aligned-current layers characterize the disturbed conditions of these regions

  9. A proposal for limited criminal liability in high-accuracy endoscopic sinus surgery.

    Science.gov (United States)

    Voultsos, P; Casini, M; Ricci, G; Tambone, V; Midolo, E; Spagnolo, A G

    2017-02-01

    The aim of the present study is to propose legal reform limiting surgeons' criminal liability in high-accuracy and high-risk surgery such as endoscopic sinus surgery (ESS). The study includes a review of the medical literature, focusing on identifying and examining reasons why ESS carries a very high risk of serious complications related to inaccurate surgical manoeuvers and reviewing British and Italian legal theory and case-law on medical negligence, especially with regard to Italian Law 189/2012 (so called "Balduzzi" Law). It was found that serious complications due to inaccurate surgical manoeuvers may occur in ESS regardless of the skill, experience and prudence/diligence of the surgeon. Subjectivity should be essential to medical negligence, especially regarding high-accuracy surgery. Italian Law 189/2012 represents a good basis for the limitation of criminal liability resulting from inaccurate manoeuvres in high-accuracy surgery such as ESS. It is concluded that ESS surgeons should be relieved of criminal liability in cases of simple/ordinary negligence where guidelines have been observed. © Copyright by Società Italiana di Otorinolaringologia e Chirurgia Cervico-Facciale, Rome, Italy.

  10. AlignMe—a membrane protein sequence alignment web server

    Science.gov (United States)

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

    2014-01-01

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

  11. Aligning Career and Technical Education with High-Wage and High-Demand Occupations in Tennessee. Issues & Answers. REL 2011-No. 111

    Science.gov (United States)

    Mokher, Christine

    2011-01-01

    This study examines the availability of career and technical education program areas in Tennessee high schools, concentrations (a three-or-more credit sequence in a program area) completed by 2007/08 high school graduates, and how these concentrations align with jobs in the labor market. It looks at how these outcomes differ, statewide and by…

  12. High current high accuracy IGBT pulse generator

    International Nuclear Information System (INIS)

    Nesterov, V.V.; Donaldson, A.R.

    1995-05-01

    A solid state pulse generator capable of delivering high current triangular or trapezoidal pulses into an inductive load has been developed at SLAC. Energy stored in a capacitor bank of the pulse generator is switched to the load through a pair of insulated gate bipolar transistors (IGBT). The circuit can then recover the remaining energy and transfer it back to the capacitor bank without reversing the capacitor voltage. A third IGBT device is employed to control the initial charge to the capacitor bank, a command charging technique, and to compensate for pulse to pulse power losses. The rack mounted pulse generator contains a 525 μF capacitor bank. It can deliver 500 A at 900V into inductive loads up to 3 mH. The current amplitude and discharge time are controlled to 0.02% accuracy by a precision controller through the SLAC central computer system. This pulse generator drives a series pair of extraction dipoles

  13. Fully aligned high-spin states in 86Zr

    International Nuclear Information System (INIS)

    Doring, J.; Hohns, G.D.; Sylvan, G.N.

    1995-01-01

    To study multi-quasiparticle excitations and their interplay with collective degrees of freedom at very high spins, a new in-beam investigation of the even-even 86 Zr has been performed via the 58 Ni( 32 S,4p) reaction at 135 MeV using the early implementation of GAMMASPHERE combined with the 47π charged particle detector system MICROBALL. The yrast positive- and negative-parity sequences have been extended up to 30 + and 27 - levels, respectively. Calculations within the configuration-dependent shell-correction method using a cranked Nilsson potential have shown that the highest spins are built from the six g 9 /2 neutrons and at most four protons excited from the p 1/2 , p 3/2 , f 5/2 subshells to the g 9 /2 subshell at a small deformation. The 30 + and 27 - states are the highest possible fully-aligned states based on holes in the N = 3 shell. Higher spins can be built by promotion of one neutron from the g 9 /2 to the g 7 /2 subshell but with a quite high energy cost

  14. Accuracy and precision of 3 intraoral scanners and accuracy of conventional impressions: A novel in vivo analysis method.

    Science.gov (United States)

    Nedelcu, R; Olsson, P; Nyström, I; Rydén, J; Thor, A

    2018-02-01

    To evaluate a novel methodology using industrial scanners as a reference, and assess in vivo accuracy of 3 intraoral scanners (IOS) and conventional impressions. Further, to evaluate IOS precision in vivo. Four reference-bodies were bonded to the buccal surfaces of upper premolars and incisors in five subjects. After three reference-scans, ATOS Core 80 (ATOS), subjects were scanned three times with three IOS systems: 3M True Definition (3M), CEREC Omnicam (OMNI) and Trios 3 (TRIOS). One conventional impression (IMPR) was taken, 3M Impregum Penta Soft, and poured models were digitized with laboratory scanner 3shape D1000 (D1000). Best-fit alignment of reference-bodies and 3D Compare Analysis was performed. Precision of ATOS and D1000 was assessed for quantitative evaluation and comparison. Accuracy of IOS and IMPR were analyzed using ATOS as reference. Precision of IOS was evaluated through intra-system comparison. Precision of ATOS reference scanner (mean 0.6 μm) and D1000 (mean 0.5 μm) was high. Pairwise multiple comparisons of reference-bodies located in different tooth positions displayed a statistically significant difference of accuracy between two scanner-groups: 3M and TRIOS, over OMNI (p value range 0.0001 to 0.0006). IMPR did not show any statistically significant difference to IOS. However, deviations of IOS and IMPR were within a similar magnitude. No statistical difference was found for IOS precision. The methodology can be used for assessing accuracy of IOS and IMPR in vivo in up to five units bilaterally from midline. 3M and TRIOS had a higher accuracy than OMNI. IMPR overlapped both groups. Intraoral scanners can be used as a replacement for conventional impressions when restoring up to ten units without extended edentulous spans. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  15. Energy band alignment of antiferroelectric (Pb,La)(Zr,Sn,Ti)O{sub 3}

    Energy Technology Data Exchange (ETDEWEB)

    Klein, Andreas, E-mail: aklein@surface.tu-darmstadt.de [Technische Universität Darmstadt, Institute of Materials Science, Surface Science Division, Jovanka-Bontschits-Straße 2, 64287 Darmstadt (Germany); Lohaus, Christian [Technische Universität Darmstadt, Institute of Materials Science, Surface Science Division, Jovanka-Bontschits-Straße 2, 64287 Darmstadt (Germany); Reiser, Patrick [Technische Universität Darmstadt, Institute of Materials Science, Surface Science Division, Jovanka-Bontschits-Straße 2, 64287 Darmstadt (Germany); InnovationLab GmbH, Speyerer Straße 4, 69115 Heidelberg (Germany); Dimesso, Lucangelo [Technische Universität Darmstadt, Institute of Materials Science, Surface Science Division, Jovanka-Bontschits-Straße 2, 64287 Darmstadt (Germany); Wang, Xiucai; Yang, Tongqing [Tongji University, Key Laboratory of Advanced Civil Engineering Materials (Ministry of Education), Functional Materials Research Laboratory, College of Materials Science and Engineering, Cao’an Road 4800, Shanghai 201804 (China)

    2017-06-15

    Highlights: • Energy band alignment of antiferroelectric PLZST studied by XPS. • A deconvolution procedure is applied to study band alignment of insulating materials. • Contribution of Pb 6s orbitals leads to higher valence band maximum. • Ferroelectric polarization does not contribute to valence band maximum energy. • The variation of Schottky barrier heights indicates no Fermi level pinning in PLZST. - Abstract: The energy band alignment of antiferroelectric (Pb,La)(Zr,Sn,Ti)O{sub 3} is studied with photoelectron spectroscopy using interfaces with high work function RuO{sub 2} and low work function Sn-doped In{sub 2}O{sub 3} (ITO). It is demonstrated how spectral deconvolution can be used to determine absolute Schottky barrier heights for insulating materials with a high accuracy. Using this approach it is found that the valence band maximum energy of (Pb,La)(Zr,Sn,Ti)O{sub 3} is found to be comparable to that of Pb- and Bi-containing ferroelectric materials, which is ∼1 eV higher than that of BaTiO{sub 3}. The results provide additional evidence for the occupation of the 6s orbitals as origin of the higher valence band maximum, which is directly related to the electrical properties of such compounds. The results also verify that the energy band alignment determined by photoelectron spectroscopy of as-deposited electrodes is not influenced by polarisation. The electronic structure of (Pb,La)(Zr,Sn,Ti)O{sub 3} should enable doping of the material without strongly modifying its insulating properties, which is crucial for high energy density capacitors. Moreover, the position of the energy bands should result in a great freedom of selecting electrode materials in terms of avoiding charge injection.

  16. High-accuracy determination for optical indicatrix rotation in ferroelectric DTGS

    OpenAIRE

    O.S.Kushnir; O.A.Bevz; O.G.Vlokh

    2000-01-01

    Optical indicatrix rotation in deuterated ferroelectric triglycine sulphate is studied with the high-accuracy null-polarimetric technique. The behaviour of the effect in ferroelectric phase is referred to quadratic spontaneous electrooptics.

  17. Mathematics Learning Assisted Geogebra using Technologically Aligned Classroom (TAC) to Improve Communication Skills of Vocasional High School Student

    Science.gov (United States)

    Yuliardi, R.; Nurjanah

    2017-09-01

    The purpose of this study to analyze mathematical communication skill’s student to resolve geometry transformation problems through computer Assisted Geogebra using Technologically Aligned Classroom (TAC). The population in this study were students from one of Vocasional High School Student in West Java. Selection of sample by purposed random sampling, the experimental class is taught Technologically Aligned Classroom (TAC) with GeoGebra, while the control class is taught by conventional learning. This study was quasi-experimental with pretest and posttest control group design. Based on the results; (1) The enhancement of student mathematical communication skills through TAC was higher than the conventional learning; (2) based on gender, there were no differences of mathematical communication skilss student who exposed with TAC and conventional learning; (3) based on KAM test, there was significant enhancement of students’ communication skills among ability of high, middle, and low KAM. The differences occur between high KAM and middle KAM, and also between high KAM and low KAM. Based on this result, mathematics learning Assisted Geogebra using Technologically Aligned Classroom (TAC) can be applied in the process of Mathematics Learning in Vocasional High School.

  18. Achieving High Accuracy in Calculations of NMR Parameters

    DEFF Research Database (Denmark)

    Faber, Rasmus

    quantum chemical methods have been developed, the calculation of NMR parameters with quantitative accuracy is far from trivial. In this thesis I address some of the issues that makes accurate calculation of NMR parameters so challenging, with the main focus on SSCCs. High accuracy quantum chemical......, but no programs were available to perform such calculations. As part of this thesis the CFOUR program has therefore been extended to allow the calculation of SSCCs using the CC3 method. CC3 calculations of SSCCs have then been performed for several molecules, including some difficult cases. These results show...... vibrations must be included. The calculation of vibrational corrections to NMR parameters has been reviewed as part of this thesis. A study of the basis set convergence of vibrational corrections to nuclear shielding constants has also been performed. The basis set error in vibrational correction...

  19. Computer navigation experience in hip resurfacing improves femoral component alignment using a conventional jig

    Directory of Open Access Journals (Sweden)

    Zachary Morison

    2013-01-01

    Full Text Available Background:The use of computer navigation has been shown to improve the accuracy of femoral component placement compared to conventional instrumentation in hip resurfacing. Whether exposure to computer navigation improves accuracy when the procedure is subsequently performed with conventional instrumentation without navigation has not been explored. We examined whether femoral component alignment utilizing a conventional jig improves following experience with the use of imageless computer navigation for hip resurfacing. Materials and Methods:Between December 2004 and December 2008, 213 consecutive hip resurfacings were performed by a single surgeon. The first 17 (Cohort 1 and the last 9 (Cohort 2 hip resurfacings were performed using a conventional guidewire alignment jig. In 187 cases, the femoral component was implanted using the imageless computer navigation. Cohorts 1 and 2 were compared for femoral component alignment accuracy. Results:All components in Cohort 2 achieved the position determined by the preoperative plan. The mean deviation of the stem-shaft angle (SSA from the preoperatively planned target position was 2.2° in Cohort 2 and 5.6° in Cohort 1 ( P = 0.01. Four implants in Cohort 1 were positioned at least 10° varus compared to the target SSA position and another four were retroverted. Conclusions: Femoral component placement utilizing conventional instrumentation may be more accurate following experience using imageless computer navigation.

  20. Spatiotemporal alignment of in utero BOLD-MRI series.

    Science.gov (United States)

    Turk, Esra Abaci; Luo, Jie; Gagoski, Borjan; Pascau, Javier; Bibbo, Carolina; Robinson, Julian N; Grant, P Ellen; Adalsteinsson, Elfar; Golland, Polina; Malpica, Norberto

    2017-08-01

    To present a method for spatiotemporal alignment of in-utero magnetic resonance imaging (MRI) time series acquired during maternal hyperoxia for enabling improved quantitative tracking of blood oxygen level-dependent (BOLD) signal changes that characterize oxygen transport through the placenta to fetal organs. The proposed pipeline for spatiotemporal alignment of images acquired with a single-shot gradient echo echo-planar imaging includes 1) signal nonuniformity correction, 2) intravolume motion correction based on nonrigid registration, 3) correction of motion and nonrigid deformations across volumes, and 4) detection of the outlier volumes to be discarded from subsequent analysis. BOLD MRI time series collected from 10 pregnant women during 3T scans were analyzed using this pipeline. To assess pipeline performance, signal fluctuations between consecutive timepoints were examined. In addition, volume overlap and distance between manual region of interest (ROI) delineations in a subset of frames and the delineations obtained through propagation of the ROIs from the reference frame were used to quantify alignment accuracy. A previously demonstrated rigid registration approach was used for comparison. The proposed pipeline improved anatomical alignment of placenta and fetal organs over the state-of-the-art rigid motion correction methods. In particular, unexpected temporal signal fluctuations during the first normoxia period were significantly decreased (P quantitative studies of placental function by improving spatiotemporal alignment across placenta and fetal organs. 1 Technical Efficacy: Stage 1 J. MAGN. RESON. IMAGING 2017;46:403-412. © 2017 International Society for Magnetic Resonance in Medicine.

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

    Energy Technology Data Exchange (ETDEWEB)

    Bushnell, Brian

    2014-03-17

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

  2. A technique for aligning sextupole systems using beam optics

    International Nuclear Information System (INIS)

    Chao, Yu-Chiu.

    1992-03-01

    A technique for beam based alignment of sextupole system is developed exploiting the enhancement effect of orbit differences by the sextupoles. This technique can in principle be applied to sextupole or sextupole strings with controlled orbit pattern and BPM configurations. This paper will discuss the theoretical basis, special optimization considerations and expected accuracy. Application to the SLC final focus is also discussed

  3. Modeling of Geometric Error in Linear Guide Way to Improved the vertical three-axis CNC Milling machine’s accuracy

    Science.gov (United States)

    Kwintarini, Widiyanti; Wibowo, Agung; Arthaya, Bagus M.; Yuwana Martawirya, Yatna

    2018-03-01

    The purpose of this study was to improve the accuracy of three-axis CNC Milling Vertical engines with a general approach by using mathematical modeling methods of machine tool geometric errors. The inaccuracy of CNC machines can be caused by geometric errors that are an important factor during the manufacturing process and during the assembly phase, and are factors for being able to build machines with high-accuracy. To improve the accuracy of the three-axis vertical milling machine, by knowing geometric errors and identifying the error position parameters in the machine tool by arranging the mathematical modeling. The geometric error in the machine tool consists of twenty-one error parameters consisting of nine linear error parameters, nine angle error parameters and three perpendicular error parameters. The mathematical modeling approach of geometric error with the calculated alignment error and angle error in the supporting components of the machine motion is linear guide way and linear motion. The purpose of using this mathematical modeling approach is the identification of geometric errors that can be helpful as reference during the design, assembly and maintenance stages to improve the accuracy of CNC machines. Mathematically modeling geometric errors in CNC machine tools can illustrate the relationship between alignment error, position and angle on a linear guide way of three-axis vertical milling machines.

  4. A prototype distributed object-oriented architecture for image-based automatic laser alignment

    International Nuclear Information System (INIS)

    Stout, E.A.; Kamm, V.J.M.; Spann, J.M.; Van Arsdall, P.J.

    1996-01-01

    Designing a computer control system for the National Ignition Facility (NIF) is a complex undertaking because of the system's large size and its distributed nature. The controls team is addressing that complexity by adopting the object-oriented programming paradigm, designing reusable software frameworks, and using the Common Object Request Broker Architecture (CORBA) for distribution. A prototype system for image-based automatic laser alignment has been developed to evaluate and gain experience with CORBA and OOP in a small distributed system. The prototype is also important in evaluating alignment concepts, image processing techniques, speed and accuracy of automatic alignment objectives for the NIF, and control hardware for aligment devices. The prototype system has met its inital objectives and provides a basis for continued development

  5. Performance analysis for W-band antenna alignment using accurate mechanical beam steering

    DEFF Research Database (Denmark)

    Morales Vicente, Alvaro; Rodríguez Páez, Juan Sebastián; Gallardo, Omar

    2017-01-01

    This article presents a study of antenna alignment impact on bit error rate for a wireless link between two directive W-band horn antennas where one of them is mechanically steered by a Stewart platform. Such a technique is applied to find the optimal alignment between transmitter and receiver...... with an accuracy of 18 both in azimuth and elevation angles. The maximum degree of misalignment which can be tolerated is also reported for different values of optical power in the generation of W-band signals by photonic up-conversion. (C) 2017 Wiley Periodicals, Inc....

  6. Large-scale synthesis of high-purity well-aligned carbon nanotubes using pyrolysis of iron(II) phthalocyanine and acetylene

    Science.gov (United States)

    Liu, B. C.; Lee, T. J.; Lee, S. H.; Park, C. Y.; Lee, C. J.

    2003-08-01

    Well-aligned carbon nanotubes (CNTs) with high purity have been produced by pyrolysis of iron(II) phthalocyanine and acetylene at 800 °C. The synthesized CNTs have a length of 75 μm and diameters ranging from 20 to 60 nm. The CNTs have a bamboo-like structure and exhibit good crystallinity of graphite sheets. The growth rate of the CNTs was rapidly increased with adding C 2H 2. Our results demonstrate that the proposed growth method is suitable to large-scale synthesis of high-purity well-aligned CNTs on various substrates.

  7. Dense Vertically Aligned Copper Nanowire Composites as High Performance Thermal Interface Materials.

    Science.gov (United States)

    Barako, Michael T; Isaacson, Scott G; Lian, Feifei; Pop, Eric; Dauskardt, Reinhold H; Goodson, Kenneth E; Tice, Jesse

    2017-12-06

    Thermal interface materials (TIMs) are essential for managing heat in modern electronics, and nanocomposite TIMs can offer critical improvements. Here, we demonstrate thermally conductive, mechanically compliant TIMs based on dense, vertically aligned copper nanowires (CuNWs) embedded into polymer matrices. We evaluate the thermal and mechanical characteristics of 20-25% dense CuNW arrays with and without polydimethylsiloxane infiltration. The thermal resistance achieved is below 5 mm 2 K W -1 , over an order of magnitude lower than commercial heat sink compounds. Nanoindentation reveals that the nonlinear deformation mechanics of this TIM are influenced by both the CuNW morphology and the polymer matrix. We also implement a flip-chip bonding protocol to directly attach CuNW composites to copper surfaces, as required in many thermal architectures. Thus, we demonstrate a rational design strategy for nanocomposite TIMs that simultaneously retain the high thermal conductivity of aligned CuNWs and the mechanical compliance of a polymer.

  8. 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

  9. 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...

  10. 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

  11. Improving the Accuracy of NMR Structures of Large Proteins Using Pseudocontact Shifts as Long-Range Restraints

    Energy Technology Data Exchange (ETDEWEB)

    Gaponenko, Vadim [National Cancer Institute, Structural Biophysics Laboratory (United States); Sarma, Siddhartha P. [Indian Institute of Science, Molecular Biophysics Unit (India); Altieri, Amanda S. [National Cancer Institute, Structural Biophysics Laboratory (United States); Horita, David A. [Wake Forest University School of Medicine, Department of Biochemistry (United States); Li, Jess; Byrd, R. Andrew [National Cancer Institute, Structural Biophysics Laboratory (United States)], E-mail: rabyrd@ncifcrf.gov

    2004-03-15

    We demonstrate improved accuracy in protein structure determination for large ({>=}30 kDa), deuterated proteins (e.g. STAT4{sub NT}) via the combination of pseudocontact shifts for amide and methyl protons with the available NOEs in methyl-protonated proteins. The improved accuracy is cross validated by Q-factors determined from residual dipolar couplings measured as a result of magnetic susceptibility alignment. The paramagnet is introduced via binding to thiol-reactive EDTA, and multiple sites can be serially engineered to obtain data from alternative orientations of the paramagnetic anisotropic susceptibility tensor. The technique is advantageous for systems where the target protein has strong interactions with known alignment media.

  12. High-Accuracy Spherical Near-Field Measurements for Satellite Antenna Testing

    DEFF Research Database (Denmark)

    Breinbjerg, Olav

    2017-01-01

    The spherical near-field antenna measurement technique is unique in combining several distinct advantages and it generally constitutes the most accurate technique for experimental characterization of radiation from antennas. From the outset in 1970, spherical near-field antenna measurements have...... matured into a well-established technique that is widely used for testing antennas for many wireless applications. In particular, for high-accuracy applications, such as remote sensing satellite missions in ESA's Earth Observation Programme with uncertainty requirements at the level of 0.05dB - 0.10d......B, the spherical near-field antenna measurement technique is generally superior. This paper addresses the means to achieving high measurement accuracy; these include the measurement technique per se, its implementation in terms of proper measurement procedures, the use of uncertainty estimates, as well as facility...

  13. Precision lens assembly with alignment turning system

    Science.gov (United States)

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

    2017-10-01

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

  14. 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...

  15. 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.

  16. Aligned, isotropic and patterned carbon nanotube substrates that control the growth and alignment of Chinese hamster ovary cells

    Energy Technology Data Exchange (ETDEWEB)

    Abdullah, Che Azurahanim Che; Asanithi, Piyapong; Brunner, Eric W; Jurewicz, Izabela; Bo, Chiara; Sear, Richard P; Dalton, Alan B [Department of Physics and Surrey Materials Institute, University of Surrey, Guildford, Surrey GU2 7XH (United Kingdom); Azad, Chihye Lewis; Ovalle-Robles, Raquel; Fang Shaoli; Lima, Marcio D; Lepro, Xavier; Collins, Steve; Baughman, Ray H, E-mail: r.sear@surrey.ac.uk [Alan G MacDiarmid NanoTech Institute, The University of Texas at Dallas, Richardson, TX 75080-3021 (United States)

    2011-05-20

    Here we culture Chinese hamster ovary cells on isotropic, aligned and patterned substrates based on multiwall carbon nanotubes. The nanotubes provide the substrate with nanoscale topography. The cells adhere to and grow on all substrates, and on the aligned substrate, the cells align strongly with the axis of the bundles of the multiwall nanotubes. This control over cell alignment is required for tissue engineering; almost all tissues consist of oriented cells. The aligned substrates are made using straightforward physical chemistry techniques from forests of multiwall nanotubes; no lithography is required to make inexpensive large-scale substrates with highly aligned nanoscale grooves. Interestingly, although the cells strongly align with the nanoscale grooves, only a few also elongate along this axis: alignment of the cells does not require a pronounced change in morphology of the cell. We also pattern the nanotube bundles over length scales comparable to the cell size and show that the cells follow this pattern.

  17. Erwartete Messung der Z Produktionsrate mit dem CMS Detektor und Simulation des Tracker Laser Alignment Systems

    CERN Document Server

    Thomas, Maarten

    2009-01-01

    The Large Hadron Collider is a two-ring, superconducting accelerator and collider which can provide both proton and heavy-ion beams. First collisions are foreseen for 2009. The Compact Muon System (CMS) detector will measure the particles created in the hadron collisions and can confirm the Standard Model by establishing the existence of the Higgs boson, but also search for new phenomena. In order to provide a robust and precise track reconstruction, which can already be used in the High-Level Trigger systems, the positions of the silicon sensors in the CMS tracker have to been known with an accuracy of O(100µm). Therefore the CMS tracker has been equipped with a dedicated alignment system. The Laser Alignment System (LAS) aligns the tracker subdetectors with respect to each other and can also monitor the stability of the sensor positions during data taking. This study describes the implementation of a realistic simulation of the LAS in the CMS software framework (CMSSW) as well as the analysis of the first ...

  18. High Accuracy Piezoelectric Kinemometer; Cinemometro piezoelectrico de alta exactitud (VUAE)

    Energy Technology Data Exchange (ETDEWEB)

    Jimenez Martinez, F. J.; Frutos, J. de; Pastor, C.; Vazquez Rodriguez, M.

    2012-07-01

    We have developed a portable computerized and low consumption, our system is called High Accuracy Piezoelectric Kinemometer measurement, herein VUAE. By the high accuracy obtained by VUAE it make able to use the VUAE to obtain references measurements of system for measuring Speeds in Vehicles. Therefore VUAE could be used how reference equipment to estimate the error of installed kinemometers. The VUAE was created with n (n=2) pairs of ultrasonic transmitter-receiver, herein E-Rult. The transmitters used in the n couples E-Rult generate n ultrasonic barriers and receivers receive the echoes when the vehicle crosses the barriers. Digital processing of the echoes signals let us to obtain acceptable signals. Later, by mean of cross correlation technics is possible make a highly exact estimation of speed of the vehicle. The log of the moments of interception and the distance between each of the n ultrasounds allows for a highly exact estimation of speed of the vehicle. VUAE speed measurements were compared to a speed reference system based on piezoelectric cables. (Author) 11 refs.

  19. 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....

  20. Self-centering fiber alignment structures for high-precision field installable single-mode fiber connectors

    Science.gov (United States)

    Van Erps, Jürgen; Ebraert, Evert; Gao, Fei; Vervaeke, Michael; Berghmans, Francis; Beri, Stefano; Watté, Jan; Thienpont, Hugo

    2014-05-01

    There is a steady increase in the demand for internet bandwidth, primarily driven by cloud services and high-definition video streaming. Europe's Digital Agenda states the ambitious objective that by 2020 all Europeans should have access to internet at speeds of 30Mb/s or above, with 50% or more of households subscribing to connections of 100Mb/s. Today however, internet access in Europe is mainly based on the first generation of broadband, meaning internet accessed over legacy telephone copper and TV cable networks. In recent years, Fiber-To-The-Home (FTTH) networks have been adopted as a replacement of traditional electrical connections for the `last mile' transmission of information at bandwidths over 1Gb/s. However, FTTH penetration is still very low (economies. The main reason for this is the high deployment cost of FTTH networks. Indeed, the success and adoption of optical access networks critically depend on the quality and reliability of connections between optical fibers. In particular a further reduction of insertion loss of field- installable connectors must be achieved without a significant increase in component cost. This requires precise alignment of fibers that can differ in terms of ellipticity, eccentricity or diameter and seems hardly achievable using today's widespread ferrule-based alignment systems. In this paper, we present a field-installable connector based on deflectable/compressible spring structures, providing a self-centering functionality for the fiber. This way, it can accommodate for possible fiber cladding diameter variations (the tolerance on the cladding diameter of G.652 fiber is typically +/-0.7μm). The mechanical properties of the cantilever are derived through an analytical approximation and a mathematical model of the spring constant, and finite element-based simulations are carried out to find the maximum first principal stress as well as the stress distribution distribution in the fiber alignment structure. Elastic

  1. Alignment at the ESRF

    International Nuclear Information System (INIS)

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

    1999-01-01

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

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

    International Nuclear Information System (INIS)

    Chen Kang; Tjandra, Nico

    2007-01-01

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

  3. Growth of high-aspect ratio horizontally-aligned ZnO nanowire arrays.

    Science.gov (United States)

    Soman, Pranav; Darnell, Max; Feldman, Marc D; Chen, Shaochen

    2011-08-01

    A method of fabricating horizontally-aligned zinc-oxide (ZnO) nanowire (NW) arrays with full control over the width and length is demonstrated. SEM images reveal the hexagonal structure typical of zinc oxide NWs. Arrays of high-aspect ratio horizontal ZnO NWs are fabricated by making use of the lateral overgrowth from dot patterns created by electron beam lithography (EBL). An array of patterned wires are lifted off and transferred to a flexible PDMS substrate with possible applications in several key nanotechnology areas.

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

    DEFF Research Database (Denmark)

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

    2010-01-01

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

  5. Accuracy of five intraoral scanners compared to indirect digitalization.

    Science.gov (United States)

    Güth, Jan-Frederik; Runkel, Cornelius; Beuer, Florian; Stimmelmayr, Michael; Edelhoff, Daniel; Keul, Christine

    2017-06-01

    Direct and indirect digitalization offer two options for computer-aided design (CAD)/ computer-aided manufacturing (CAM)-generated restorations. The aim of this study was to evaluate the accuracy of different intraoral scanners and compare them to the process of indirect digitalization. A titanium testing model was directly digitized 12 times with each intraoral scanner: (1) CS 3500 (CS), (2) Zfx Intrascan (ZFX), (3) CEREC AC Bluecam (BLU), (4) CEREC AC Omnicam (OC) and (5) True Definition (TD). As control, 12 polyether impressions were taken and the referring plaster casts were digitized indirectly with the D-810 laboratory scanner (CON). The accuracy (trueness/precision) of the datasets was evaluated by an analysing software (Geomagic Qualify 12.1) using a "best fit alignment" of the datasets with a highly accurate reference dataset of the testing model, received from industrial computed tomography. Direct digitalization using the TD showed the significant highest overall "trueness", followed by CS. Both performed better than CON. BLU, ZFX and OC showed higher differences from the reference dataset than CON. Regarding the overall "precision", the CS 3500 intraoral scanner and the True Definition showed the best performance. CON, BLU and OC resulted in significantly higher precision than ZFX did. Within the limitations of this in vitro study, the accuracy of the ascertained datasets was dependent on the scanning system. The direct digitalization was not superior to indirect digitalization for all tested systems. Regarding the accuracy, all tested intraoral scanning technologies seem to be able to reproduce a single quadrant within clinical acceptable accuracy. However, differences were detected between the tested systems.

  6. Iridium catalyzed growth of vertically aligned CNTs by APCVD

    International Nuclear Information System (INIS)

    Sahoo, R.K.; Jacob, C.

    2014-01-01

    Highlights: • Growth of uniform-diameter vertically-aligned multi-walled CNTs by APCVD. • Use of high melting point low carbon solubility iridium nanoparticles as catalyst. • Optimization of growth time for uniform sized, uniformly aligned CNTs. • Growth model for the various features in the vertically aligned CNTs is proposed. - Abstract: Vertically aligned carbon nanotubes (VA-CNTs) have been synthesized using high temperature catalyst nanoparticles of iridium. The catalyst layer was prepared by DC sputtering. Particle density, circularity and average particle size of the catalyst were analyzed using field emission scanning electron microscopy. The alignment, morphology and the length of the as-grown CNTs were analyzed using field-emission scanning electron microscopy. High resolution transmission electron microscopy was carried out to observe the layers of graphitic stacking which form the carbon nanotubes. Micro Raman measurement was used for the analysis of the graphitic crystallinity of the as-grown carbon nano structures. Effects of growth time variation on growth morphology and alignment have been studied. The alignment has been explained on the basis of the crowding effect of the neighboring nanoparticles

  7. Iridium catalyzed growth of vertically aligned CNTs by APCVD

    Energy Technology Data Exchange (ETDEWEB)

    Sahoo, R.K.; Jacob, C., E-mail: cxj14_holiday@yahoo.com

    2014-07-01

    Highlights: • Growth of uniform-diameter vertically-aligned multi-walled CNTs by APCVD. • Use of high melting point low carbon solubility iridium nanoparticles as catalyst. • Optimization of growth time for uniform sized, uniformly aligned CNTs. • Growth model for the various features in the vertically aligned CNTs is proposed. - Abstract: Vertically aligned carbon nanotubes (VA-CNTs) have been synthesized using high temperature catalyst nanoparticles of iridium. The catalyst layer was prepared by DC sputtering. Particle density, circularity and average particle size of the catalyst were analyzed using field emission scanning electron microscopy. The alignment, morphology and the length of the as-grown CNTs were analyzed using field-emission scanning electron microscopy. High resolution transmission electron microscopy was carried out to observe the layers of graphitic stacking which form the carbon nanotubes. Micro Raman measurement was used for the analysis of the graphitic crystallinity of the as-grown carbon nano structures. Effects of growth time variation on growth morphology and alignment have been studied. The alignment has been explained on the basis of the crowding effect of the neighboring nanoparticles.

  8. Aligning Career and Technical Education with High-Wage and High-Demand Occupations in Tennessee. Summary. Issues & Answers. REL 2011-No. 111

    Science.gov (United States)

    Mokher, Christine

    2011-01-01

    This study examines the availability of career and technical education program areas in Tennessee high schools, concentrations (a three-or-more credit sequence in a program area) completed by 2007/08 high school graduates, and how these concentrations align with jobs in the labor market. It looks at how these outcomes differ, statewide and by…

  9. 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/.

  10. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Penzel, Florian Olivier

    2015-07-01

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

  12. 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, ...

  13. Why is a high accuracy needed in dosimetry

    International Nuclear Information System (INIS)

    Lanzl, L.H.

    1976-01-01

    Dose and exposure intercomparisons on a national or international basis have become an important component of quality assurance in the practice of good radiotherapy. A high degree of accuracy of γ and x radiation dosimetry is essential in our international society, where medical information is so readily exchanged and used. The value of accurate dosimetry lies mainly in the avoidance of complications in normal tissue and an optimal degree of tumor control

  14. 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

  15. Aligning with New Digital Strategy

    DEFF Research Database (Denmark)

    Yeow, Adrian; Soh, Christina; Hansen, Rina

    2018-01-01

    Prior IS research has not fully addressed the aligning process in the highly dynamic context of digital strategy. To address this gap, we conduct a longitudinal analysis of a B2B company's journey to enact its B2C digital strategy, using the dynamic capabilities approach. We found...... that as an organization shifts towards a digital strategy, misalignments between the emergent strategy and resources give rise to tension. Our study resulted in the development of an aligning process model that is comprised of three phases (exploratory, building, and extending) and generalizable organizational aligning...... actions that form the organization's sensing, seizing, and transforming capacities. These aligning actions iteratively reconfigured organizational resources and refined strategy in order to respond to both changes in the environment and internal tensions. We also recognized that there are challenges...

  16. Note: A simple image processing based fiducial auto-alignment method for sample registration.

    Science.gov (United States)

    Robertson, Wesley D; Porto, Lucas R; Ip, Candice J X; Nantel, Megan K T; Tellkamp, Friedjof; Lu, Yinfei; Miller, R J Dwayne

    2015-08-01

    A simple method for the location and auto-alignment of sample fiducials for sample registration using widely available MATLAB/LabVIEW software is demonstrated. The method is robust, easily implemented, and applicable to a wide variety of experiment types for improved reproducibility and increased setup speed. The software uses image processing to locate and measure the diameter and center point of circular fiducials for distance self-calibration and iterative alignment and can be used with most imaging systems. The method is demonstrated to be fast and reliable in locating and aligning sample fiducials, provided here by a nanofabricated array, with accuracy within the optical resolution of the imaging system. The software was further demonstrated to register, load, and sample the dynamically wetted array.

  17. A novel micromachined shadow mask system with self-alignment and gap control capability

    International Nuclear Information System (INIS)

    Hong, Jung Moo; Zou Jun

    2008-01-01

    We present a novel micromachined shadow mask system, which is capable of accurate self-alignment and mask-substrate gap control. The shadow mask system consists of a silicon shadow mask and a silicon carrier wafer with pyramidal cavities fabricated with bulk micromachining. Self-alignment and gap control of the shadow mask and the fabrication substrate can readily be achieved by using matching pairs of pyramidal cavities and steel spheres placed between. The layer-to-layer alignment accuracy of the new shadow mask system has been experimentally characterized and verified using both optical and atomic force microscopic measurements. As an application of this new shadow mask system, an organic thin-film transistor (OTFT) using pentacene as the semiconductor layer has been successfully fabricated and tested

  18. 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 ...

  19. An Alignment of J-PARC Linac

    CERN Document Server

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

    2005-01-01

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

  20. The use of an intermediate wavelength laser for alignment to inertial confinement fusion targets

    International Nuclear Information System (INIS)

    English, R.E. Jr.; Seppala, L.G.; Vann, C.S.; Bliss, E.S.

    1995-01-01

    The conceptual design of the National Ignition Facility (NIF) 192 beam laser incorporates a low-power alignment beam injected in the pinhole plane of the final spatial filter with a wave length intermediate between the 1053 mn laser output and the 351 mn frequency-converted beam that illuminates the target Choosing the specific wavelength for which the spatial filter plane is reimaged in the same target chamber plane as the frequency-converted main laser pulse, achieves optimum accuracy without the need for additional means to insure precise overlap between the two beams. Insertion of the alignment beam after the last laser amplifier also allows alignment to the target while the amplifiers are still cooling from a previous shot

  1. Subfamily logos: visualization of sequence deviations at alignment positions with high information content

    Directory of Open Access Journals (Sweden)

    Beitz Eric

    2006-06-01

    Full Text Available Abstract Background Recognition of relevant sequence deviations can be valuable for elucidating functional differences between protein subfamilies. Interesting residues at highly conserved positions can then be mutated and experimentally analyzed. However, identification of such sites is tedious because automated approaches are scarce. Results Subfamily logos visualize subfamily-specific sequence deviations. The display is similar to classical sequence logos but extends into the negative range. Positive, upright characters correspond to residues which are characteristic for the subfamily, negative, upside-down characters to residues typical for the remaining sequences. The symbol height is adjusted to the information content of the alignment position. Residues which are conserved throughout do not appear. Conclusion Subfamily logos provide an intuitive display of relevant sequence deviations. The method has proven to be valid using a set of 135 aligned aquaporin sequences in which established subfamily-specific positions were readily identified by the algorithm.

  2. Innovative Fiber-Optic Gyroscopes (FOGs) for High Accuracy Space Applications, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — This project aims to develop a compact, highly innovative Inertial Reference/Measurement Unit (IRU/IMU) that pushes the state-of-the-art in high accuracy performance...

  3. High accuracy acoustic relative humidity measurement in duct flow with air.

    Science.gov (United States)

    van Schaik, Wilhelm; Grooten, Mart; Wernaart, Twan; van der Geld, Cees

    2010-01-01

    An acoustic relative humidity sensor for air-steam mixtures in duct flow is designed and tested. Theory, construction, calibration, considerations on dynamic response and results are presented. The measurement device is capable of measuring line averaged values of gas velocity, temperature and relative humidity (RH) instantaneously, by applying two ultrasonic transducers and an array of four temperature sensors. Measurement ranges are: gas velocity of 0-12 m/s with an error of ± 0.13 m/s, temperature 0-100 °C with an error of ± 0.07 °C and relative humidity 0-100% with accuracy better than 2 % RH above 50 °C. Main advantage over conventional humidity sensors is the high sensitivity at high RH at temperatures exceeding 50 °C, with accuracy increasing with increasing temperature. The sensors are non-intrusive and resist highly humid environments.

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

    Energy Technology Data Exchange (ETDEWEB)

    Brudno, Michael; Poliakov, Alexander; Salamov, Asaf; Cooper, Gregory M.; Sidow, Arend; Rubin, Edward M.; Solovyev, Victor; Batzoglou, Serafim; Dubchak, Inna

    2004-07-04

    We have built a whole genome multiple alignment of the three currently available mammalian genomes using a fully automated pipeline which combines the local/global approach of the Berkeley Genome Pipeline and the LAGAN program. The strategy is based on progressive alignment, and consists of two main steps: (1) alignment of the mouse and rat genomes; and (2) alignment of human to either the mouse-rat alignments from step 1, or the remaining unaligned mouse and rat sequences. The resulting alignments demonstrate high sensitivity, with 87% of all human gene-coding areas aligned in both mouse and rat. The specificity is also high: <7% of the rat contigs are aligned to multiple places in human and 97% of all alignments with human sequence > 100kb agree with a three-way synteny map built independently using predicted exons in the three genomes. At the nucleotide level <1% of the rat nucleotides are mapped to multiple places in the human sequence in the alignment; and 96.5% of human nucleotides within all alignments agree with the synteny map. The alignments are publicly available online, with visualization through the novel Multi-VISTA browser that we also present.

  5. Two high accuracy digital integrators for Rogowski current transducers

    Science.gov (United States)

    Luo, Pan-dian; Li, Hong-bin; Li, Zhen-hua

    2014-01-01

    The Rogowski current transducers have been widely used in AC current measurement, but their accuracy is mainly subject to the analog integrators, which have typical problems such as poor long-term stability and being susceptible to environmental conditions. The digital integrators can be another choice, but they cannot obtain a stable and accurate output for the reason that the DC component in original signal can be accumulated, which will lead to output DC drift. Unknown initial conditions can also result in integral output DC offset. This paper proposes two improved digital integrators used in Rogowski current transducers instead of traditional analog integrators for high measuring accuracy. A proportional-integral-derivative (PID) feedback controller and an attenuation coefficient have been applied in improving the Al-Alaoui integrator to change its DC response and get an ideal frequency response. For the special design in the field of digital signal processing, the improved digital integrators have better performance than analog integrators. Simulation models are built for the purpose of verification and comparison. The experiments prove that the designed integrators can achieve higher accuracy than analog integrators in steady-state response, transient-state response, and temperature changing condition.

  6. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.

    Science.gov (United States)

    Treangen, Todd J; Ondov, Brian D; Koren, Sergey; Phillippy, Adam M

    2014-01-01

    Whole-genome sequences are now available for many microbial species and clades, however existing whole-genome alignment methods are limited in their ability to perform sequence comparisons of multiple sequences simultaneously. Here we present the Harvest suite of core-genome alignment and visualization tools for the rapid and simultaneous analysis of thousands of intraspecific microbial strains. Harvest includes Parsnp, a fast core-genome multi-aligner, and Gingr, a dynamic visual platform. Together they provide interactive core-genome alignments, variant calls, recombination detection, and phylogenetic trees. Using simulated and real data we demonstrate that our approach exhibits unrivaled speed while maintaining the accuracy of existing methods. The Harvest suite is open-source and freely available from: http://github.com/marbl/harvest.

  7. Measuring the distance between multiple sequence alignments.

    Science.gov (United States)

    Blackburne, Benjamin P; Whelan, Simon

    2012-02-15

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

  8. Aligned carbon nanotubes patterned photolithographically by silver

    Science.gov (United States)

    Huang, Shaoming; Mau, Albert H. W.

    2003-02-01

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

  9. Electron ray tracing with high accuracy

    International Nuclear Information System (INIS)

    Saito, K.; Okubo, T.; Takamoto, K.; Uno, Y.; Kondo, M.

    1986-01-01

    An electron ray tracing program is developed to investigate the overall geometrical and chromatic aberrations in electron optical systems. The program also computes aberrations due to manufacturing errors in lenses and deflectors. Computation accuracy is improved by (1) calculating electrostatic and magnetic scalar potentials using the finite element method with third-order isoparametric elements, and (2) solving the modified ray equation which the aberrations satisfy. Computation accuracy of 4 nm is achieved for calculating optical properties of the system with an electrostatic lens

  10. High accuracy 3D electromagnetic finite element analysis

    International Nuclear Information System (INIS)

    Nelson, Eric M.

    1997-01-01

    A high accuracy 3D electromagnetic finite element field solver employing quadratic hexahedral elements and quadratic mixed-order one-form basis functions will be described. The solver is based on an object-oriented C++ class library. Test cases demonstrate that frequency errors less than 10 ppm can be achieved using modest workstations, and that the solutions have no contamination from spurious modes. The role of differential geometry and geometrical physics in finite element analysis will also be discussed

  11. High accuracy 3D electromagnetic finite element analysis

    International Nuclear Information System (INIS)

    Nelson, E.M.

    1996-01-01

    A high accuracy 3D electromagnetic finite element field solver employing quadratic hexahedral elements and quadratic mixed-order one-form basis functions will be described. The solver is based on an object-oriented C++ class library. Test cases demonstrate that frequency errors less than 10 ppm can be achieved using modest workstations, and that the solutions have no contamination from spurious modes. The role of differential geometry and geometrical physics in finite element analysis will also be discussed

  12. Aligned, plasma sprayed SmCo5 deposits

    International Nuclear Information System (INIS)

    Kumar, K.; Das, D.

    1986-01-01

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

  13. A High-Throughput, High-Accuracy System-Level Simulation Framework for System on Chips

    Directory of Open Access Journals (Sweden)

    Guanyi Sun

    2011-01-01

    Full Text Available Today's System-on-Chips (SoCs design is extremely challenging because it involves complicated design tradeoffs and heterogeneous design expertise. To explore the large solution space, system architects have to rely on system-level simulators to identify an optimized SoC architecture. In this paper, we propose a system-level simulation framework, System Performance Simulation Implementation Mechanism, or SPSIM. Based on SystemC TLM2.0, the framework consists of an executable SoC model, a simulation tool chain, and a modeling methodology. Compared with the large body of existing research in this area, this work is aimed at delivering a high simulation throughput and, at the same time, guaranteeing a high accuracy on real industrial applications. Integrating the leading TLM techniques, our simulator can attain a simulation speed that is not slower than that of the hardware execution by a factor of 35 on a set of real-world applications. SPSIM incorporates effective timing models, which can achieve a high accuracy after hardware-based calibration. Experimental results on a set of mobile applications proved that the difference between the simulated and measured results of timing performance is within 10%, which in the past can only be attained by cycle-accurate models.

  14. MEMS Integrated Submount Alignment for Optoelectronics

    Science.gov (United States)

    Shakespeare, W. Jeffrey; Pearson, Raymond A.; Grenestedt, Joachim L.; Hutapea, Parsaoran; Gupta, Vikas

    2005-02-01

    One of the most expensive and time-consuming production processes for single-mode fiber-optic components is the alignment of the photonic chip or waveguide to the fiber. The alignment equipment is capital intensive and usually requires trained technicians to achieve desired results. Current technology requires active alignment since tolerances are only ~0.2 μ m or less for a typical laser diode. This is accomplished using piezoelectric actuated stages and active optical feedback. Joining technologies such as soldering, epoxy bonding, or laser welding may contribute significant postbond shift, and final coupling efficiencies are often less than 80%. This paper presents a method of adaptive optical alignment to freeze in place directly on an optical submount using a microelectromechanical system (MEMS) shape memory alloy (SMA) actuation technology. Postbond shift is eliminated since the phase change is the alignment actuation. This technology is not limited to optical alignment but can be applied to a variety of MEMS actuations, including nano-actuation and nano-alignment for biomedical applications. Experimental proof-of-concept results are discussed, and a simple analytical model is proposed to predict the stress strain behavior of the optical submount. Optical coupling efficiencies and alignment times are compared with traditional processes. The feasibility of this technique in high-volume production is discussed.

  15. Image-guided system versus manual marking for toric intraocular lens alignment in cataract surgery

    NARCIS (Netherlands)

    Webers, V.S.C.; Bauer, N.J.C.; Visser, N.; Berendschot, T.T.J.M.; van den Biggelaar, F.J.H.M.; Nuijts, R.M.M.A.

    2017-01-01

    Purpose To compare the accuracy of toric intraocular lens (IOL) alignment using the Verion Image-Guided System versus a conventional manual ink-marking procedure. Setting University Eye Clinic Maastricht, Maastricht, the Netherlands. Design Prospective randomized clinical trial. Methods Eyes with

  16. Disruption of myoblast alignment by highly motile rhabdomyosarcoma cell in tissue structure.

    Science.gov (United States)

    Li, Menglu; Nagamori, Eiji; Kino-Oka, Masahiro

    2017-02-01

    Rhabdomyosarcoma (RMS) is a highly malignant tumor type of skeletal muscle origin, hallmarked by local invasion. Interaction between invasive tumor cells and normal cells plays a major role in tumor invasion and metastasis. Culturing tumor cells in a three-dimensional (3D) model can translate tumor malignancy relevant cell-cell interaction. To mimic tumor heterogeneity in vitro, a co-culture system consisting of a malignant embryonal rhabdomyosarcoma (ERMS) cell line RD and a normal human skeletal muscle myoblast (HSMM) cell line was established by cell sheet technology. Various ratios of RDs to HSMMs were employed to understand the quantitative effect on intercellular interactions. Disruption of sheet structure was observed in heterogeneous cell sheets having a low ratio of RDs to HSMMs, whereas homogeneous HSMM or RD sheets maintained intact structure. Deeper exploration of dynamic tumor cell behavior inside HSMM sheets revealed that HSMM cell alignment was disrupted by highly motile RDs. This study demonstrated that RMS cells are capable of compromising their surrounding environment through induced decay of HSMMs alignment in a cell-based 3D system. This suggests that muscle disruption might be a major consequence of RMS cell invasion into muscles, which could be a promising target to preventing tumor invasion. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  17. Continuous high-yield production of vertically aligned carbon nanotubes on 2D and 3D substrates.

    Science.gov (United States)

    Guzmán de Villoria, Roberto; Hart, A John; Wardle, Brian L

    2011-06-28

    Vertically aligned carbon nanotubes (VACNTs) have certain advantages over bulk CNT powders and randomly oriented CNT mats for applications in flexible electronic devices, filtration membranes, biosensors and multifunctional aerospace materials. Here, a machine and a process to synthesize VACNTs in a continuous manner are presented showing uniform growth on 2D and 3D substrates, including alumina fibers, silicon wafer pieces, and stainless steel foils. Aligned multiwalled carbon nanotubes (MWNT) are synthesized at substrate feed rates of up to 6.8 cm/min, and the CNTs reach up to 60 μm in length depending on residence time in the reactor. In addition to the aligned morphology indicative of high yield growth, transmission electron microscopy and Raman spectroscopy reveal that the CNTs are of comparable quality to CNTs grown via a similar batch process. A significant reduction in time, reaction products, gases, and energy is demonstrated relative to batch processing, paving the way for industrial production of VACNTs.

  18. Accuracy of hiatal hernia detection with esophageal high-resolution manometry

    NARCIS (Netherlands)

    Weijenborg, P. W.; van Hoeij, F. B.; Smout, A. J. P. M.; Bredenoord, A. J.

    2015-01-01

    The diagnosis of a sliding hiatal hernia is classically made with endoscopy or barium esophagogram. Spatial separation of the lower esophageal sphincter (LES) and diaphragm, the hallmark of hiatal hernia, can also be observed on high-resolution manometry (HRM), but the diagnostic accuracy of this

  19. Self-aligned metallization on organic semiconductor through 3D dual-layer thermal nanoimprint

    International Nuclear Information System (INIS)

    Jung, Y; Cheng, X

    2014-01-01

    High-resolution patterning of metal structures on organic semiconductors is important to the realization of high-performance organic transistors for organic integrated circuit applications. The traditional shadow mask technique has a limited resolution, precluding sub-micron metal structures on organic semiconductors. Thus organic transistors cannot benefit from scaling into the deep sub-micron region to improve their dc and ac performances. In this work, we report an efficient multiple-level metallization on poly (3-hexylthiophene) (P3HT) with a deep sub-micron lateral gap. By using a 3D nanoimprint mold in a dual-layer thermal nanoimprint process, we achieved self-aligned two-level metallization on P3HT. The 3D dual-layer thermal nanoimprint enables the first metal patterns to have suspending side-wings that can clearly define a distance from the second metal patterns. Isotropic and anisotropic side-wing structures can be fabricated through two different schemes. The process based on isotropic side-wings achieves a lateral-gap in the order of 100 nm (scheme 1). A gap of 60 nm can be achieved from the process with anisotropic side-wings (scheme 2). Because of the capability of nanoscale metal patterning on organic semiconductors with high overlay accuracy, this self-aligned metallization technique can be utilized to fabricate high-performance organic metal semiconductor field-effect transistor. (paper)

  20. 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.

  1. High Accuracy Acoustic Relative Humidity Measurement inDuct Flow with Air

    Directory of Open Access Journals (Sweden)

    Cees van der Geld

    2010-08-01

    Full Text Available An acoustic relative humidity sensor for air-steam mixtures in duct flow is designed and tested. Theory, construction, calibration, considerations on dynamic response and results are presented. The measurement device is capable of measuring line averaged values of gas velocity, temperature and relative humidity (RH instantaneously, by applying two ultrasonic transducers and an array of four temperature sensors. Measurement ranges are: gas velocity of 0–12 m/s with an error of ±0.13 m/s, temperature 0–100 °C with an error of ±0.07 °C and relative humidity 0–100% with accuracy better than 2 % RH above 50 °C. Main advantage over conventional humidity sensors is the high sensitivity at high RH at temperatures exceeding 50 °C, with accuracy increasing with increasing temperature. The sensors are non-intrusive and resist highly humid environments.

  2. Highly efficient growth of vertically aligned carbon nanotubes on Fe-Ni based metal alloy foils for supercapacitors

    Science.gov (United States)

    Amalina Raja Seman, Raja Noor; Asyadi Azam, Mohd; Ambri Mohamed, Mohd

    2016-12-01

    Supercapacitors are highly promising energy devices with superior charge storage performance and a long lifecycle. Construction of the supercapacitor cell, especially electrode fabrication, is critical to ensure good performance in applications. This work demonstrates direct growth of vertically aligned carbon nanotubes (CNTs) on Fe-Ni based metal alloy foils, namely SUS 310S, Inconel 600 and YEF 50, and their use in symmetric vertically aligned CNT supercapacitor electrodes. Alumina and cobalt thin film catalysts were deposited onto the foils, and then CNT growth was performed using alcohol catalytic chemical vapour deposition. By this method, vertically aligned CNTs were successfully grown and used directly as a binder-free supercapacitor electrode to deliver excellent electrochemical performance. The device showed relatively good specific capacitance, a superior rate capability and excellent cycle stability, maintaining about 96% capacitance up to 1000 cycles.

  3. Realizing one-dimensional quantum and high-frequency transport features in aligned single-walled carbon nanotube ropes

    Energy Technology Data Exchange (ETDEWEB)

    Ncube, Siphephile; Chimowa, George; Chiguvare, Zivayi; Bhattacharyya, Somnath, E-mail: Somnath.Bhattacharyya@wits.ac.za [Nano-Scale Transport Physics Laboratory, School of Physics and DST/NRF Centre of Excellence in Strong Materials, University of the Witwatersrand, Private Bag 3, WITS 2050, Johannesburg (South Africa)

    2014-07-14

    The superiority of the electronic transport properties of single-walled carbon nanotube (SWNT) ropes over SWNT mats is verified from low temperature and frequency-dependent transport. The overall change of resistance versus in nanotube mats shows that 3D variable range hopping is the dominant conduction mechanism within the 2–300 K range. The magneto-resistance (MR) is found to be predominantly negative with a parabolic nature, which can also be described by the hopping model. Although the positive upturn of the MR at low temperatures establishes the contribution from quantum interference, the inherent quantum transport in individual tubes is suppressed at elevated temperatures. Therefore, to minimize multi-channel effects from inter-tube interactions and other defects, two-terminal devices were fabricated from aligned SWNT (extracted from a mat) for low temperature transport as well as high-frequency measurements. In contrast to the mat, the aligned ropes exhibit step-like features in the differential conductance within the 80–300 K temperature range. The effects of plasmon propagation, unique to one dimension, were identified in electronic transport as a non-universal power-law dependence of the differential conductance on temperature and source-drain voltage. The complex impedance showed high power transmission capabilities up to 65 GHz as well as oscillations in the frequency range up to 30 GHz. The measurements suggest that aligned SWNT ropes have a realistic potential for high-speed device applications.

  4. Realizing one-dimensional quantum and high-frequency transport features in aligned single-walled carbon nanotube ropes

    Science.gov (United States)

    Ncube, Siphephile; Chimowa, George; Chiguvare, Zivayi; Bhattacharyya, Somnath

    2014-07-01

    The superiority of the electronic transport properties of single-walled carbon nanotube (SWNT) ropes over SWNT mats is verified from low temperature and frequency-dependent transport. The overall change of resistance versus in nanotube mats shows that 3D variable range hopping is the dominant conduction mechanism within the 2-300 K range. The magneto-resistance (MR) is found to be predominantly negative with a parabolic nature, which can also be described by the hopping model. Although the positive upturn of the MR at low temperatures establishes the contribution from quantum interference, the inherent quantum transport in individual tubes is suppressed at elevated temperatures. Therefore, to minimize multi-channel effects from inter-tube interactions and other defects, two-terminal devices were fabricated from aligned SWNT (extracted from a mat) for low temperature transport as well as high-frequency measurements. In contrast to the mat, the aligned ropes exhibit step-like features in the differential conductance within the 80-300 K temperature range. The effects of plasmon propagation, unique to one dimension, were identified in electronic transport as a non-universal power-law dependence of the differential conductance on temperature and source-drain voltage. The complex impedance showed high power transmission capabilities up to 65 GHz as well as oscillations in the frequency range up to 30 GHz. The measurements suggest that aligned SWNT ropes have a realistic potential for high-speed device applications.

  5. A highly sensitive hydrogen peroxide amperometric sensor based on MnO2-modified vertically aligned multiwalled carbon nanotubes.

    Science.gov (United States)

    Xu, Bin; Ye, Min-Ling; Yu, Yu-Xiang; Zhang, Wei-De

    2010-07-26

    In this report, a highly sensitive amperometric sensor based on MnO(2)-modified vertically aligned multiwalled carbon nanotubes (MnO(2)/VACNTs) for determination of hydrogen peroxide (H(2)O(2)) was fabricated by electrodeposition. The morphology of the nanocomposite was characterized by scanning electron microscopy, energy-dispersive X-ray spectrometer and X-ray diffraction. Cyclic voltammetry, chronoamperometry and electrochemical impedance spectroscopy were applied to investigate the electrochemical properties of the MnO(2)/VACNTs nanocomposite electrode. The mechanism for the electrochemical reaction of H(2)O(2) at the MnO(2)/VACNTs nanocomposite electrode was also discussed. In borate buffer (pH 7.8, 0.20 M), the MnO(2)/VACNTs nanocomposite electrode exhibits a linear dependence (R=0.998) on the concentration of H(2)O(2) from 1.2 x 10(-6)M to 1.8 x 10(-3)M, a high sensitivity of 1.08 x 10(6) microA M(-1) cm(-2) and a detection limit of 8.0 x 10(-7) M (signal/noise=3). Meanwhile, the MnO(2)/VACNTs nanocomposite electrode is also highly resistant towards typical inorganic salts and some biomolecules such as acetic acid, citric acid, uric acid and D-(+)-glucose, etc. In addition, the sensor based on the MnO(2)/VACNTs nanocomposite electrode was applied for the determination of trace of H(2)O(2) in milk with high accuracy, demonstrating its potential for practical application. Copyright 2010 Elsevier B.V. All rights reserved.

  6. Highly polarized light emission by isotropic quantum dots integrated with magnetically aligned segmented nanowires

    International Nuclear Information System (INIS)

    Uran, Can; Erdem, Talha; Guzelturk, Burak; Perkgöz, Nihan Kosku; Jun, Shinae; Jang, Eunjoo; Demir, Hilmi Volkan

    2014-01-01

    In this work, we demonstrate a proof-of-concept system for generating highly polarized light from colloidal quantum dots (QDs) coupled with magnetically aligned segmented Au/Ni/Au nanowires (NWs). Optical characterizations reveal that the optimized QD-NW coupled structures emit highly polarized light with an s-to p-polarization (s/p) contrast as high as 15:1 corresponding to a degree of polarization of 0.88. These experimental results are supported by the finite-difference time-domain simulations, which demonstrate the interplay between the inter-NW distance and the degree of polarization.

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

    KAUST Repository

    Wei, Yaguang

    2010-09-08

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

  8. Alignment performance monitoring for ASML systems

    Science.gov (United States)

    Chung, Woong-Jae; Temchenko, Vlad; Hauck, Tarja; Schmidt, Sebastian

    2006-03-01

    In today's semiconductor industry downscaling of the IC design puts a stringent requirement on pattern overlay control. Tighter overlay requirements lead to exceedingly higher rework rates, meaning additional costs to manufacturing. Better alignment control became a target of engineering efforts to decrease rework rate for high-end technologies. Overlay performance is influenced by known parameters such as "Shift, Scaling, Rotation, etc", and unknown parameters defined as "Process Induced Variation", which are difficult to control by means of a process automation system. In reality, this process-induced variation leads to a strong wafer to wafer, or lot to lot variation, which are not easy to detect in the mass-production environment which uses sampling overlay measurements for only several wafers in a lot. An engineering task of finding and correcting a root cause for Process Induced Variations of overlay performance will be greatly simplified if the unknown parameters could be tracked for each wafer. This paper introduces an alignment performance monitoring method based on analysis of automatically generated "AWE" files for ASML scanner systems. Because "AWE" files include alignment results for each aligned wafer, it is possible to use them for monitoring, controlling and correcting the causes of "process induced" overlay performance without requiring extra measurement time. Since "AWE" files include alignment information for different alignment marks, it is also possible to select and optimize the best alignment recipe for each alignment strategy. Several case studies provided in our paper will demonstrate how AWE file analysis can be used to assist engineer in interpreting pattern alignment data. Since implementing our alignment data monitoring method, we were able to achieve significant improvement of alignment and overlay performance without additional overlay measurement time. We also noticed that the rework rate coming from alignment went down and

  9. Comparative Analysis of Mass Spectral Similarity Measures on Peak Alignment for Comprehensive Two-Dimensional Gas Chromatography Mass Spectrometry

    Science.gov (United States)

    2013-01-01

    Peak alignment is a critical procedure in mass spectrometry-based biomarker discovery in metabolomics. One of peak alignment approaches to comprehensive two-dimensional gas chromatography mass spectrometry (GC×GC-MS) data is peak matching-based alignment. A key to the peak matching-based alignment is the calculation of mass spectral similarity scores. Various mass spectral similarity measures have been developed mainly for compound identification, but the effect of these spectral similarity measures on the performance of peak matching-based alignment still remains unknown. Therefore, we selected five mass spectral similarity measures, cosine correlation, Pearson's correlation, Spearman's correlation, partial correlation, and part correlation, and examined their effects on peak alignment using two sets of experimental GC×GC-MS data. The results show that the spectral similarity measure does not affect the alignment accuracy significantly in analysis of data from less complex samples, while the partial correlation performs much better than other spectral similarity measures when analyzing experimental data acquired from complex biological samples. PMID:24151524

  10. A hybrid cloud read aligner based on MinHash and kmer voting that preserves privacy

    Science.gov (United States)

    Popic, Victoria; Batzoglou, Serafim

    2017-05-01

    Low-cost clouds can alleviate the compute and storage burden of the genome sequencing data explosion. However, moving personal genome data analysis to the cloud can raise serious privacy concerns. Here, we devise a method named Balaur, a privacy preserving read mapper for hybrid clouds based on locality sensitive hashing and kmer voting. Balaur can securely outsource a substantial fraction of the computation to the public cloud, while being highly competitive in accuracy and speed with non-private state-of-the-art read aligners on short read data. We also show that the method is significantly faster than the state of the art in long read mapping. Therefore, Balaur can enable institutions handling massive genomic data sets to shift part of their analysis to the cloud without sacrificing accuracy or exposing sensitive information to an untrusted third party.

  11. 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...

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

    Directory of Open Access Journals (Sweden)

    Brejnev Muhizi Muhire

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

  13. Aligning Metabolic Pathways Exploiting Binary Relation of Reactions.

    Directory of Open Access Journals (Sweden)

    Yiran Huang

    Full Text Available Metabolic pathway alignment has been widely used to find one-to-one and/or one-to-many reaction mappings to identify the alternative pathways that have similar functions through different sets of reactions, which has important applications in reconstructing phylogeny and understanding metabolic functions. The existing alignment methods exhaustively search reaction sets, which may become infeasible for large pathways. To address this problem, we present an effective alignment method for accurately extracting reaction mappings between two metabolic pathways. We show that connected relation between reactions can be formalized as binary relation of reactions in metabolic pathways, and the multiplications of zero-one matrices for binary relations of reactions can be accomplished in finite steps. By utilizing the multiplications of zero-one matrices for binary relation of reactions, we efficiently obtain reaction sets in a small number of steps without exhaustive search, and accurately uncover biologically relevant reaction mappings. Furthermore, we introduce a measure of topological similarity of nodes (reactions by comparing the structural similarity of the k-neighborhood subgraphs of the nodes in aligning metabolic pathways. We employ this similarity metric to improve the accuracy of the alignments. The experimental results on the KEGG database show that when compared with other state-of-the-art methods, in most cases, our method obtains better performance in the node correctness and edge correctness, and the number of the edges of the largest common connected subgraph for one-to-one reaction mappings, and the number of correct one-to-many reaction mappings. Our method is scalable in finding more reaction mappings with better biological relevance in large metabolic pathways.

  14. DNAAlignEditor: DNA alignment editor tool

    Directory of Open Access Journals (Sweden)

    Guill Katherine E

    2008-03-01

    Full Text Available Abstract Background With advances in DNA re-sequencing methods and Next-Generation parallel sequencing approaches, there has been a large increase in genomic efforts to define and analyze the sequence variability present among individuals within a species. For very polymorphic species such as maize, this has lead to a need for intuitive, user-friendly software that aids the biologist, often with naïve programming capability, in tracking, editing, displaying, and exporting multiple individual sequence alignments. To fill this need we have developed a novel DNA alignment editor. Results We have generated a nucleotide sequence alignment editor (DNAAlignEditor that provides an intuitive, user-friendly interface for manual editing of multiple sequence alignments with functions for input, editing, and output of sequence alignments. The color-coding of nucleotide identity and the display of associated quality score aids in the manual alignment editing process. DNAAlignEditor works as a client/server tool having two main components: a relational database that collects the processed alignments and a user interface connected to database through universal data access connectivity drivers. DNAAlignEditor can be used either as a stand-alone application or as a network application with multiple users concurrently connected. Conclusion We anticipate that this software will be of general interest to biologists and population genetics in editing DNA sequence alignments and analyzing natural sequence variation regardless of species, and will be particularly useful for manual alignment editing of sequences in species with high levels of polymorphism.

  15. Compositions for directed alignment of conjugated polymers

    Science.gov (United States)

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

    2016-04-19

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

  16. Diffusion of dilute gas in arrays of randomly distributed, vertically aligned, high-aspect-ratio cylinders

    Directory of Open Access Journals (Sweden)

    Wojciech Szmyt

    2017-01-01

    Full Text Available In this work we modelled the diffusive transport of a dilute gas along arrays of randomly distributed, vertically aligned nanocylinders (nanotubes or nanowires as opposed to gas diffusion in long pores, which is described by the well-known Knudsen theory. Analytical expressions for (i the gas diffusion coefficient inside such arrays, (ii the time between collisions of molecules with the nanocylinder walls (mean time of flight, (iii the surface impingement rate, and (iv the Knudsen number of such a system were rigidly derived based on a random-walk model of a molecule that undergoes memoryless, diffusive reflections from nanocylinder walls assuming the molecular regime of gas transport. It can be specifically shown that the gas diffusion coefficient inside such arrays is inversely proportional to the areal density of cylinders and their mean diameter. An example calculation of a diffusion coefficient is delivered for a system of titanium isopropoxide molecules diffusing between vertically aligned carbon nanotubes. Our findings are important for the correct modelling and optimisation of gas-based deposition techniques, such as atomic layer deposition or chemical vapour deposition, frequently used for surface functionalisation of high-aspect-ratio nanocylinder arrays in solar cells and energy storage applications. Furthermore, gas sensing devices with high-aspect-ratio nanocylinder arrays and the growth of vertically aligned carbon nanotubes need the fundamental understanding and precise modelling of gas transport to optimise such processes.

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

    Science.gov (United States)

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

    2018-04-01

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

  18. High accuracy 3D electromagnetic finite element analysis

    International Nuclear Information System (INIS)

    Nelson, E.M.

    1997-01-01

    A high accuracy 3D electromagnetic finite element field solver employing quadratic hexahedral elements and quadratic mixed-order one-form basis functions will be described. The solver is based on an object-oriented C++ class library. Test cases demonstrate that frequency errors less than 10 ppm can be achieved using modest workstations, and that the solutions have no contamination from spurious modes. The role of differential geometry and geometrical physics in finite element analysis will also be discussed. copyright 1997 American Institute of Physics

  19. High resolution Fresnel zone plate laser alignment system

    International Nuclear Information System (INIS)

    Bressler, V.E.; Fischer, G.E.; Ruland, R.E.; Wang, T.

    1992-03-01

    The existing Fresnel zone plate laser alignment system is currently being extended and upgraded for the Final Focus Test Beam (FFTB). Previously, the resolution of this system has been several tens of micrometers. After the upgrade, the resolution will be a few micrometers. Details of the upgrade as well as simulation and experimental results will be presented

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

    Science.gov (United States)

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

    2013-07-01

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

  1. Expected measurement of the Z production rate with the CMS detector and simulation of the Tracker Laser Alignment System

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, Maarten

    2009-06-16

    The Large Hadron Collider is a two-ring, superconducting accelerator and collider which can provide both proton and heavy-ion beams. First collisions are foreseen for 2009. The Compact Muon System (CMS) detector will measure the particles created in the hadron collisions and can confirm the Standard Model by establishing the existence of the Higgs boson, but also search for new phenomena. In order to provide a robust and precise track reconstruction, which can already be used in the High-Level Trigger systems, the positions of the silicon sensors in the CMS tracker have to been known with an accuracy of O(100 {mu}m). Therefore the CMS tracker has been equipped with a dedicated alignment system. The Laser Alignment System (LAS) aligns the tracker subdetectors with respect to each other and can also monitor the stability of the sensor positions during data taking. This study describes the implementation of a realistic simulation of the LAS in the CMS software framework (CMSSW) as well as the analysis of the first data collected during the integration of one of the tracker endcaps. In the present study it has been found that the alignment of the endcaps is possible with an accuracy of approximately 76 {mu}m. These results are in agreement with independent measurements of the TEC geometry using cosmic muons or photogrammetry measurements. The accuracy of approximately 100 {mu}m needed for track pattern recognition and reconstruction can be assured by the Laser Alignment System as shown in this study. Accurate knowledge of the luminosity delivered by the LHC to the experiments is an essential ingredient for many physics studies. The present work uses the production of lepton pairs via the Drell-Yan mechanism to determine the integrated luminosity with the CMS detector. A Monte Carlo generator (MC rate at NLO) including next-to-leading order QCD diagrams has been used to generate Drell-Yan events decaying into two muons. After a full CMS detector simulation, the events

  2. Expected measurement of the Z production rate with the CMS detector and simulation of the Tracker Laser Alignment System

    International Nuclear Information System (INIS)

    Thomas, Maarten

    2009-01-01

    The Large Hadron Collider is a two-ring, superconducting accelerator and collider which can provide both proton and heavy-ion beams. First collisions are foreseen for 2009. The Compact Muon System (CMS) detector will measure the particles created in the hadron collisions and can confirm the Standard Model by establishing the existence of the Higgs boson, but also search for new phenomena. In order to provide a robust and precise track reconstruction, which can already be used in the High-Level Trigger systems, the positions of the silicon sensors in the CMS tracker have to been known with an accuracy of O(100 μm). Therefore the CMS tracker has been equipped with a dedicated alignment system. The Laser Alignment System (LAS) aligns the tracker subdetectors with respect to each other and can also monitor the stability of the sensor positions during data taking. This study describes the implementation of a realistic simulation of the LAS in the CMS software framework (CMSSW) as well as the analysis of the first data collected during the integration of one of the tracker endcaps. In the present study it has been found that the alignment of the endcaps is possible with an accuracy of approximately 76 μm. These results are in agreement with independent measurements of the TEC geometry using cosmic muons or photogrammetry measurements. The accuracy of approximately 100 μm needed for track pattern recognition and reconstruction can be assured by the Laser Alignment System as shown in this study. Accurate knowledge of the luminosity delivered by the LHC to the experiments is an essential ingredient for many physics studies. The present work uses the production of lepton pairs via the Drell-Yan mechanism to determine the integrated luminosity with the CMS detector. A Monte Carlo generator (MC rate at NLO) including next-to-leading order QCD diagrams has been used to generate Drell-Yan events decaying into two muons. After a full CMS detector simulation, the events have

  3. 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.

  4. Ultrasonic inspections of fuel alignment pins

    International Nuclear Information System (INIS)

    Rathgeb, W.; Schmid, R.

    1994-01-01

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

  5. 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...

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

    Science.gov (United States)

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

    2016-12-15

    MSAProbs is a state-of-the-art protein multiple sequence alignment tool based on hidden Markov models. It can achieve high alignment accuracy at the expense of relatively long runtimes for large-scale input datasets. In this work we present MSAProbs-MPI, a distributed-memory parallel version of the multithreaded MSAProbs tool that is able to reduce runtimes by exploiting the compute capabilities of common multicore CPU clusters. Our performance evaluation on a cluster with 32 nodes (each containing two Intel Haswell processors) shows reductions in execution time of over one order of magnitude for typical input datasets. Furthermore, MSAProbs-MPI using eight nodes is faster than the GPU-accelerated QuickProbs running on a Tesla K20. Another strong point is that MSAProbs-MPI can deal with large datasets for which MSAProbs and QuickProbs might fail due to time and memory constraints, respectively. Source code in C ++ and MPI running on Linux systems as well as a reference manual are available at http://msaprobs.sourceforge.net CONTACT: jgonzalezd@udc.esSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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

    Science.gov (United States)

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

    2006-12-15

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

  8. 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 ...

  9. 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...

  10. High-Mobility Aligned Pentacene Films Grown by Zone-Casting

    DEFF Research Database (Denmark)

    Duffy, Claudia M.; Andreasen, Jens Wenzel; Breiby, Dag W.

    2008-01-01

    We investigate the growth and field-effect transistor performance of aligned pentacene thin films deposited by zone-casting from a solution of unsubstituted pentacene molecules in a chlorinated solvent. Polarized optical microscopy shows that solution processed pentacene films grow as large...

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

    Science.gov (United States)

    Lee, Hui Sun; Im, Wonpil

    2013-01-01

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

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

    International Nuclear Information System (INIS)

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

    1998-01-01

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

  13. The Laser Alignment System for the CMS silicon strip tracker

    CERN Document Server

    Olzem, Jan

    2009-01-01

    The Laser Alignment System (LAS) of the CMS silicon strip Tracker has been designed for surveying the geometry of the large-scale Tracker support structures. It uses 40 laser beams ($\\lambda$ = 1075 nm) that induce signals on a subset of the Tracker silicon sensors. The positions in space of the laser spots on the sensors are reconstructed with a resolution of 30 $\\mu$m. From this, the LAS is capable of permanent in-time monitoring of the different Tracker components relative to each other with better than 30 $\\mu$m precision. Additionally, it can provide an absolute measurement of the Tracker mechanical structure with an accuracy better than 70 $\\mu$m, thereby supplying additional input to the track based alignment at detector startup. 31 out of the 40 LAS beams have been successfully operated during the CMS cosmic muon data taking campaign in autumn 2008. The alignment of the Tracker Endcap Discs and of the discs with respect to the Tracker Inner Barrel and Tracker Outer Barrel subdetectors was measured w...

  14. 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

  15. A Method for SINS Alignment with Large Initial Misalignment Angles Based on Kalman Filter with Parameters Resetting

    Directory of Open Access Journals (Sweden)

    Xixiang Liu

    2014-01-01

    Full Text Available In the initial alignment process of strapdown inertial navigation system (SINS, large initial misalignment angles always bring nonlinear problem, which causes alignment failure when the classical linear error model and standard Kalman filter are used. In this paper, the problem of large misalignment angles in SINS initial alignment is investigated, and the key reason for alignment failure is given as the state covariance from Kalman filter cannot represent the true one during the steady filtering process. According to the analysis, an alignment method for SINS based on multiresetting the state covariance matrix of Kalman filter is designed to deal with large initial misalignment angles, in which classical linear error model and standard Kalman filter are used, but the state covariance matrix should be multireset before the steady process until large misalignment angles are decreased to small ones. The performance of the proposed method is evaluated by simulation and car test, and the results indicate that the proposed method can fulfill initial alignment with large misalignment angles effectively and the alignment accuracy of the proposed method is as precise as that of alignment with small misalignment angles.

  16. Planar self-aligned imprint lithography for coplanar plasmonic nanostructures fabrication

    KAUST Repository

    Wan, Weiwei; Lin, Liang; Xu, Yelong; Guo, Xu; Liu, Xiaoping; Ge, Haixiong; Lu, Minghui; Cui, Bo; Chen, Yanfeng

    2014-01-01

    manufacturing remains a challenge due to the high cost of achieving mechanical alignment precision. Although self-aligned imprint lithography was developed to avoid the need of alignment for the vertical layered structures, it has limited usage

  17. The effect of pattern overlap on the accuracy of high resolution electron backscatter diffraction measurements

    Energy Technology Data Exchange (ETDEWEB)

    Tong, Vivian, E-mail: v.tong13@imperial.ac.uk [Department of Materials, Imperial College London, Prince Consort Road, London SW7 2AZ (United Kingdom); Jiang, Jun [Department of Materials, Imperial College London, Prince Consort Road, London SW7 2AZ (United Kingdom); Wilkinson, Angus J. [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Britton, T. Ben [Department of Materials, Imperial College London, Prince Consort Road, London SW7 2AZ (United Kingdom)

    2015-08-15

    High resolution, cross-correlation-based, electron backscatter diffraction (EBSD) measures the variation of elastic strains and lattice rotations from a reference state. Regions near grain boundaries are often of interest but overlap of patterns from the two grains could reduce accuracy of the cross-correlation analysis. To explore this concern, patterns from the interior of two grains have been mixed to simulate the interaction volume crossing a grain boundary so that the effect on the accuracy of the cross correlation results can be tested. It was found that the accuracy of HR-EBSD strain measurements performed in a FEG-SEM on zirconium remains good until the incident beam is less than 18 nm from a grain boundary. A simulated microstructure was used to measure how often pattern overlap occurs at any given EBSD step size, and a simple relation was found linking the probability of overlap with step size. - Highlights: • Pattern overlap occurs at grain boundaries and reduces HR-EBSD accuracy. • A test is devised to measure the accuracy of HR-EBSD in the presence of overlap. • High pass filters can sometimes, but not generally, improve HR-EBSD measurements. • Accuracy of HR-EBSD remains high until the reference pattern intensity is <72%. • 9% of points near a grain boundary will have significant error for 200nm step size in Zircaloy-4.

  18. Preparation of aligned W{sub 18}O{sub 49} nanowire clusters with high photocatalytic activity

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Ning [State Key Laboratory of Inorganic Synthesis & Preparative Chemistry, Jilin University, Changchun 130012 (China); Zhao, Yafei, E-mail: zhaoyafei007@126.com [State Key Laboratory of Inorganic Synthesis & Preparative Chemistry, Jilin University, Changchun 130012 (China); School of Chemical Engineering and Energy, Zhengzhou University, Zhengzhou, Henan 450001 (China); Lu, Yanjie [School of Chemical Engineering and Energy, Zhengzhou University, Zhengzhou, Henan 450001 (China); Zhu, Guangshan, E-mail: zhugs@jlu.edu.cn [State Key Laboratory of Inorganic Synthesis & Preparative Chemistry, Jilin University, Changchun 130012 (China)

    2017-04-15

    Highlights: • Aligned W{sub 18}O{sub 49} nanowire clusters were prepared by a facile hydrothermal method. • W{sub 18}O{sub 49} has unique structure, high degree of crystallinity and large surface area. • W{sub 18}O{sub 49} nanowire clusters exhibited high photocatalytic degradation activity. - Abstract: The aligned W{sub 18}O{sub 49} nanowire clusters were synthesized via a facile and economic ethanol-assisted hydrothermal method using peroxopolytungstic acid as precursor. Results show that the as-prepared W{sub 18}O{sub 49} exhibits a high yield and ultrathin structure with preferential growth direction along [0 1 0]. The amount of peroxopolytungstic acid and reaction time play significant role on the morphology of W{sub 18}O{sub 49} nanowires. The nanowires have unique structure, high degree of crystallinity, large specific surface area, and large number of defects such as oxygen vacancies, which are responsible for their high photocatalytic performance for degradation of methylene blue. The photocatalytic conversion of methylene blue can reach above 98% after degradation. W{sub 18}O{sub 49} also exhibits good photodegradation stability after five cycles of reuse. The results demonstrate that the as-prepared W{sub 18}O{sub 49} nanowire clusters are expected to be a promising material for applications in the field of environment.

  19. Capillary Self-Alignment of Microchips on Soft Substrates

    Directory of Open Access Journals (Sweden)

    Bo Chang

    2016-03-01

    Full Text Available Soft micro devices and stretchable electronics have attracted great interest for their potential applications in sensory skins and wearable bio-integrated devices. One of the most important steps in building printed circuits is the alignment of assembled micro objects. Previously, the capillary self-alignment of microchips driven by surface tension effects has been shown to be able to achieve high-throughput and high-precision in the integration of micro parts on rigid hydrophilic/superhydrophobic patterned surfaces. In this paper, the self-alignment of microchips on a patterned soft and stretchable substrate, which consists of hydrophilic pads surrounded by a superhydrophobic polydimethylsiloxane (PDMS background, is demonstrated for the first time. A simple process has been developed for making superhydrophobic soft surface by replicating nanostructures of black silicon onto a PDMS surface. Different kinds of PDMS have been investigated, and the parameters for fabricating superhydrophobic PDMS have been optimized. A self-alignment strategy has been proposed that can result in reliable self-alignment on a soft PDMS substrate. Our results show that capillary self-alignment has great potential for building soft printed circuits.

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

    Directory of Open Access Journals (Sweden)

    Alexander Kawrykow

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

  1. Optical System Error Analysis and Calibration Method of High-Accuracy Star Trackers

    Directory of Open Access Journals (Sweden)

    Zheng You

    2013-04-01

    Full Text Available The star tracker is a high-accuracy attitude measurement device widely used in spacecraft. Its performance depends largely on the precision of the optical system parameters. Therefore, the analysis of the optical system parameter errors and a precise calibration model are crucial to the accuracy of the star tracker. Research in this field is relatively lacking a systematic and universal analysis up to now. This paper proposes in detail an approach for the synthetic error analysis of the star tracker, without the complicated theoretical derivation. This approach can determine the error propagation relationship of the star tracker, and can build intuitively and systematically an error model. The analysis results can be used as a foundation and a guide for the optical design, calibration, and compensation of the star tracker. A calibration experiment is designed and conducted. Excellent calibration results are achieved based on the calibration model. To summarize, the error analysis approach and the calibration method are proved to be adequate and precise, and could provide an important guarantee for the design, manufacture, and measurement of high-accuracy star trackers.

  2. Optical system error analysis and calibration method of high-accuracy star trackers.

    Science.gov (United States)

    Sun, Ting; Xing, Fei; You, Zheng

    2013-04-08

    The star tracker is a high-accuracy attitude measurement device widely used in spacecraft. Its performance depends largely on the precision of the optical system parameters. Therefore, the analysis of the optical system parameter errors and a precise calibration model are crucial to the accuracy of the star tracker. Research in this field is relatively lacking a systematic and universal analysis up to now. This paper proposes in detail an approach for the synthetic error analysis of the star tracker, without the complicated theoretical derivation. This approach can determine the error propagation relationship of the star tracker, and can build intuitively and systematically an error model. The analysis results can be used as a foundation and a guide for the optical design, calibration, and compensation of the star tracker. A calibration experiment is designed and conducted. Excellent calibration results are achieved based on the calibration model. To summarize, the error analysis approach and the calibration method are proved to be adequate and precise, and could provide an important guarantee for the design, manufacture, and measurement of high-accuracy star trackers.

  3. Tantalum electrodes modified with well-aligned carbon nanotube-Au nanoparticles: application to the highly sensitive electrochemical determination of cefazolin.

    Science.gov (United States)

    Fayazfar, Haniyeh; Afshar, Abdollah; Dolati, Abolghasem

    2014-07-01

    Carbon nanotube/nanoparticle hybrid materials have been proven to exhibit high electrocatalytic activity suggesting broad potential applications in the field of electroanalysis. For the first time, modification of Ta electrode with aligned multi-walled carbon nanotubes/Au nanoparticles introduced for the sensitive determination of the antibiotic drug, cefazolin (CFZ). The electrochemical response characteristics of the modified electrode toward CFZ were investigated by means of cyclic and linear sweep voltammetry. The modified electrode showed an efficient catalytic activity for the reduction of CFZ, leading to a remarkable decrease in reduction overpotential and a significant increase of peak current. Under optimum conditions, the highly sensitive modified electrode showed a wide linear range from 50 pM to 50 μM with a sufficiently low detection limit of 1 ± 0.01 pM (S/N = 3). The results indicated that the prepared electrode presents suitable characteristics in terms of sensitivity (458.2 ± 2.6 μAcm(-2)/μM), accuracy, repeatability (RSD of 1.8 %), reproducibility (RSD of 2.9 %), stability (14 days), and good catalytic activity in physiological conditions. The method was successfully applied for accurate determination of trace amounts of CFZ in pharmaceutical and clinical preparations without the necessity for samples pretreatment or any time-consuming extraction or evaporation steps prior to the analysis.

  4. Patient-specific guides do not improve accuracy in total knee arthroplasty: a prospective randomized controlled trial.

    Science.gov (United States)

    Victor, Jan; Dujardin, Jan; Vandenneucker, Hilde; Arnout, Nele; Bellemans, Johan

    2014-01-01

    Recently, patient-specific guides (PSGs) have been introduced, claiming a significant improvement in accuracy and reproducibility of component positioning in TKA. Despite intensive marketing by the manufacturers, this claim has not yet been confirmed in a controlled prospective trial. We (1) compared three-planar component alignment and overall coronal mechanical alignment between PSG and conventional instrumentation and (2) logged the need for applying changes in the suggested position of the PSG. In this randomized controlled trial, we enrolled 128 patients. In the PSG cohort, surgical navigation was used as an intraoperative control. When the suggested cut deviated more than 3° from target, the use of PSG was abandoned and marked as an outlier. When cranial-caudal position or size was adapted, the PSG was marked as modified. All patients underwent long-leg standing radiography and CT scan. Deviation of more than 3° from the target in any plane was defined as an outlier. The PSG and conventional cohorts showed similar numbers of outliers in overall coronal alignment (25% versus 28%; p = 0.69), femoral coronal alignment (7% versus 14%) (p = 0.24), and femoral axial alignment (23% versus 17%; p = 0.50). There were more outliers in tibial coronal (15% versus 3%; p = 0.03) and sagittal 21% versus 3%; p = 0.002) alignment in the PSG group than in the conventional group. PSGs were abandoned in 14 patients (22%) and modified in 18 (28%). PSGs do not improve accuracy in TKA and, in our experience, were somewhat impractical in that the procedure needed to be either modified or abandoned with some frequency.

  5. 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.

  6. Octahedral Tin Dioxide Nanocrystals Anchored on Vertically Aligned Carbon Aerogels as High Capacity Anode Materials for Lithium-Ion Batteries

    OpenAIRE

    Mingkai Liu; Yuqing Liu; Yuting Zhang; Yiliao Li; Peng Zhang; Yan Yan; Tianxi Liu

    2016-01-01

    A novel binder-free graphene - carbon nanotubes - SnO2 (GCNT-SnO2) aerogel with vertically aligned pores was prepared via a simple and efficient directional freezing method. SnO2 octahedrons exposed of {221} high energy facets were uniformly distributed and tightly anchored on multidimensional graphene/carbon nanotube (GCNT) composites. Vertically aligned pores can effectively prevent the emersion of ?closed? pores which cannot load the active SnO2 nanoparticles, further ensure quick immersio...

  7. Kinematic analysis and experimental verification of a eccentric wheel based precision alignment mechanism for LINAC

    International Nuclear Information System (INIS)

    Mundra, G.; Jain, V.; Singh, K.K.; Saxena, P.; Khare, R.K.; Bagre, M.

    2011-01-01

    Eccentric wheel based precision alignment system was designed for the remote motorized alignment of proposed proton injector LINAC (SFDTL). As a part of the further development for the alignment and monitoring scheme, a menu driven alignment system is being developed. The paper describes a general kinematic equation (with base line tilt correction) based on the various parameters of the mechanism like eccentricity, wheel diameter, distance between the wheels and the diameter of the cylindrical accelerator component. Based on this equation the extent of the alignment range for the 4 degree of freedom is evaluated and analysis on some of the parameters variation and the theoretical accuracy/resolution is computed. For the same a computer program is written which can compute the various points for the each discrete position of the two motor combinations. The paper also describes the experimentally evaluated values of these positions (for the full extent of area) and the matching/comparison of the two data. These data now can be used for the movement computation required for alignment of the four motors (two front and two rear motors of the support structure). (author)

  8. Innovative Fiber-Optic Gyroscopes (FOGs) for High Accuracy Space Applications, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — NASA's future science and exploratory missions will require much lighter, smaller, and longer life rate sensors that can provide high accuracy navigational...

  9. Measuring covariation in RNA alignments: Physical realism improves information measures

    DEFF Research Database (Denmark)

    Lindgreen, Stinus; Gardner, Paul Phillip; Krogh, Anders

    2006-01-01

    Motivation: The importance of non-coding RNAs is becoming increasingly evident, and often the function of these molecules depends on the structure. It is common to use alignments of related RNA sequences to deduce the consensus secondary structure by detecting patterns of co-evolution. A central...... part of such an analysis is to measure covariation between two positions in an alignment. Here, we rank various measures ranging from simple mutual information to more advanced covariation measures. Results: Mutual information is still used for secondary structure prediction, but the results...... of this study indicate which measures are useful. Incorporating more structural information by considering e.g. indels and stacking improves accuracy, suggesting that physically realistic measures yield improved predictions. This can be used to improve both current and future programs for secondary structure...

  10. Monitoring of absolute mirror alignment at COMPASS RICH-1 detector

    Energy Technology Data Exchange (ETDEWEB)

    Alexeev, M. [INFN, Sezione di Torino and University of East Piemonte, Alessandria (Italy); INFN, Sezione di Trieste and University of Bari, Bari (Italy); Birsa, R. [INFN, Sezione di Trieste, Trieste (Italy); Bradamante, F.; Bressan, A. [INFN, Sezione di Trieste and University of Trieste, Trieste (Italy); Chiosso, M. [INFN, Sezione di Torino and University of Torino, Torino (Italy); Ciliberti, P. [INFN, Sezione di Trieste and University of Trieste, Trieste (Italy); Dalla Torre, S. [INFN, Sezione di Trieste, Trieste (Italy); Denisov, O. [INFN, Sezione di Torino, Torino (Italy); Duic, V. [INFN, Sezione di Trieste and University of Trieste, Trieste (Italy); Ferrero, A. [INFN, Sezione di Torino and University of Torino, Torino (Italy); Finger, M.; Finger, M. [Charles University, Prague (Czech Republic); JINR, Dubna (Russian Federation); Gayde, J.Ch. [CERN, European Organization for Nuclear Research, Geneva (Switzerland); Giorgi, M. [INFN, Sezione di Trieste and University of Trieste, Trieste (Italy); Gobbo, B.; Levorato, S. [INFN, Sezione di Trieste, Trieste (Italy); Maggiora, A. [INFN, Sezione di Torino, Torino (Italy); Martin, A. [INFN, Sezione di Trieste and University of Trieste, Trieste (Italy); Menon, G. [INFN, Sezione di Trieste, Trieste (Italy); Panzieri, D. [INFN, Sezione di Torino and University of East Piemonte, Alessandria (Italy); and others

    2014-12-01

    The gaseous COMPASS RICH-1 detector uses two spherical mirror surfaces, segmented into 116 individual mirrors, to focus the Cherenkov photons onto the detector plane. Any mirror misalignment directly affects the detector resolution. The on-line Continuous Line Alignment and Monitoring (CLAM) photogrammetry-based method has been implemented to measure the alignment of individual mirrors which can be characterized by the center of curvature. The mirror wall reflects a regular grid of retroreflective strips placed inside the detector vessel. Then, the position of each mirror is determined from the image of the grid reflection. The images are collected by four cameras. Any small mirror misalignment results in changes of the grid lines’ positions in the image. The accuracy limits of the CLAM method were checked by laser interferometry and are below 0.1 mrad.

  11. 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 ...

  12. Real-time high-resolution measurement of collagen alignment in dynamically loaded soft tissue.

    Science.gov (United States)

    York, Timothy; Kahan, Lindsey; Lake, Spencer P; Gruev, Viktor

    2014-06-01

    A technique for creating maps of the direction and strength of fiber alignment in collagenous soft tissues is presented. The method uses a division of focal plane polarimeter to measure circularly polarized light transmitted through the tissue. The architecture of the sensor allows measurement of the retardance and fiber alignment at the full frame rate of the sensor without any moving optics. The technique compares favorably to the standard method of using a rotating polarizer. How the new technique enables real-time capture of the full angular spread of fiber alignment and retardance under various cyclic loading conditions is illustrated.

  13. Highly Stretchable Supercapacitors Based on Aligned Carbon Nanotube/Molybdenum Disulfide Composites.

    Science.gov (United States)

    Lv, Tian; Yao, Yao; Li, Ning; Chen, Tao

    2016-08-01

    Stretchable supercapacitors that can sustain their performance under unpredictable tensile force are important elements for practical applications of various portable and wearable electronics. However, the stretchability of most reported supercapacitors was often lower than 100 % because of the limitation of the electrodes used. Herein we developed all-solid-state supercapacitors with a stretchability as high as 240 % by using aligned carbon nanotube composites with compact structure as electrodes. By combined with pseudocapacitive molybdenum disulfide nanosheets, the newly developed supercapacitor showed a specific capacitance of 13.16 F cm(-3) , and also showed excellent cycling retention (98 %) after 10 000 charge-discharge cycles. This work also presents a general and effective approach in developing high-performance electrodes for flexible and stretchable electronics. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. A Workflow to Improve the Alignment of Prostate Imaging with Whole-mount Histopathology.

    Science.gov (United States)

    Yamamoto, Hidekazu; Nir, Dror; Vyas, Lona; Chang, Richard T; Popert, Rick; Cahill, Declan; Challacombe, Ben; Dasgupta, Prokar; Chandra, Ashish

    2014-08-01

    Evaluation of prostate imaging tests against whole-mount histology specimens requires accurate alignment between radiologic and histologic data sets. Misalignment results in false-positive and -negative zones as assessed by imaging. We describe a workflow for three-dimensional alignment of prostate imaging data against whole-mount prostatectomy reference specimens and assess its performance against a standard workflow. Ethical approval was granted. Patients underwent motorized transrectal ultrasound (Prostate Histoscanning) to generate a three-dimensional image of the prostate before radical prostatectomy. The test workflow incorporated steps for axial alignment between imaging and histology, size adjustments following formalin fixation, and use of custom-made parallel cutters and digital caliper instruments. The control workflow comprised freehand cutting and assumed homogeneous block thicknesses at the same relative angles between pathology and imaging sections. Thirty radical prostatectomy specimens were histologically and radiologically processed, either by an alignment-optimized workflow (n = 20) or a control workflow (n = 10). The optimized workflow generated tissue blocks of heterogeneous thicknesses but with no significant drifting in the cutting plane. The control workflow resulted in significantly nonparallel blocks, accurately matching only one out of four histology blocks to their respective imaging data. The image-to-histology alignment accuracy was 20% greater in the optimized workflow (P alignment was observed in the optimized workflow. Evaluation of prostate imaging biomarkers using whole-mount histology references should include a test-to-reference spatial alignment workflow. Copyright © 2014 AUR. Published by Elsevier Inc. All rights reserved.

  15. A flexible statistical model for alignment of label-free proteomics data--incorporating ion mobility and product ion information.

    Science.gov (United States)

    Benjamin, Ashlee M; Thompson, J Will; Soderblom, Erik J; Geromanos, Scott J; Henao, Ricardo; Kraus, Virginia B; Moseley, M Arthur; Lucas, Joseph E

    2013-12-16

    The goal of many proteomics experiments is to determine the abundance of proteins in biological samples, and the variation thereof in various physiological conditions. High-throughput quantitative proteomics, specifically label-free LC-MS/MS, allows rapid measurement of thousands of proteins, enabling large-scale studies of various biological systems. Prior to analyzing these information-rich datasets, raw data must undergo several computational processing steps. We present a method to address one of the essential steps in proteomics data processing--the matching of peptide measurements across samples. We describe a novel method for label-free proteomics data alignment with the ability to incorporate previously unused aspects of the data, particularly ion mobility drift times and product ion information. We compare the results of our alignment method to PEPPeR and OpenMS, and compare alignment accuracy achieved by different versions of our method utilizing various data characteristics. Our method results in increased match recall rates and similar or improved mismatch rates compared to PEPPeR and OpenMS feature-based alignment. We also show that the inclusion of drift time and product ion information results in higher recall rates and more confident matches, without increases in error rates. Based on the results presented here, we argue that the incorporation of ion mobility drift time and product ion information are worthy pursuits. Alignment methods should be flexible enough to utilize all available data, particularly with recent advancements in experimental separation methods.

  16. Wave drag reduction due to a self-aligning aerodisk

    Science.gov (United States)

    Schnepf, Ch.; Wysocki, O.; Schülein, E.

    2015-06-01

    The effect of a self-aligning aerodisk on the wave drag of a blunt slender body in a pitching maneuver has been numerically investigated. The self-alignment was realized by a coupling of the flow solver and a flight mechanics tool. The slender body was pitched with high repetition rate between α = 0° and 20° at M = 1.41. Even at high α, the concept could align the aerodisk to the oncoming flow. In comparison to the reference body without a self-aligning aerodisk, a distinct drag reduction is achieved. A comparison with existing experimental data shows a qualitatively good agreement considering the shock and separation structure and the kinematics of the aerodisk.

  17. Magnet-assisted device-level alignment for the fabrication of membrane-sandwiched polydimethylsiloxane microfluidic devices

    International Nuclear Information System (INIS)

    Lu, J-C; Liao, W-H; Tung, Y-C

    2012-01-01

    Polydimethylsiloxane (PDMS) microfluidic device is one of the most essential techniques that advance microfluidics research in recent decades. PDMS is broadly exploited to construct microfluidic devices due to its unique and advantageous material properties. To realize more functionalities, PDMS microfluidic devices with multi-layer architectures, especially those with sandwiched membranes, have been developed for various applications. However, existing alignment methods for device fabrication are mainly based on manual observations, which are time consuming, inaccurate and inconsistent. This paper develops a magnet-assisted alignment method to enhance device-level alignment accuracy and precision without complicated fabrication processes. In the developed alignment method, magnets are embedded into PDMS layers at the corners of the device. The paired magnets are arranged in symmetric positions at each PDMS layer, and the magnetic attraction force automatically pulls the PDMS layers into the aligned position during assembly. This paper also applies the method to construct a practical microfluidic device, a tunable chaotic micromixer. The results demonstrate the successful operation of the device without failure, which suggests the accurate alignment and reliable bonding achieved by the method. Consequently, the fabrication method developed in this paper is promising to be exploited to construct various membrane-sandwiched PDMS microfluidic devices with more integrated functionalities to advance microfluidics research. (paper)

  18. 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.

  19. Accuracy of Digital vs. Conventional Implant Impressions

    Science.gov (United States)

    Lee, Sang J.; Betensky, Rebecca A.; Gianneschi, Grace E.; Gallucci, German O.

    2015-01-01

    The accuracy of digital impressions greatly influences the clinical viability in implant restorations. The aim of this study is to compare the accuracy of gypsum models acquired from the conventional implant impression to digitally milled models created from direct digitalization by three-dimensional analysis. Thirty gypsum and 30 digitally milled models impressed directly from a reference model were prepared. The models were scanned by a laboratory scanner and 30 STL datasets from each group were imported to an inspection software. The datasets were aligned to the reference dataset by a repeated best fit algorithm and 10 specified contact locations of interest were measured in mean volumetric deviations. The areas were pooled by cusps, fossae, interproximal contacts, horizontal and vertical axes of implant position and angulation. The pooled areas were statistically analysed by comparing each group to the reference model to investigate the mean volumetric deviations accounting for accuracy and standard deviations for precision. Milled models from digital impressions had comparable accuracy to gypsum models from conventional impressions. However, differences in fossae and vertical displacement of the implant position from the gypsum and digitally milled models compared to the reference model, exhibited statistical significance (p<0.001, p=0.020 respectively). PMID:24720423

  20. Preparation and Mechanical Properties of Aligned Discontinuous Carbon Fiber Composites

    OpenAIRE

    DENG Hua; GAO Junpeng; BAO Jianwen

    2018-01-01

    Aligned discontinuous carbon fiber composites were fabricated from aligned discontinuous carbon fiber prepreg, which was prepared from continuous carbon fiber prepreg via mechanical high-frequency cutting. The internal quality and mechanical properties were characterized and compared with continuous carbon fiber composites. The results show that the internal quality of the aligned discontinuous carbon fiber composites is fine and the mechanical properties have high retention rate after the fi...

  1. High Accuracy Evaluation of the Finite Fourier Transform Using Sampled Data

    Science.gov (United States)

    Morelli, Eugene A.

    1997-01-01

    Many system identification and signal processing procedures can be done advantageously in the frequency domain. A required preliminary step for this approach is the transformation of sampled time domain data into the frequency domain. The analytical tool used for this transformation is the finite Fourier transform. Inaccuracy in the transformation can degrade system identification and signal processing results. This work presents a method for evaluating the finite Fourier transform using cubic interpolation of sampled time domain data for high accuracy, and the chirp Zeta-transform for arbitrary frequency resolution. The accuracy of the technique is demonstrated in example cases where the transformation can be evaluated analytically. Arbitrary frequency resolution is shown to be important for capturing details of the data in the frequency domain. The technique is demonstrated using flight test data from a longitudinal maneuver of the F-18 High Alpha Research Vehicle.

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

    Science.gov (United States)

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

    2006-12-01

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

  3. 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.

  4. High accuracy interface characterization of three phase material systems in three dimensions

    DEFF Research Database (Denmark)

    Jørgensen, Peter Stanley; Hansen, Karin Vels; Larsen, Rasmus

    2010-01-01

    Quantification of interface properties such as two phase boundary area and triple phase boundary length is important in the characterization ofmanymaterial microstructures, in particular for solid oxide fuel cell electrodes. Three-dimensional images of these microstructures can be obtained...... by tomography schemes such as focused ion beam serial sectioning or micro-computed tomography. We present a high accuracy method of calculating two phase surface areas and triple phase length of triple phase systems from subvoxel accuracy segmentations of constituent phases. The method performs a three phase...... polygonization of the interface boundaries which results in a non-manifold mesh of connected faces. We show how the triple phase boundaries can be extracted as connected curve loops without branches. The accuracy of the method is analyzed by calculations on geometrical primitives...

  5. XUV ionization of aligned molecules

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-11-15

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

  6. XUV ionization of aligned molecules

    International Nuclear Information System (INIS)

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

    2011-01-01

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

  7. 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.

  8. Intrinsically aligned chemo-mechanical functionalization of twin cantilever structures

    International Nuclear Information System (INIS)

    Toffoli, V; Esch, F; Melli, M; Pozzato, A; Tormen, M; Lazzarino, M; Cataruzza, F; Carrato, S; Scoles, G

    2008-01-01

    Mechanical oscillators became a main focus of research in recent years for potential applications in biomolecule detectors. We recently demonstrated the feasibility of a scheme based on twin cantilevers with a sensitivity down to the single molecule. This approach is extremely promising under the condition that the two terminals of the device can be functionalized with high selectivity and nanometric accuracy by linker molecules. Here we demonstrate a chemo-mechanical method to achieve the intrinsically aligned functionalization of two silicon surfaces, which can be separated by a gap controllable with nanometric precision. The chemical binding of the target molecules in the selected position is obtained through a cycloaddition reaction which exploits the reactivity of the freshly cleaved surfaces that form when the cantilever gap is created. The general validity of this approach is shown by the use in different chemical environments of two compounds with different reactive functional groups.

  9. Design and fabrication of advanced fiber alignment structures for field-installable fiber connectors

    Science.gov (United States)

    Van Erps, Jürgen; Vervaeke, Michael; Sánchez Martínez, Alberto; Beri, Stefano; Debaes, Christof; Watté, Jan; Thienpont, Hugo

    2012-06-01

    Fiber-To-The-Home (FTTH) networks have been adopted as a potential replacement of traditional electrical connections for the 'last mile' transmission of information at bandwidths over 1Gb/s. However, the success and adoption of optical access networks critically depend on the quality and reliability of connections between optical fibers. In particular a further reduction of insertion loss of field-installable connectors must be achieved without a significant increase in component cost. This requires precise alignment of fibers that can differ in terms of ellipticity, eccentricity or diameter and seems hardly achievable using today's widespread ferrule-based alignment systems. Novel low-cost structures for bare fiber alignment with outstanding positioning accuracies are strongly desired as they would allow reducing loss beyond the level achievable with ferrule-bore systems. However, the realization of such alignment system is challenging as it should provide sufficient force to position the fiber with sub-micron accuracy required in positioning the fiber. In this contribution we propose, design and prototype a bare-fiber alignment system which makes use of deflectable/compressible micro-cantilevers. Such cantilevers behave as springs and provide self-centering functionality to the structure. Simulations of the mechanical properties of the cantilevers are carried out in order to get an analytical approximation and a mathematical model of the spring constant and stress in the structure. Elastic constants of the order of 104 to 105N/m are found out to be compatible with a proof stress of 70 MPa. Finally a first self-centering structure is prototyped in PMMA using our Deep Proton Writing technology. The spring constants of the fabricated cantilevers are in the range of 4 to 6 × 104N/m and the stress is in the range 10 to 20 MPa. These self-centering structures have the potential to become the basic building blocks for a new generation of field-installable connectors.

  10. Preparation of highly aligned silicon oxide nanowires with stable intensive photoluminescence

    International Nuclear Information System (INIS)

    Duraia, El-Shazly M.; Mansurov, Z.A.; Tokmolden, S.; Beall, Gary W.

    2010-01-01

    In this work we report the successful formation of highly aligned vertical silicon oxide nanowires. The source of silicon was from the substrate itself without any additional source of silicon. X-ray measurement demonstrated that our nanowires are amorphous. Photoluminescence measurements were conducted through 18 months and indicated that there is a very good intensive emission peaks near the violet regions. The FTIR measurements indicated the existence of peaks at 463, 604, 795 and a wide peak at 1111 cm -1 and this can be attributed to Si-O-Si and Si-O stretching vibrations. We also report the formation of the octopus-like silicon oxide nanowires and the growth mechanism of these structures was discussed.

  11. Preparation of highly aligned silicon oxide nanowires with stable intensive photoluminescence

    Energy Technology Data Exchange (ETDEWEB)

    Duraia, El-Shazly M., E-mail: duraia_physics@yahoo.co [Suez Canal University, Faculty of Science, Physics Department, Ismailia (Egypt); Al-Farabi Kazakh National University, Almaty (Kazakhstan); Institute of Physics and Technology, 11 Ibragimov Street, 050032 Almaty (Kazakhstan); Mansurov, Z.A. [Al-Farabi Kazakh National University, Almaty (Kazakhstan); Tokmolden, S. [Institute of Physics and Technology, 11 Ibragimov Street, 050032 Almaty (Kazakhstan); Beall, Gary W. [Texas State University-San Marcos, Department of Chemistry and Biochemistry, 601 University Dr., San Marcos, TX 78666 (United States)

    2010-02-15

    In this work we report the successful formation of highly aligned vertical silicon oxide nanowires. The source of silicon was from the substrate itself without any additional source of silicon. X-ray measurement demonstrated that our nanowires are amorphous. Photoluminescence measurements were conducted through 18 months and indicated that there is a very good intensive emission peaks near the violet regions. The FTIR measurements indicated the existence of peaks at 463, 604, 795 and a wide peak at 1111 cm{sup -1} and this can be attributed to Si-O-Si and Si-O stretching vibrations. We also report the formation of the octopus-like silicon oxide nanowires and the growth mechanism of these structures was discussed.

  12. Simulation based assembly and alignment process ability analysis for line replaceable units of the high power solid state laser facility

    International Nuclear Information System (INIS)

    Wang, Junfeng; Lu, Cong; Li, Shiqi

    2016-01-01

    Highlights: • Discrete event simulation is applied to analyze the assembly and alignment process ability of LRUs in SG-III facility. • The overall assembly and alignment process of LRUs with specific characteristics is described. • An extended-directed graph is proposed to express the assembly and alignment process of LRUs. • Different scenarios have been simulated to evaluate assembling process ability of LRUs and decision making is supported to ensure the construction millstone. - Abstract: Line replaceable units (LRUs) are important components of the very large high power solid state laser facilities. The assembly and alignment process ability of LRUs will impact the construction milestone of facilities. This paper describes the use of discrete event simulation method for assembly and alignment process analysis of LRUs in such facilities. The overall assembly and alignment process for LRUs is presented based on the layout of the optics assembly laboratory and the process characteristics are analyzed. An extended-directed graph is proposed to express the assembly and alignment process of LRUs. Taking the LRUs of disk amplifier system in Shen Guang-III (SG-III) facility as the example, some process simulation models are built based on the Quest simulation platform. The constraints, such as duration, equipment, technician and part supply, are considered in the simulation models. Different simulation scenarios have been carried out to evaluate the assembling process ability of LRUs. The simulation method can provide a valuable decision making and process optimization tool for the optics assembly laboratory layout and the process working out of such facilities.

  13. Simulation based assembly and alignment process ability analysis for line replaceable units of the high power solid state laser facility

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Junfeng; Lu, Cong; Li, Shiqi, E-mail: sqli@hust.edu.cn

    2016-11-15

    Highlights: • Discrete event simulation is applied to analyze the assembly and alignment process ability of LRUs in SG-III facility. • The overall assembly and alignment process of LRUs with specific characteristics is described. • An extended-directed graph is proposed to express the assembly and alignment process of LRUs. • Different scenarios have been simulated to evaluate assembling process ability of LRUs and decision making is supported to ensure the construction millstone. - Abstract: Line replaceable units (LRUs) are important components of the very large high power solid state laser facilities. The assembly and alignment process ability of LRUs will impact the construction milestone of facilities. This paper describes the use of discrete event simulation method for assembly and alignment process analysis of LRUs in such facilities. The overall assembly and alignment process for LRUs is presented based on the layout of the optics assembly laboratory and the process characteristics are analyzed. An extended-directed graph is proposed to express the assembly and alignment process of LRUs. Taking the LRUs of disk amplifier system in Shen Guang-III (SG-III) facility as the example, some process simulation models are built based on the Quest simulation platform. The constraints, such as duration, equipment, technician and part supply, are considered in the simulation models. Different simulation scenarios have been carried out to evaluate the assembling process ability of LRUs. The simulation method can provide a valuable decision making and process optimization tool for the optics assembly laboratory layout and the process working out of such facilities.

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

    DEFF Research Database (Denmark)

    Wernersson, Rasmus; Pedersen, Anders Gorm

    2003-01-01

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

  15. A Smart High Accuracy Silicon Piezoresistive Pressure Sensor Temperature Compensation System

    Directory of Open Access Journals (Sweden)

    Guanwu Zhou

    2014-07-01

    Full Text Available Theoretical analysis in this paper indicates that the accuracy of a silicon piezoresistive pressure sensor is mainly affected by thermal drift, and varies nonlinearly with the temperature. Here, a smart temperature compensation system to reduce its effect on accuracy is proposed. Firstly, an effective conditioning circuit for signal processing and data acquisition is designed. The hardware to implement the system is fabricated. Then, a program is developed on LabVIEW which incorporates an extreme learning machine (ELM as the calibration algorithm for the pressure drift. The implementation of the algorithm was ported to a micro-control unit (MCU after calibration in the computer. Practical pressure measurement experiments are carried out to verify the system’s performance. The temperature compensation is solved in the interval from −40 to 85 °C. The compensated sensor is aimed at providing pressure measurement in oil-gas pipelines. Compared with other algorithms, ELM acquires higher accuracy and is more suitable for batch compensation because of its higher generalization and faster learning speed. The accuracy, linearity, zero temperature coefficient and sensitivity temperature coefficient of the tested sensor are 2.57% FS, 2.49% FS, 8.1 × 10−5/°C and 29.5 × 10−5/°C before compensation, and are improved to 0.13%FS, 0.15%FS, 1.17 × 10−5/°C and 2.1 × 10−5/°C respectively, after compensation. The experimental results demonstrate that the proposed system is valid for the temperature compensation and high accuracy requirement of the sensor.

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

    International Nuclear Information System (INIS)

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

    2006-01-01

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

  17. Inertial Measures of Motion for Clinical Biomechanics: Comparative Assessment of Accuracy under Controlled Conditions – Changes in Accuracy over Time

    Science.gov (United States)

    Lebel, Karina; Boissy, Patrick; Hamel, Mathieu; Duval, Christian

    2015-01-01

    Background Interest in 3D inertial motion tracking devices (AHRS) has been growing rapidly among the biomechanical community. Although the convenience of such tracking devices seems to open a whole new world of possibilities for evaluation in clinical biomechanics, its limitations haven’t been extensively documented. The objectives of this study are: 1) to assess the change in absolute and relative accuracy of multiple units of 3 commercially available AHRS over time; and 2) to identify different sources of errors affecting AHRS accuracy and to document how they may affect the measurements over time. Methods This study used an instrumented Gimbal table on which AHRS modules were carefully attached and put through a series of velocity-controlled sustained motions including 2 minutes motion trials (2MT) and 12 minutes multiple dynamic phases motion trials (12MDP). Absolute accuracy was assessed by comparison of the AHRS orientation measurements to those of an optical gold standard. Relative accuracy was evaluated using the variation in relative orientation between modules during the trials. Findings Both absolute and relative accuracy decreased over time during 2MT. 12MDP trials showed a significant decrease in accuracy over multiple phases, but accuracy could be enhanced significantly by resetting the reference point and/or compensating for initial Inertial frame estimation reference for each phase. Interpretation The variation in AHRS accuracy observed between the different systems and with time can be attributed in part to the dynamic estimation error, but also and foremost, to the ability of AHRS units to locate the same Inertial frame. Conclusions Mean accuracies obtained under the Gimbal table sustained conditions of motion suggest that AHRS are promising tools for clinical mobility assessment under constrained conditions of use. However, improvement in magnetic compensation and alignment between AHRS modules are desirable in order for AHRS to reach their

  18. INTRINSIC ALIGNMENT OF CLUSTER GALAXIES: THE REDSHIFT EVOLUTION

    International Nuclear Information System (INIS)

    Hao Jiangang; Kubo, Jeffrey M.; Feldmann, Robert; Annis, James; Johnston, David E.; Lin Huan; McKay, Timothy A.

    2011-01-01

    We present measurements of two types of cluster galaxy alignments based on a volume limited and highly pure (≥90%) sample of clusters from the GMBCG catalog derived from Data Release 7 of the Sloan Digital Sky Survey (SDSS DR7). We detect a clear brightest cluster galaxy (BCG) alignment (the alignment of major axis of the BCG toward the distribution of cluster satellite galaxies). We find that the BCG alignment signal becomes stronger as the redshift and BCG absolute magnitude decrease and becomes weaker as BCG stellar mass decreases. No dependence of the BCG alignment on cluster richness is found. We can detect a statistically significant (≥3σ) satellite alignment (the alignment of the major axes of the cluster satellite galaxies toward the BCG) only when we use the isophotal fit position angles (P.A.s), and the satellite alignment depends on the apparent magnitudes rather than the absolute magnitudes of the BCGs. This suggests that the detected satellite alignment based on isophotal P.A.s from the SDSS pipeline is possibly due to the contamination from the diffuse light of nearby BCGs. We caution that this should not be simply interpreted as non-existence of the satellite alignment, but rather that we cannot detect them with our current photometric SDSS data. We perform our measurements on both SDSS r-band and i-band data, but do not observe a passband dependence of the alignments.

  19. Alignment and vibration issues in TeV linear collider design

    International Nuclear Information System (INIS)

    Fischer, G.E.

    1989-07-01

    The next generation of linear colliders will require alignment accuracies and stabilities of component placement at least one, perhaps two, orders of magnitude better than can be achieved by the conventional methods and procedures in practice today. The magnitudes of these component-placement tolerances for current designs of various linear collider subsystems are tabulated. In the micron range, long-term ground motion is sufficiently rapid that on-line reference and mechanical correction systems are called for. Some recent experiences with the upgraded SLAC laser alignment systems and examples of some conceivable solutions for the future are described. The so called ''girder'' problem is discussed in the light of ambient and vibratory disturbances. The importance of the quality of the underlying geology is stressed. The necessity and limitations of public-beam-derived placement information are mentioned. 40 refs., 4 figs., 1 tab

  20. Controlling residual dipolar couplings in high-resolution NMR of proteins by strain induced alignment in a gel

    International Nuclear Information System (INIS)

    Ishii, Yoshitaka; Markus, Michelle A.; Tycko, Robert

    2001-01-01

    Water-soluble biological macromolecules can be weakly aligned by dissolution in a strained, hydrated gel such as cross-linked polyacrylamide, an effect termed 'strain-induced alignment in a gel' (SAG). SAG induces nonzero nuclear magnetic dipole-dipole couplings that can be measured in high-resolution NMR spectra and used as structural constraints. The dependence of experimental 15 N- 1 H dipolar couplings extracted from two-dimensional heteronuclear single quantum coherence (HSQC) spectra on several properties of compressed polyacrylamide, including the extent of compression, the polyacrylamide concentration, and the cross-link density, is reported for the B1 immunoglobulin binding domain of streptococcal protein G (protein G/B1, 57 residues). It is shown that the magnitude of macromolecular alignment can be widely varied by adjusting these properties, although the orientation and asymmetry of the alignment tensor are not affected significantly. The dependence of the 15 N relaxation times T 1 and T 2 of protein G/B1 on polyacrylamide concentration are also reported. In addition, the results of 15 N relaxation and HSQC experiments on the RNA binding domain of prokaryotic protein S4 from Bacillus stearothermophilus (S4 Δ41, residues 43-200) in a compressed polyacrylamide gel are presented. These results demonstrate the applicability of SAG to proteins of higher molecular weight and greater complexity. A modified in-phase/anti-phase (IPAP) HSQC technique is described that suppresses natural-abundance 15 N background signals from amide groups in polyacrylamide, resulting in cleaner HSQC spectra in SAG experiments. The mechanism of protein alignment in strained polyacrylamide gels is contrasted with that in liquid crystalline media

  1. High-rate capability silicon decorated vertically aligned carbon nanotubes for Li-ion batteries

    Energy Technology Data Exchange (ETDEWEB)

    Gohier, Aurelien; Kim, Ki-Hwan; Maurice, Jean-Luc; Cojocaru, Costel Sorin [Laboratoire de Physique des Interfaces et des Couches Minces, LPICM, Ecole Polytechnique, route de Saclay, 91128 Palaiseau Cedex (France); Laik, Barbara; Pereira-Ramos, Jean-Pierre [Institut de Chimie et des Materiaux Paris-Est, ICMPE/GESMAT, UMR 7182 CNRS-UPEC, 2 rue Henri Dunant, 94320 Thiais (France); Van, Pierre Tran [Renault SAS, DREAM/DETA/SEE, 1, avenue du Golf, 78288 Guyancourt (France)

    2012-05-15

    The concept of a hybrid nanostructured collector made of thin vertically aligned carbon nanotubes (CNTs) decorated with Si nanoparticles provides high power density anodes in lithium-ion batteries. An impressive rate capability is achieved due to the efficient electronic conduction of CNTs combined with well defined electroactive Si nanoparticles: capacities of 3000 mAh g{sup -1} at 1.3C and 800 mAh g{sup -1} at 15C are achieved. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  2. High-yield growth of vertically aligned carbon nanotubes on a continuously moving substrate

    International Nuclear Information System (INIS)

    Guzman de Villoria, R; Hart, A J; Steiner, S A III; Wardle, B L; Figueredo, S L; Slocum, A H

    2009-01-01

    Vertically aligned carbon nanotube (CNT) arrays are grown on a moving substrate, demonstrating continuous growth of nanoscale materials with long-range order. A cold-wall chamber with an oscillating moving platform is used to locally heat a silicon growth substrate coated with an Fe/Al 2 O 3 catalyst film for CNT growth via chemical vapor deposition. The reactant gases are introduced over the substrate through a directed nozzle to attain high-yield CNT growth. Aligned multi-wall carbon nanotube arrays (or 'forests') with heights of ∼1 mm are achieved at substrate speeds up to 2.4 mm s -1 . Arrays grown on moving substrates at different velocities are studied in order to identify potential physical limitations of repeatable and fast growth on a continuous basis. No significant differences are noted between static and moving growth as characterized by scanning electron microscopy and Raman spectroscopy, although overall growth height is marginally reduced at the highest substrate velocity. CNT arrays produced on moving substrates are also found to be comparable to those produced through well-characterized batch processes consistent with a base-growth mechanism. Growth parameters required for the moving furnace are found to differ only slightly from those used in a comparable batch process; thermal uniformity appears to be the critical parameter for achieving large-area uniform array growth. If the continuous-growth technology is combined with a reaction zone isolation scheme common in other types of processing (e.g., in the manufacture of carbon fibers), large-scale dense and aligned CNT arrays may be efficiently grown and harvested for numerous applications including providing interlayers for advanced composite reinforcement and improved electrical and thermal transport.

  3. High-yield growth of vertically aligned carbon nanotubes on a continuously moving substrate.

    Science.gov (United States)

    Guzmán de Villoria, R; Figueredo, S L; Hart, A J; Steiner, S A; Slocum, A H; Wardle, B L

    2009-10-07

    Vertically aligned carbon nanotube (CNT) arrays are grown on a moving substrate, demonstrating continuous growth of nanoscale materials with long-range order. A cold-wall chamber with an oscillating moving platform is used to locally heat a silicon growth substrate coated with an Fe/Al2O3 catalyst film for CNT growth via chemical vapor deposition. The reactant gases are introduced over the substrate through a directed nozzle to attain high-yield CNT growth. Aligned multi-wall carbon nanotube arrays (or 'forests') with heights of approximately 1 mm are achieved at substrate speeds up to 2.4 mm s(-1). Arrays grown on moving substrates at different velocities are studied in order to identify potential physical limitations of repeatable and fast growth on a continuous basis. No significant differences are noted between static and moving growth as characterized by scanning electron microscopy and Raman spectroscopy, although overall growth height is marginally reduced at the highest substrate velocity. CNT arrays produced on moving substrates are also found to be comparable to those produced through well-characterized batch processes consistent with a base-growth mechanism. Growth parameters required for the moving furnace are found to differ only slightly from those used in a comparable batch process; thermal uniformity appears to be the critical parameter for achieving large-area uniform array growth. If the continuous-growth technology is combined with a reaction zone isolation scheme common in other types of processing (e.g., in the manufacture of carbon fibers), large-scale dense and aligned CNT arrays may be efficiently grown and harvested for numerous applications including providing interlayers for advanced composite reinforcement and improved electrical and thermal transport.

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

    Science.gov (United States)

    Huang, Jiaxiang; Gong, Maoguo; Ma, Lijia

    2016-10-19

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

  5. Highly aligned vertical GaN nanowires using submonolayer metal catalysts

    Science.gov (United States)

    Wang, George T [Albuquerque, NM; Li, Qiming [Albuquerque, NM; Creighton, J Randall [Albuquerque, NM

    2010-06-29

    A method for forming vertically oriented, crystallographically aligned nanowires (nanocolumns) using monolayer or submonolayer quantities of metal atoms to form uniformly sized metal islands that serve as catalysts for MOCVD growth of Group III nitride nanowires.

  6. NiftyPET: a High-throughput Software Platform for High Quantitative Accuracy and Precision PET Imaging and Analysis.

    Science.gov (United States)

    Markiewicz, Pawel J; Ehrhardt, Matthias J; Erlandsson, Kjell; Noonan, Philip J; Barnes, Anna; Schott, Jonathan M; Atkinson, David; Arridge, Simon R; Hutton, Brian F; Ourselin, Sebastien

    2018-01-01

    We present a standalone, scalable and high-throughput software platform for PET image reconstruction and analysis. We focus on high fidelity modelling of the acquisition processes to provide high accuracy and precision quantitative imaging, especially for large axial field of view scanners. All the core routines are implemented using parallel computing available from within the Python package NiftyPET, enabling easy access, manipulation and visualisation of data at any processing stage. The pipeline of the platform starts from MR and raw PET input data and is divided into the following processing stages: (1) list-mode data processing; (2) accurate attenuation coefficient map generation; (3) detector normalisation; (4) exact forward and back projection between sinogram and image space; (5) estimation of reduced-variance random events; (6) high accuracy fully 3D estimation of scatter events; (7) voxel-based partial volume correction; (8) region- and voxel-level image analysis. We demonstrate the advantages of this platform using an amyloid brain scan where all the processing is executed from a single and uniform computational environment in Python. The high accuracy acquisition modelling is achieved through span-1 (no axial compression) ray tracing for true, random and scatter events. Furthermore, the platform offers uncertainty estimation of any image derived statistic to facilitate robust tracking of subtle physiological changes in longitudinal studies. The platform also supports the development of new reconstruction and analysis algorithms through restricting the axial field of view to any set of rings covering a region of interest and thus performing fully 3D reconstruction and corrections using real data significantly faster. All the software is available as open source with the accompanying wiki-page and test data.

  7. Metrology and Alignment of Light Weight Grazing Incidence X-Ray Mirrors

    Science.gov (United States)

    Zhang, William; Content, David; Petre, Robert; Saha, Timo

    2000-01-01

    Metrology and alignment of light weight X-ray optics have been a challenge for two reasons: (1) that the intrinsic mirror quality and distortions caused by handling can not be easily separated, and (2) the diffraction limits of the visible light become a severe problem at the order of one arc-minute. Traditional methods of using a normal incident pencil or small parallel beam which monitors a tiny fraction of the mirror in question at a given time can not adequately monitor those distortions. We are developing a normal incidence setup that monitors a large fraction, if not the whole, of the mirror at any given time. It will allow us to align thin X-ray mirrors to-an accuracy of a few arc seconds or to a limit dominated by the mirror intrinsic quality.

  8. 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...

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

    International Nuclear Information System (INIS)

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

    2017-01-01

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

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

    Science.gov (United States)

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

    2017-04-01

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

  11. 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

  12. Registration accuracy and quality of real-life images.

    Directory of Open Access Journals (Sweden)

    Wei-Yen Hsu

    Full Text Available BACKGROUND: A common registration problem for the application of consumer device is to align all the acquired image sequences into a complete scene. Image alignment requires a registration algorithm that will compensate as much as possible for geometric variability among images. However, images captured views from a real scene usually produce different distortions. Some are derived from the optic characteristics of image sensors, and others are caused by the specific scenes and objects. METHODOLOGY/PRINCIPAL FINDINGS: An image registration algorithm considering the perspective projection is proposed for the application of consumer devices in this study. It exploits a multiresolution wavelet-based method to extract significant features. An analytic differential approach is then proposed to achieve fast convergence of point matching. Finally, the registration accuracy is further refined to obtain subpixel precision by a feature-based modified Levenberg-Marquardt method. Due to its feature-based and nonlinear characteristic, it converges considerably faster than most other methods. In addition, vignette compensation and color difference adjustment are also performed to further improve the quality of registration results. CONCLUSIONS/SIGNIFICANCE: The performance of the proposed method is evaluated by testing the synthetic and real images acquired by a hand-held digital still camera and in comparison with two registration techniques in terms of the squared sum of intensity differences (SSD and correlation coefficient (CC. The results indicate that the proposed method is promising in registration accuracy and quality, which are statistically significantly better than other two approaches.

  13. High-accuracy self-mixing interferometer based on single high-order orthogonally polarized feedback effects.

    Science.gov (United States)

    Zeng, Zhaoli; Qu, Xueming; Tan, Yidong; Tan, Runtao; Zhang, Shulian

    2015-06-29

    A simple and high-accuracy self-mixing interferometer based on single high-order orthogonally polarized feedback effects is presented. The single high-order feedback effect is realized when dual-frequency laser reflects numerous times in a Fabry-Perot cavity and then goes back to the laser resonator along the same route. In this case, two orthogonally polarized feedback fringes with nanoscale resolution are obtained. This self-mixing interferometer has the advantages of higher sensitivity to weak signal than that of conventional interferometer. In addition, two orthogonally polarized fringes are useful for discriminating the moving direction of measured object. The experiment of measuring 2.5nm step is conducted, which shows a great potential in nanometrology.

  14. Automated novel high-accuracy miniaturized positioning system for use in analytical instrumentation

    Science.gov (United States)

    Siomos, Konstadinos; Kaliakatsos, John; Apostolakis, Manolis; Lianakis, John; Duenow, Peter

    1996-01-01

    The development of three-dimensional automotive devices (micro-robots) for applications in analytical instrumentation, clinical chemical diagnostics and advanced laser optics, depends strongly on the ability of such a device: firstly to be positioned with high accuracy, reliability, and automatically, by means of user friendly interface techniques; secondly to be compact; and thirdly to operate under vacuum conditions, free of most of the problems connected with conventional micropositioners using stepping-motor gear techniques. The objective of this paper is to develop and construct a mechanically compact computer-based micropositioning system for coordinated motion in the X-Y-Z directions with: (1) a positioning accuracy of less than 1 micrometer, (the accuracy of the end-position of the system is controlled by a hard/software assembly using a self-constructed optical encoder); (2) a heat-free propulsion mechanism for vacuum operation; and (3) synchronized X-Y motion.

  15. Identification and delineation of areas flood hazard using high accuracy of DEM data

    Science.gov (United States)

    Riadi, B.; Barus, B.; Widiatmaka; Yanuar, M. J. P.; Pramudya, B.

    2018-05-01

    Flood incidents that often occur in Karawang regency need to be mitigated. These expectations exist on technologies that can predict, anticipate and reduce disaster risks. Flood modeling techniques using Digital Elevation Model (DEM) data can be applied in mitigation activities. High accuracy DEM data used in modeling, will result in better flooding flood models. The result of high accuracy DEM data processing will yield information about surface morphology which can be used to identify indication of flood hazard area. The purpose of this study was to identify and describe flood hazard areas by identifying wetland areas using DEM data and Landsat-8 images. TerraSAR-X high-resolution data is used to detect wetlands from landscapes, while land cover is identified by Landsat image data. The Topography Wetness Index (TWI) method is used to detect and identify wetland areas with basic DEM data, while for land cover analysis using Tasseled Cap Transformation (TCT) method. The result of TWI modeling yields information about potential land of flood. Overlay TWI map with land cover map that produces information that in Karawang regency the most vulnerable areas occur flooding in rice fields. The spatial accuracy of the flood hazard area in this study was 87%.

  16. Accuracy of Estimating Highly Eccentric Binary Black Hole Parameters with Gravitational-wave Detections

    Science.gov (United States)

    Gondán, László; Kocsis, Bence; Raffai, Péter; Frei, Zsolt

    2018-03-01

    Mergers of stellar-mass black holes on highly eccentric orbits are among the targets for ground-based gravitational-wave detectors, including LIGO, VIRGO, and KAGRA. These sources may commonly form through gravitational-wave emission in high-velocity dispersion systems or through the secular Kozai–Lidov mechanism in triple systems. Gravitational waves carry information about the binaries’ orbital parameters and source location. Using the Fisher matrix technique, we determine the measurement accuracy with which the LIGO–VIRGO–KAGRA network could measure the source parameters of eccentric binaries using a matched filtering search of the repeated burst and eccentric inspiral phases of the waveform. We account for general relativistic precession and the evolution of the orbital eccentricity and frequency during the inspiral. We find that the signal-to-noise ratio and the parameter measurement accuracy may be significantly higher for eccentric sources than for circular sources. This increase is sensitive to the initial pericenter distance, the initial eccentricity, and the component masses. For instance, compared to a 30 {M}ȯ –30 {M}ȯ non-spinning circular binary, the chirp mass and sky-localization accuracy can improve by a factor of ∼129 (38) and ∼2 (11) for an initially highly eccentric binary assuming an initial pericenter distance of 20 M tot (10 M tot).

  17. MaxAlign: maximizing usable data in an alignment

    DEFF Research Database (Denmark)

    Oliveira, Rodrigo Gouveia; Sackett, Peter Wad; Pedersen, Anders Gorm

    2007-01-01

    Align. In this paper we also introduce a new simple measure of tree similarity, Normalized Symmetric Similarity (NSS) that we consider useful for comparing tree topologies. CONCLUSION: We demonstrate how MaxAlign is helpful in detecting misaligned or defective sequences without requiring manual inspection. We also...

  18. Rapid detection, classification and accurate alignment of up to a million or more related protein sequences.

    Science.gov (United States)

    Neuwald, Andrew F

    2009-08-01

    The patterns of sequence similarity and divergence present within functionally diverse, evolutionarily related proteins contain implicit information about corresponding biochemical similarities and differences. A first step toward accessing such information is to statistically analyze these patterns, which, in turn, requires that one first identify and accurately align a very large set of protein sequences. Ideally, the set should include many distantly related, functionally divergent subgroups. Because it is extremely difficult, if not impossible for fully automated methods to align such sequences correctly, researchers often resort to manual curation based on detailed structural and biochemical information. However, multiply-aligning vast numbers of sequences in this way is clearly impractical. This problem is addressed using Multiply-Aligned Profiles for Global Alignment of Protein Sequences (MAPGAPS). The MAPGAPS program uses a set of multiply-aligned profiles both as a query to detect and classify related sequences and as a template to multiply-align the sequences. It relies on Karlin-Altschul statistics for sensitivity and on PSI-BLAST (and other) heuristics for speed. Using as input a carefully curated multiple-profile alignment for P-loop GTPases, MAPGAPS correctly aligned weakly conserved sequence motifs within 33 distantly related GTPases of known structure. By comparison, the sequence- and structurally based alignment methods hmmalign and PROMALS3D misaligned at least 11 and 23 of these regions, respectively. When applied to a dataset of 65 million protein sequences, MAPGAPS identified, classified and aligned (with comparable accuracy) nearly half a million putative P-loop GTPase sequences. A C++ implementation of MAPGAPS is available at http://mapgaps.igs.umaryland.edu. Supplementary data are available at Bioinformatics online.

  19. Aligning for Innovation - Alignment Strategy to Drive Innovation

    Science.gov (United States)

    Johnson, Hurel; Teltschik, David; Bussey, Horace, Jr.; Moy, James

    2010-01-01

    With the sudden need for innovation that will help the country achieve its long-term space exploration objectives, the question of whether NASA is aligned effectively to drive the innovation that it so desperately needs to take space exploration to the next level should be entertained. Authors such as Robert Kaplan and David North have noted that companies that use a formal system for implementing strategy consistently outperform their peers. They have outlined a six-stage management systems model for implementing strategy, which includes the aligning of the organization towards its objectives. This involves the alignment of the organization from the top down. This presentation will explore the impacts of existing U.S. industrial policy on technological innovation; assess the current NASA organizational alignment and its impacts on driving technological innovation; and finally suggest an alternative approach that may drive the innovation needed to take the world to the next level of space exploration, with NASA truly leading the way.

  20. Octahedral Tin Dioxide Nanocrystals Anchored on Vertically Aligned Carbon Aerogels as High Capacity Anode Materials for Lithium-Ion Batteries

    Science.gov (United States)

    Liu, Mingkai; Liu, Yuqing; Zhang, Yuting; Li, Yiliao; Zhang, Peng; Yan, Yan; Liu, Tianxi

    2016-01-01

    A novel binder-free graphene - carbon nanotubes - SnO2 (GCNT-SnO2) aerogel with vertically aligned pores was prepared via a simple and efficient directional freezing method. SnO2 octahedrons exposed of {221} high energy facets were uniformly distributed and tightly anchored on multidimensional graphene/carbon nanotube (GCNT) composites. Vertically aligned pores can effectively prevent the emersion of “closed” pores which cannot load the active SnO2 nanoparticles, further ensure quick immersion of electrolyte throughout the aerogel, and can largely shorten the transport distance between lithium ions and active sites of SnO2. Especially, excellent electrical conductivity of GCNT-SnO2 aerogel was achieved as a result of good interconnected networks of graphene and CNTs. Furthermore, meso- and macroporous structures with large surface area created by the vertically aligned pores can provide great benefit to the favorable transport kinetics for both lithium ion and electrons and afford sufficient space for volume expansion of SnO2. Due to the well-designed architecture of GCNT-SnO2 aerogel, a high specific capacity of 1190 mAh/g with good long-term cycling stability up to 1000 times was achieved. This work provides a promising strategy for preparing free-standing and binder-free active electrode materials with high performance for lithium ion batteries and other energy storage devices. PMID:27510357

  1. First performance evaluation of software for automatic segmentation, labeling and reformation of anatomical aligned axial images of the thoracolumbar spine at CT

    Energy Technology Data Exchange (ETDEWEB)

    Scholtz, Jan-Erik, E-mail: janerikscholtz@gmail.com; Wichmann, Julian L.; Kaup, Moritz; Fischer, Sebastian; Kerl, J. Matthias; Lehnert, Thomas; Vogl, Thomas J.; Bauer, Ralf W.

    2015-03-15

    Highlights: •Automatic segmentation and labeling of the thoracolumbar spine. •Automatically generated double-angulated and aligned axial images of spine segments. •High grade of accurateness for the symmetric depiction of anatomical structures. •Time-saving and may improve workflow in daily practice. -- Abstract: Objectives: To evaluate software for automatic segmentation, labeling and reformation of anatomical aligned axial images of the thoracolumbar spine on CT in terms of accuracy, potential for time savings and workflow improvement. Material and methods: 77 patients (28 women, 49 men, mean age 65.3 ± 14.4 years) with known or suspected spinal disorders (degenerative spine disease n = 32; disc herniation n = 36; traumatic vertebral fractures n = 9) underwent 64-slice MDCT with thin-slab reconstruction. Time for automatic labeling of the thoracolumbar spine and reconstruction of double-angulated axial images of the pathological vertebrae was compared with manually performed reconstruction of anatomical aligned axial images. Reformatted images of both reconstruction methods were assessed by two observers regarding accuracy of symmetric depiction of anatomical structures. Results: In 33 cases double-angulated axial images were created in 1 vertebra, in 28 cases in 2 vertebrae and in 16 cases in 3 vertebrae. Correct automatic labeling was achieved in 72 of 77 patients (93.5%). Errors could be manually corrected in 4 cases. Automatic labeling required 1 min in average. In cases where anatomical aligned axial images of 1 vertebra were created, reconstructions made by hand were significantly faster (p < 0.05). Automatic reconstruction was time-saving in cases of 2 and more vertebrae (p < 0.05). Both reconstruction methods revealed good image quality with excellent inter-observer agreement. Conclusion: The evaluated software for automatic labeling and anatomically aligned, double-angulated axial image reconstruction of the thoracolumbar spine on CT is time

  2. Nonintrusive Finger-Vein Recognition System Using NIR Image Sensor and Accuracy Analyses According to Various Factors

    Directory of Open Access Journals (Sweden)

    Tuyen Danh Pham

    2015-07-01

    Full Text Available Biometrics is a technology that enables an individual person to be identified based on human physiological and behavioral characteristics. Among biometrics technologies, face recognition has been widely used because of its advantages in terms of convenience and non-contact operation. However, its performance is affected by factors such as variation in the illumination, facial expression, and head pose. Therefore, fingerprint and iris recognitions are preferred alternatives. However, the performance of the former can be adversely affected by the skin condition, including scarring and dryness. In addition, the latter has the disadvantages of high cost, large system size, and inconvenience to the user, who has to align their eyes with the iris camera. In an attempt to overcome these problems, finger-vein recognition has been vigorously researched, but an analysis of its accuracies according to various factors has not received much attention. Therefore, we propose a nonintrusive finger-vein recognition system using a near infrared (NIR image sensor and analyze its accuracies considering various factors. The experimental results obtained with three databases showed that our system can be operated in real applications with high accuracy; and the dissimilarity of the finger-veins of different people is larger than that of the finger types and hands.

  3. Nonintrusive Finger-Vein Recognition System Using NIR Image Sensor and Accuracy Analyses According to Various Factors.

    Science.gov (United States)

    Pham, Tuyen Danh; Park, Young Ho; Nguyen, Dat Tien; Kwon, Seung Yong; Park, Kang Ryoung

    2015-07-13

    Biometrics is a technology that enables an individual person to be identified based on human physiological and behavioral characteristics. Among biometrics technologies, face recognition has been widely used because of its advantages in terms of convenience and non-contact operation. However, its performance is affected by factors such as variation in the illumination, facial expression, and head pose. Therefore, fingerprint and iris recognitions are preferred alternatives. However, the performance of the former can be adversely affected by the skin condition, including scarring and dryness. In addition, the latter has the disadvantages of high cost, large system size, and inconvenience to the user, who has to align their eyes with the iris camera. In an attempt to overcome these problems, finger-vein recognition has been vigorously researched, but an analysis of its accuracies according to various factors has not received much attention. Therefore, we propose a nonintrusive finger-vein recognition system using a near infrared (NIR) image sensor and analyze its accuracies considering various factors. The experimental results obtained with three databases showed that our system can be operated in real applications with high accuracy; and the dissimilarity of the finger-veins of different people is larger than that of the finger types and hands.

  4. Nucleation, Growth, and Alignment of Poly(3-hexylthiophene) Nanofibers for High-Performance OFETs.

    Science.gov (United States)

    Persson, Nils E; Chu, Ping-Hsun; McBride, Michael; Grover, Martha; Reichmanis, Elsa

    2017-04-18

    Conjugated semiconducting polymers have been the subject of intense study for over two decades with promising advances toward a printable electronics manufacturing ecosystem. These materials will deliver functional electronic devices that are lightweight, flexible, large-area, and cost-effective, with applications ranging from biomedical sensors to solar cells. Synthesis of novel molecules has led to significant improvements in charge carrier mobility, a defining electrical performance metric for many applications. However, the solution processing and thin film deposition of conjugated polymers must also be properly controlled to obtain reproducible device performance. This has led to an abundance of research on the process-structure-property relationships governing the microstructural evolution of the model semicrystalline poly(3-hexylthiophene) (P3HT) as applied to organic field effect transistor (OFET) fabrication. What followed was the production of an expansive body of work on the crystallization, self-assembly, and charge transport behavior of this semiflexible polymer whose strong π-π stacking interactions allow for highly creative methods of structural control, including the modulation of solvent and solution properties, flow-induced crystallization and alignment techniques, structural templating, and solid-state thermal and mechanical processing. This Account relates recent progress in the microstructural control of P3HT thin films through the nucleation, growth, and alignment of P3HT nanofibers. Solution-based nanofiber formation allows one to develop structural order prior to thin film deposition, mitigating the need for intricate deposition processes and enabling the use of batch and continuous chemical processing steps. Fiber growth is framed as a traditional crystallization problem, with the balance between nucleation and growth rates determining the fiber size and ultimately the distribution of grain boundaries in the solid state. Control of

  5. Structural re-alignment in an immunologic surface region of ricin A chain

    Energy Technology Data Exchange (ETDEWEB)

    Zemla, A T; Zhou, C E

    2007-07-24

    We compared structure alignments generated by several protein structure comparison programs to determine whether existing methods would satisfactorily align residues at a highly conserved position within an immunogenic loop in ribosome inactivating proteins (RIPs). Using default settings, structure alignments generated by several programs (CE, DaliLite, FATCAT, LGA, MAMMOTH, MATRAS, SHEBA, SSM) failed to align the respective conserved residues, although LGA reported correct residue-residue (R-R) correspondences when the beta-carbon (Cb) position was used as the point of reference in the alignment calculations. Further tests using variable points of reference indicated that points distal from the beta carbon along a vector connecting the alpha and beta carbons yielded rigid structural alignments in which residues known to be highly conserved in RIPs were reported as corresponding residues in structural comparisons between ricin A chain, abrin-A, and other RIPs. Results suggest that approaches to structure alignment employing alternate point representations corresponding to side chain position may yield structure alignments that are more consistent with observed conservation of functional surface residues than do standard alignment programs, which apply uniform criteria for alignment (i.e., alpha carbon (Ca) as point of reference) along the entirety of the peptide chain. We present the results of tests that suggest the utility of allowing user-specified points of reference in generating alternate structural alignments, and we present a web server for automatically generating such alignments.

  6. High accuracy positioning using carrier-phases with the opensource GPSTK software

    OpenAIRE

    Salazar Hernández, Dagoberto José; Hernández Pajares, Manuel; Juan Zornoza, José Miguel; Sanz Subirana, Jaume

    2008-01-01

    The objective of this work is to show how using a proper GNSS data management strategy, combined with the flexibility provided by the open source "GPS Toolkit" (GPSTk), it is possible to easily develop both simple code-based processing strategies as well as basic high accuracy carrier-phase positioning techniques like Precise Point Positioning (PPP

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

    Science.gov (United States)

    Martin, Andrew C R

    2014-01-01

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

  8. Control rod housing alignment

    International Nuclear Information System (INIS)

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

    1990-01-01

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

  9. 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

  10. Accuracy of Implant Placement Utilizing Customized Patient Instrumentation in Total Knee Arthroplasty

    Directory of Open Access Journals (Sweden)

    William D. Bugbee

    2013-01-01

    Full Text Available Customized patient instrumentation (CPI combines preoperative planning with customized cutting jigs to position and align implants during total knee arthroplasty (TKA. We compared postoperative implant alignment of patients undergoing surgery with CPI to traditional TKA instrumentation for accuracy of implant placement. Twenty-five consecutive TKAs using CPI were analyzed. Preoperative CT scans of the lower extremities were segmented using a computer program. Limb alignment and mechanical axis were computed. Virtual implantation of computer-aided design models was done. Postoperative coronal and sagittal view radiographs were obtained. Using 3D image-matching software, relative positions of femoral and tibial implants were determined. Twenty-five TKAs implanted using traditional instrumentation were also analyzed. For CPI, difference in alignment from the preoperative plan was calculated. In the CPI group, the mean absolute difference between the planned and actual femoral placements was 0.67° in the coronal plane and 1.2° in the sagittal plane. For tibial alignment, the mean absolute difference was 0.9° in the coronal plane and 1.3° in the sagittal plane. For traditional instrumentation, difference from ideal placement for the femur was 1.5° in the coronal plane and 2.3° in the sagittal plane. For the tibia, the difference was 1.8° in the coronal plane. CPI achieved accurate implant positioning and was superior to traditional TKA instrumentation.

  11. SU-F-J-44: Development of a Room Laser Based Real-Time Alignment Monitoring System Using An Array of Photodiodes

    International Nuclear Information System (INIS)

    Noh, Y; Kim, T; Kang, S; Kim, D; Cho, M; Kim, K; Shin, D; Suh, T; Kim, S

    2016-01-01

    Purpose: To develop a real-time alignment monitoring system (RAMS) to compensate for the limitations of the conventional room laser based alignment system, and to verify the feasibility of the RAMS. Methods: The RAMS was composed of a room laser sensing array (RLSA), an analog-todigital converter, and a control PC. In the RLSA, seven photodiodes (each in 1 mm width) are arranged in a pattern that the RAMS provides alignment in 1 mm resolution. It works based on detecting laser light aligned on one of photodiodes. When misaligned, the laser would match with different photodiode(s) giving signal at unexpected location. Thus, how much displaced can be determined. To verify the reproducibility of the system with respect to time as well as repeated set-ups, temporal reproducibility and repeatability test was conducted. The accuracy of the system was tested by obtaining detection signals with varying laser-match positions. Results: The signal of the RAMS was found to be stable with respect to time. The repeatability test resulted in a maximum coefficient of variance of 1.14%, suggesting that the signal of the RAMS was stable over repeated set-ups. In the accuracy test, signals between when the laser was aligned and notaligned with any of sensors could be distinguished by signal intensity. The signals of not-aligned sensors were always below 75% of the signal of the aligned sensor. It was confirmed that the system could detect 1 mm of movement by monitoring the pattern of signals, and could observe the movement of the system in real-time. Conclusion: We developed a room laser based alignment monitoring system. The feasibility test verified that the system is capable of quantitative alignment monitoring in real time. The system is relatively simple, not expensive, and considered to be easily incorporated into conventional room laser systems for real-time alignment monitoring. This research was supported by the Mid-career Researcher Program through NRF funded by the

  12. 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...

  13. A New Approach to High-accuracy Road Orthophoto Mapping Based on Wavelet Transform

    Directory of Open Access Journals (Sweden)

    Ming Yang

    2011-12-01

    Full Text Available Existing orthophoto map based on satellite photography and aerial photography is not precise enough for road marking. This paper proposes a new approach to high-accuracy orthophoto mapping. The approach uses inverse perspective transformation to process the image information and generates the orthophoto fragment. The offline interpolation algorithm is used to process the location information. It processes the dead reckoning and the EKF location information, and uses the result to transform the fragments to the global coordinate system. At last it uses wavelet transform to divides the image to two frequency bands and uses weighted median algorithm to deal with them separately. The result of experiment shows that the map produced with this method has high accuracy.

  14. Optical metrology alignment and impact on the measurement performance of the LISA Technology Package

    Energy Technology Data Exchange (ETDEWEB)

    Hirth, M; Fichter, W; Brandt, N; Gerardi, D [iFR, Universitaet Stuttgart, Pfaffenwaldring 7a, 70569 Stuttgart (Germany); Schleicher, A [Astrium GmbH, 88039 Friedrichshafen (Germany); Wanner, G, E-mail: marc.hirth@ifr.uni-stuttgart.d [Albert Einstein Institut, Callinstrasse 38, 30167 Hannover (Germany)

    2009-03-01

    Aside from LISA Pathfinder's top-level acceleration requirement, there is a stringent independent requirement for the accuracy of the optical metrology system. In case of a perfectly aligned metrology system (optical bench and test masses) it should rather be independent of residual displacement jitter due to control. However, this ideal case will not be achieved as mechanical tolerances and uncertainties lead to a direct impact of test mass and spacecraft displacement jitter on the optical measurement accuracy. In this paper, we present a strategy how to cover these effects for a systematic requirement breakdown. We use a simplified nonlinear geometrical model for the differential distance measurement of the test masses which is linearized and linked to the equations of motion for both the spacecraft and the two test masses. This leads from test mass relative displacement to a formulation in terms of applied force/torque and thus allows to distinguish the absolute motion of each of the three bodies. It further shows how motions in each degree of freedom couple linearly into the optical measurement via DC misalignments of the laser beam and the test masses. This finally allows for deriving requirements on the alignment accuracy of components and on permittable closed-loop acceleration noise. In the last part a budget for the expected measurement performance is compiled from simulations as no measurement data is available yet.

  15. Optical metrology alignment and impact on the measurement performance of the LISA Technology Package

    International Nuclear Information System (INIS)

    Hirth, M; Fichter, W; Brandt, N; Gerardi, D; Schleicher, A; Wanner, G

    2009-01-01

    Aside from LISA Pathfinder's top-level acceleration requirement, there is a stringent independent requirement for the accuracy of the optical metrology system. In case of a perfectly aligned metrology system (optical bench and test masses) it should rather be independent of residual displacement jitter due to control. However, this ideal case will not be achieved as mechanical tolerances and uncertainties lead to a direct impact of test mass and spacecraft displacement jitter on the optical measurement accuracy. In this paper, we present a strategy how to cover these effects for a systematic requirement breakdown. We use a simplified nonlinear geometrical model for the differential distance measurement of the test masses which is linearized and linked to the equations of motion for both the spacecraft and the two test masses. This leads from test mass relative displacement to a formulation in terms of applied force/torque and thus allows to distinguish the absolute motion of each of the three bodies. It further shows how motions in each degree of freedom couple linearly into the optical measurement via DC misalignments of the laser beam and the test masses. This finally allows for deriving requirements on the alignment accuracy of components and on permittable closed-loop acceleration noise. In the last part a budget for the expected measurement performance is compiled from simulations as no measurement data is available yet.

  16. A new ultra-high-accuracy angle generator: current status and future direction

    Science.gov (United States)

    Guertin, Christian F.; Geckeler, Ralf D.

    2017-09-01

    Lack of an extreme high-accuracy angular positioning device available in the United States has left a gap in industrial and scientific efforts conducted there, requiring certain user groups to undertake time-consuming work with overseas laboratories. Specifically, in x-ray mirror metrology the global research community is advancing the state-of-the-art to unprecedented levels. We aim to fill this U.S. gap by developing a versatile high-accuracy angle generator as a part of the national metrology tool set for x-ray mirror metrology and other important industries. Using an established calibration technique to measure the errors of the encoder scale graduations for full-rotation rotary encoders, we implemented an optimized arrangement of sensors positioned to minimize propagation of calibration errors. Our initial feasibility research shows that upon scaling to a full prototype and including additional calibration techniques we can expect to achieve uncertainties at the level of 0.01 arcsec (50 nrad) or better and offer the immense advantage of a highly automatable and customizable product to the commercial market.

  17. 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

  18. Design and Performance of the Alignment System for the CMS Muon Endcaps

    CERN Document Server

    Hohlmann, Marcus; Browngold, Max; Dehmelt, Klaus; Guragain, Samir; Andreev, Valery; Yang, Xiaofeng; Bellinger, James; Carlsmith, Duncan; Feyzi, Farshid; Loveless, Richard J; Northacker, David; Case, Michael; Eartly, David P; Prokofiev, Oleg; Sknar, Vladimir; Sytnik, Valeri

    2008-01-01

    The alignment system for the CMS Muon Endcap detector employs several hundred sensors such as optical 1-D CCD sensors illuminated by lasers and analog distance- and tilt-sensors to monitor the positions of one sixth of 468 large Cathode Strip Chambers. The chambers mounted on the endcap yoke disks undergo substantial deformation on the order of centimeters when the 4T field is switched on and off. The Muon Endcap alignment system is required to monitor chamber positions with \\mbox{75-200 $\\mu$m} accuracy in the R$\\phi$ plane, $\\approx$400 $\\mu$m in the radial direction, and $\\approx$1 mm in the z-direction along the beam axis. The complete alignment hardware for one of the two endcaps has been installed at CERN. A major system test was performed when the 4T solenoid magnet was ramped up to full field for the first time in August 2006. We present the overall system design and first results on disk deformations, which indicate that the measurements agree with expectations.

  19. Planar self-aligned imprint lithography for coplanar plasmonic nanostructures fabrication

    KAUST Repository

    Wan, Weiwei

    2014-03-01

    Nanoimprint lithography (NIL) is a cost-efficient nanopatterning technology because of its promising advantages of high throughput and high resolution. However, accurate multilevel overlay capability of NIL required for integrated circuit manufacturing remains a challenge due to the high cost of achieving mechanical alignment precision. Although self-aligned imprint lithography was developed to avoid the need of alignment for the vertical layered structures, it has limited usage in the manufacture of the coplanar structures, such as integrated plasmonic devices. In this paper, we develop a new process of planar self-alignment imprint lithography (P-SAIL) to fabricate the metallic and dielectric structures on the same plane. P-SAIL transfers the multilevel imprint processes to a single-imprint process which offers higher efficiency and less cost than existing manufacturing methods. Such concept is demonstrated in an example of fabricating planar plasmonic structures consisting of different materials. © 2014 Springer-Verlag Berlin Heidelberg.

  20. 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

  1. DIDA: Distributed Indexing Dispatched Alignment.

    Directory of Open Access Journals (Sweden)

    Hamid Mohamadi

    Full Text Available One essential application in bioinformatics that is affected by the high-throughput sequencing data deluge is the sequence alignment problem, where nucleotide or amino acid sequences are queried against targets to find regions of close similarity. When queries are too many and/or targets are too large, the alignment process becomes computationally challenging. This is usually addressed by preprocessing techniques, where the queries and/or targets are indexed for easy access while searching for matches. When the target is static, such as in an established reference genome, the cost of indexing is amortized by reusing the generated index. However, when the targets are non-static, such as contigs in the intermediate steps of a de novo assembly process, a new index must be computed for each run. To address such scalability problems, we present DIDA, a novel framework that distributes the indexing and alignment tasks into smaller subtasks over a cluster of compute nodes. It provides a workflow beyond the common practice of embarrassingly parallel implementations. DIDA is a cost-effective, scalable and modular framework for the sequence alignment problem in terms of memory usage and runtime. It can be employed in large-scale alignments to draft genomes and intermediate stages of de novo assembly runs. The DIDA source code, sample files and user manual are available through http://www.bcgsc.ca/platform/bioinfo/software/dida. The software is released under the British Columbia Cancer Agency License (BCCA, and is free for academic use.

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

    International Nuclear Information System (INIS)

    Touze, T.

    2011-01-01

    The compact linear collider (CLIC) is the particle accelerator project proposed by the european organization for nuclear research (CERN) for high energy physics after the large hadron collider (LHC). Because of the nano-metric scale of the CLIC leptons beams, the emittance growth budget is very tight. It induces alignment tolerances on the positions of the CLIC components that have never been achieved before. The last step of the CLIC alignment will be done according to the beam itself. It falls within the competence of the physicists. However, in order to implement the beam-based feedback, a challenging pre-alignment is required: 10 μm at 3σ along a 200 m sliding window. For such a precision, the proposed solution must be compatible with a feedback between the measurement and repositioning systems. The CLIC pre-alignment will have to be active. This thesis does not demonstrate the feasibility of the CLIC active pre-alignment but shows the way to the last developments that have to be done for that purpose. A method is proposed. Based on the management of the Helmert transformations between Euclidean coordinate systems, from the geodetic networks to the metrological measurements, this method is likely to solve the CLIC pre-alignment problem. Large scale facilities have been built and Monte-Carlo simulations have been made in order to validate the mathematical modeling of the measurement systems and of the alignment references. When this is done, it will be possible to extrapolate the modeling to the entire CLIC length. It will be the last step towards the demonstration of the CLIC pre-alignment feasibility. (author)

  3. 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

  4. Alignment and Distortion-Free Integration of Lightweight Mirrors into Meta-Shells for High-Resolution Astronomical X-Ray Optics

    Science.gov (United States)

    Chan, Kai-Wing; Zhang, William W.; Schofield, Mark J.; Numata, Ai; Mazzarella, James R.; Saha, Timo T.; Biskach, Michael P.; McCelland, Ryan S.; Niemeyer, Jason; Sharpe, Marton V.; hide

    2016-01-01

    High-resolution, high throughput optics for x-ray astronomy requires fabrication of well-formed mirror segments and their integration with arc-second level precision. Recently, advances of fabrication of silicon mirrors developed at NASA/Goddard prompted us to develop a new method of mirror integration. The new integration scheme takes advantage of the stiffer, more thermally conductive, and lower-CTE silicon, compared to glass, to build a telescope of much lighter weight. In this paper, we address issues of aligning and bonding mirrors with this method. In this preliminary work, we demonstrated the basic viability of such scheme. Using glass mirrors, we demonstrated that alignment error of 1" and bonding error 2" can be achieved for mirrors in a single shell. We will address the immediate plan to demonstrate the bonding reliability and to develop technology to build up a mirror stack and a whole "meta-shell".

  5. Image-guided small animal radiation research platform: calibration of treatment beam alignment

    International Nuclear Information System (INIS)

    Matinfar, Mohammad; Iordachita, Iulian; Kazanzides, Peter; Ford, Eric; Wong, John

    2009-01-01

    Small animal research allows detailed study of biological processes, disease progression and response to therapy with the potential to provide a natural bridge to the clinical environment. The small animal radiation research platform (SARRP) is a portable system for precision irradiation with beam sizes down to approximately 0.5 mm and optimally planned radiation with on-board cone-beam CT (CBCT) guidance. This paper focuses on the geometric calibration of the system for high-precision irradiation. A novel technique for the calibration of the treatment beam is presented, which employs an x-ray camera whose precise positioning need not be known. Using the camera system we acquired a digitally reconstructed 3D 'star shot' for gantry calibration and then developed a technique to align each beam to a common isocenter with the robotic animal positioning stages. The calibration incorporates localization by cone-beam CT guidance. Uncorrected offsets of the beams with respect to the calibration origin ranged from 0.4 mm to 5.2 mm. With corrections, these alignment errors can be reduced to the sub-millimeter range. The calibration technique was used to deliver a stereotactic-like arc treatment to a phantom constructed with EBT Gafchromic films. All beams were shown to intersect at a common isocenter with a measured beam (FWHM) of approximately 1.07 mm using the 0.5 mm collimated beam. The desired positioning accuracy of the SARRP is 0.25 mm and the results indicate an accuracy of 0.2 mm. To fully realize the radiation localization capabilities of the SARRP, precise geometric calibration is required, as with any such system. The x-ray camera-based technique presented here provides a straightforward and semi-automatic method for system calibration.

  6. Self-aligned inkjet printing of highly conducting gold electrodes with submicron resolution

    Science.gov (United States)

    Zhao, Ni; Chiesa, Marco; Sirringhaus, Henning; Li, Yuning; Wu, Yiliang; Ong, Beng

    2007-03-01

    Self-aligned printing is a recently developed bottom-up printing technique which utilizes the unique droplet motion on heterogeneous surfaces to define sub-100-nm critical features and surpasses the resolution which can commonly be achieved by direct printing by two orders of magnitude. Here we extend this method, which was originally implemented with conductive polymer inks, to fabrication of functional conductive nanostructures with gold nanoparticle ink. We also designed a configuration where the ink was printed between two lithographically defined patterns to facilitate the study of the channel formation. Channel lengths from 4μm down to 60nm were achieved by controlling the surface tension and drying time of the ink. A fluid dynamical model is presented to explain the mechanism by which the channel forms in the self-aligned printing technique. Field-effect transistors fabricated using gold self-aligned printed source-drain electrodes exhibit significantly improved output currents than those using conducting polymers. Unambiguous evidence for the submicrometer channel dimension is obtained by imaging the potential drop along the channel using scanning Kelvin probe microscopy.

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

    Science.gov (United States)

    Coyle, Laura Elizabeth

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

  8. High-Stacking-Density, Superior-Roughness LDH Bridged with Vertically Aligned Graphene for High-Performance Asymmetric Supercapacitors.

    Science.gov (United States)

    Guo, Wei; Yu, Chang; Li, Shaofeng; Yang, Juan; Liu, Zhibin; Zhao, Changtai; Huang, Huawei; Zhang, Mengdi; Han, Xiaotong; Niu, Yingying; Qiu, Jieshan

    2017-10-01

    The high-performance electrode materials with tuned surface and interface structure and functionalities are highly demanded for advanced supercapacitors. A novel strategy is presented to conFigure high-stacking-density, superior-roughness nickel manganese layered double hydroxide (LDH) bridged by vertically aligned graphene (VG) with nickel foam (NF) as the conductive collector, yielding the LDH-NF@VG hybrids for asymmetric supercapacitors. The VG nanosheets provide numerous electron transfer channels for quick redox reactions, and well-developed open structure for fast mass transport. Moreover, the high-stacking-density LDH grown and assembled on VG nanosheets result in a superior hydrophilicity derived from the tuned nano/microstructures, especially microroughness. Such a high stacking density with abundant active sites and superior wettability can be easily accessed by aqueous electrolytes. Benefitting from the above features, the LDH-NF@VG can deliver a high capacitance of 2920 F g -1 at a current density of 2 A g -1 , and the asymmetric supercapacitor with the LDH-NF@VG as positive electrode and activated carbon as negative electrode can deliver a high energy density of 56.8 Wh kg -1 at a power density of 260 W kg -1 , with a high specific capacitance retention rate of 87% even after 10 000 cycles. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Principles of alignment of multibeam lasers for thermonuclear purposes

    International Nuclear Information System (INIS)

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

    1980-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Lefkowitz Elliot J

    2005-08-01

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

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

    International Nuclear Information System (INIS)

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

    2006-01-01

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

  12. Effects of variable attachment shapes and aligner material on aligner retention.

    Science.gov (United States)

    Dasy, Hiltrud; Dasy, Andreas; Asatrian, Greg; Rózsa, Noémi; Lee, Hao-Fu; Kwak, Jin Hee

    2015-11-01

    To evaluate the retention of four types of aligners on a dental arch with various attachments. For this study, three casts were manufactured, two of which contained attachments (ellipsoid and beveled), and one without any attachments to serve as a control. Four types of aligners were thermoformed: Clear-Aligner (CA)-soft, CA-medium, and CA-hard, with various thicknesses, and Essix ACE. Measurements of vertical displacement force during aligner removal were performed with the Gabo Qualimeter Eplexor. Means and standard deviations were next compared between different aligner thicknesses and attachment shapes. CA-soft, CA-medium, and CA-hard did not present a significant increase in retention, except when used in the presence of attachments. Additionally, CA-medium and CA-hard required significantly more force for removal. Essix ACE demonstrated a significant decrease in retention when used with ellipsoid attachments. The force value for Essix ACE removal from the cast with beveled attachments was comparable to that of CA-medium. Forces for aligner removal from the model without attachments showed a linear trend. Essix ACE did not show a continuous increase in retention for each model. Overall, ellipsoid attachments did not present a significant change in retention. In contrast, beveled attachments improved retention. Ellipsoid attachments had no significant influence on the force required for aligner removal and hence on aligner retention. Essix ACE showed significantly less retention than CA-hard on the models with attachments. Furthermore, beveled attachments were observed to increase retention significantly, compared with ellipsoid attachments and when using no attachments.

  13. Calibration and alignment of the CMS silicon tracking detector

    International Nuclear Information System (INIS)

    Stoye, M.

    2007-07-01

    The Large Hadron Collider (LHC) will dominate the high energy physics program in the coming decade. The discovery of the standard model Higgs boson and the discovery of super-symmetric particles are within the reach at the energy scale explored by the LHC. However, the high luminosity and the high energy of the colliding protons lead to challenging demands on the detectors. The hostile radiation environment requires irradiation hard detectors, where the innermost subdetectors, consisting of silicon modules, are most affected. This thesis is devoted to the calibration and alignment of the silicon tracking detector. Electron test beam data, taken at DESY, have been used to investigate the performance of detector modules which previously were irradiated with protons up to a dose expected after 10 years of operation. The irradiated sensors turned out to be still better than required. The performance of the inner tracking systems will be dominated by the degree to which the positions of the sensors can be determined. Only a track based alignment procedure can reach the 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, as many sources of information as possible are used, and all correlations between the position parameters of the detectors are taken into account. Utilizing simulated data, a proof of concept of the alignment strategy is shown. (orig.)

  14. Calibration and alignment of the CMS silicon tracking detector

    Energy Technology Data Exchange (ETDEWEB)

    Stoye, M.

    2007-07-15

    The Large Hadron Collider (LHC) will dominate the high energy physics program in the coming decade. The discovery of the standard model Higgs boson and the discovery of super-symmetric particles are within the reach at the energy scale explored by the LHC. However, the high luminosity and the high energy of the colliding protons lead to challenging demands on the detectors. The hostile radiation environment requires irradiation hard detectors, where the innermost subdetectors, consisting of silicon modules, are most affected. This thesis is devoted to the calibration and alignment of the silicon tracking detector. Electron test beam data, taken at DESY, have been used to investigate the performance of detector modules which previously were irradiated with protons up to a dose expected after 10 years of operation. The irradiated sensors turned out to be still better than required. The performance of the inner tracking systems will be dominated by the degree to which the positions of the sensors can be determined. Only a track based alignment procedure can reach the 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 {chi}{sup 2} minimization program Millepede II an alignment strategy has been developed in which all detector components are aligned simultaneously, as many sources of information as possible are used, and all correlations between the position parameters of the detectors are taken into account. Utilizing simulated data, a proof of concept of the alignment strategy is shown. (orig.)

  15. Construction and calibration of the laser alignment system for the CMS tracker

    International Nuclear Information System (INIS)

    Adolphi, R.

    2006-01-01

    A robust and reliable optical system able to measure and control the large CMS tracker geometry with high accuracy has been developed and validated. The construction and integration of the LAS fulfilling the requirements, as well as its calibration and performance are described in this thesis. The working principle is based on the partial transparency of silicon for light wavelengths in the near infrared region. The absorbed part of the laser beam generates a signal in the corresponding silicon strip module serving to reconstruct its position. The transmitted part reaches the subsequent module layer generating an optical link between the two layers. Investigation of the light generation and distribution led to a definition of the optical components and their optimization for Laser Alignment purposes. Laser diodes have been qualified as light sources and singlemode optical fibres, terminated by special connectors, distribute the light to the CMS tracker detector. The beamsplitting device, a key component of the LAS light distribution inside the CMS tracker, has been studied in detail. The challenge of splitting one collimated beam into two back-to-back beams inside a small available volume has been solved by using the polarization principle. Special test setups were developed to determine the collinearity of the two outgoing beams with a precision better than 50 μrad and it has been shown that their relative orientation remains constant under working conditions. The interface between the tracker and the LAS is given by the silicon sensors which are responsible both for particle detection and for the determination of the position of the laser spot. An anti-reflex-coating has been applied on the backside of all alignment sensors to improve their optical properties without deterioration of their tracking performance. A test setup has been developed to simultaneously study the transmission and reflection properties of the alignment sensors. The working principle of the

  16. Construction and calibration of the laser alignment system for the CMS tracker

    Energy Technology Data Exchange (ETDEWEB)

    Adolphi, R.

    2006-11-28

    A robust and reliable optical system able to measure and control the large CMS tracker geometry with high accuracy has been developed and validated. The construction and integration of the LAS fulfilling the requirements, as well as its calibration and performance are described in this thesis. The working principle is based on the partial transparency of silicon for light wavelengths in the near infrared region. The absorbed part of the laser beam generates a signal in the corresponding silicon strip module serving to reconstruct its position. The transmitted part reaches the subsequent module layer generating an optical link between the two layers. Investigation of the light generation and distribution led to a definition of the optical components and their optimization for Laser Alignment purposes. Laser diodes have been qualified as light sources and singlemode optical fibres, terminated by special connectors, distribute the light to the CMS tracker detector. The beamsplitting device, a key component of the LAS light distribution inside the CMS tracker, has been studied in detail. The challenge of splitting one collimated beam into two back-to-back beams inside a small available volume has been solved by using the polarization principle. Special test setups were developed to determine the collinearity of the two outgoing beams with a precision better than 50 {mu}rad and it has been shown that their relative orientation remains constant under working conditions. The interface between the tracker and the LAS is given by the silicon sensors which are responsible both for particle detection and for the determination of the position of the laser spot. An anti-reflex-coating has been applied on the backside of all alignment sensors to improve their optical properties without deterioration of their tracking performance. A test setup has been developed to simultaneously study the transmission and reflection properties of the alignment sensors. The working principle of

  17. Alignment following Au L$_{3}$ photoionization by synchrotron radiation

    CERN Document Server

    Yamaoka, H; Takahiro, K; Morikawa, T; Ito, S; Mizumaki, M; Semenov, S; Cherepkov, N; Kabachnik, N M; Mukoyama, T; 10.1088/0953-4075/36/19/001

    2003-01-01

    The alignment of Au/sup +/ ions following L/sub 3/ photoionization has been studied using a high-resolution X-ray spectrometer. We observed a small anisotropy for the angular dependence of Au L/sub l/ and L alpha emissions. The alignment parameter A/sub 20/ derived from the experimental results is compared with theoretical calculations by Hartree-Fock approximation and random phase approximation with exchange. The contribution to the alignment of quadruple interaction is discussed. (40 refs).

  18. 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.

  19. 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.

  20. High-Throughput Image Analysis of Fibrillar Materials: A Case Study on Polymer Nanofiber Packing, Alignment, and Defects in Organic Field Effect Transistors.

    Science.gov (United States)

    Persson, Nils E; Rafshoon, Joshua; Naghshpour, Kaylie; Fast, Tony; Chu, Ping-Hsun; McBride, Michael; Risteen, Bailey; Grover, Martha; Reichmanis, Elsa

    2017-10-18

    High-throughput discovery of process-structure-property relationships in materials through an informatics-enabled empirical approach is an increasingly utilized technique in materials research due to the rapidly expanding availability of data. Here, process-structure-property relationships are extracted for the nucleation, growth, and deposition of semiconducting poly(3-hexylthiophene) (P3HT) nanofibers used in organic field effect transistors, via high-throughput image analysis. This study is performed using an automated image analysis pipeline combining existing open-source software and new algorithms, enabling the rapid evaluation of structural metrics for images of fibrillar materials, including local orientational order, fiber length density, and fiber length distributions. We observe that microfluidic processing leads to fibers that pack with unusually high density, while sonication yields fibers that pack sparsely with low alignment. This is attributed to differences in their crystallization mechanisms. P3HT nanofiber packing during thin film deposition exhibits behavior suggesting that fibers are confined to packing in two-dimensional layers. We find that fiber alignment, a feature correlated with charge carrier mobility, is driven by increasing fiber length, and that shorter fibers tend to segregate to the buried dielectric interface during deposition, creating potentially performance-limiting defects in alignment. Another barrier to perfect alignment is the curvature of P3HT fibers; we propose a mechanistic simulation of fiber growth that reconciles both this curvature and the log-normal distribution of fiber lengths inherent to the fiber populations under consideration.