WorldWideScience

Sample records for dynamics based alignment

  1. Sequence Alignment with Dynamic Divisor Generation for Keystroke Dynamics Based User Authentication

    OpenAIRE

    Jiacang Ho; Dae-Ki Kang

    2015-01-01

    Keystroke dynamics based authentication is one of the prevention mechanisms used to protect one’s account from criminals’ illegal access. In this authentication mechanism, keystroke dynamics are used to capture patterns in a user typing behavior. Sequence alignment is shown to be one of effective algorithms for keystroke dynamics based authentication, by comparing the sequences of keystroke data to detect imposter’s anomalous sequences. In previous research, static divisor has been used for s...

  2. Sequence Alignment with Dynamic Divisor Generation for Keystroke Dynamics Based User Authentication

    Directory of Open Access Journals (Sweden)

    Jiacang Ho

    2015-01-01

    Full Text Available Keystroke dynamics based authentication is one of the prevention mechanisms used to protect one’s account from criminals’ illegal access. In this authentication mechanism, keystroke dynamics are used to capture patterns in a user typing behavior. Sequence alignment is shown to be one of effective algorithms for keystroke dynamics based authentication, by comparing the sequences of keystroke data to detect imposter’s anomalous sequences. In previous research, static divisor has been used for sequence generation from the keystroke data, which is a number used to divide a time difference of keystroke data into an equal-length subinterval. After the division, the subintervals are mapped to alphabet letters to form sequences. One major drawback of this static divisor is that the amount of data for this subinterval generation is often insufficient, which leads to premature termination of subinterval generation and consequently causes inaccurate sequence alignment. To alleviate this problem, we introduce sequence alignment of dynamic divisor (SADD in this paper. In SADD, we use mean of Horner’s rule technique to generate dynamic divisors and apply them to produce the subintervals with different length. The comparative experimental results with SADD and other existing algorithms indicate that SADD is usually comparable to and often outperforms other existing algorithms.

  3. Shift dynamics of capillary self-alignment

    NARCIS (Netherlands)

    Arutinov, G.; Mastrangeli, M.; Smits, E.C.P.; Heck, G.V.; Schoo, H.F.M.; Toonder, J.J.M. den; Dietzel, A.H.

    2014-01-01

    This paper describes the dynamics of capillary self-alignment of components with initial shift offsets from matching receptor sites. The analysis of the full uniaxial self-alignment dynamics of foil-based mesoscopic dies from pre-alignment to final settling evidenced three distinct, sequential regim

  4. Group Based Interference Alignment

    CERN Document Server

    Ma, Yanjun; Chen, Rui; Yao, Junliang

    2010-01-01

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

  5. SVM with discriminative dynamic time alignment

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    In the past several years, support vector machines (SVM) have achieved a huge success in many field, especially in pattern recognition. But the standard SVM cannot deal with length-variable vectors, which is one severe obstacle for its applications to some important areas, such as speech recognition and part-of-speech tagging. The paper proposed a novel SVM with discriminative dynamic time alignment (DDTA-SVM) to solve this problem. When training DDTA-SVM classifier, according to the category information of the training Samples, different time alignment strategies were adopted to manipulate them in the kernel functions, which contributed to great improvement for training speed and generalization capability of the classifier. Since the alignment operator was embedded in kernel functions, the training algorithms of standard SVM were still compatible in DDTA-SVM. In order to increase the reliability of the classification, a new classification algorithm was suggested. The preliminary experimental results on Chinese confusable syllables speech classification task show that DDTA-SVM obtains faster convergence speed and better classification performance than dynamic time alignment kernel SVM (DTAK-SVM).Moreover, DDTA-SVM also gives higher classification precision compared to the conventional HMM. This proves that the proposed method is effective, especially for confusable lengthvariable pattern classification tasks.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1997-12-01

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

  7. Enhanced Dynamic Algorithm of Genome Sequence Alignments

    Directory of Open Access Journals (Sweden)

    Arabi E. keshk

    2014-05-01

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

  8. Comparative genomics beyond sequence-based alignments

    DEFF Research Database (Denmark)

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

    2008-01-01

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

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

    CERN Document Server

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

    2010-01-01

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

  10. Semiautomatic beam-based LHC collimator alignment

    CERN Document Server

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

    2012-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Skolnick Jeffrey

    2008-12-01

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

  12. Measures of frontal plane lower limb alignment obtained from static radiographs and dynamic gait analysis.

    Science.gov (United States)

    Hunt, Michael A; Birmingham, Trevor B; Jenkyn, Thomas R; Giffin, J Robert; Jones, Ian C

    2008-05-01

    Currently, lower limb alignment is measured statically from radiographs that may not accurately represent the condition of the limb when moving and weight-bearing. Thus, the purpose of the present study was to introduce and examine a novel measure of dynamic lower limb alignment obtained during walking in patients with knee OA. In this cross-sectional study, standing, full-length lower limb radiographs were acquired from 80 individuals with confirmed knee OA, who also underwent three-dimensional gait analyses with reflective markers placed on the segments of the lower limb. Frontal plane lower limb alignment was measured using the static radiographs (mechanical axis) and gait analyses (marker-based alignment) by identifying the centres of the hip, knee, and ankle from both methods. Simple linear regression indicated these measures were highly correlated (r=0.84), however, 30% of the variance in the marker-based measure of lower limb alignment was not explained by the mechanical axis despite using the same anatomical landmarks. Results from this study suggest that a valid measure of dynamic lower limb alignment can be obtained from a standard quantitative gait analysis and highlight the differences in measures of lower limb alignment obtained in static and dynamic situations. Future research into the clinical utility of measures of dynamic alignment in the treatment of OA may aid in the development of interventions specifically tailored to one's dynamic lower limb biomechanics during gait.

  13. 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

  14. On-the-move Alignment for SINS Based on Vehicle Dynamic Model%车辆运动数学模型辅助的动基座对准方法

    Institute of Scientific and Technical Information of China (English)

    李浩; 杨家胜

    2014-01-01

    针对车载捷联惯导(SINS)在外部传感器失效时无法实现动基座对准的问题,提出了基于车辆运动模型辅助的动基座对准方法。与传统方法不同的是,该方法利用车辆在路面上的运动特性,利用车辆运动模型测得的虚拟观测量来提供辅助信息,从而实现SINS的动基座对准,仿真结果表明:对于中等精度惯导,在外部传感器失效时,利用车辆运动模型提供的辅助信息,水平对准精度为0.37°,方位对准精度为5.86°,对准时间小于150 s,依然能够快速有效地实现动基座对准。%To solve the problem of the moving base alignment for the vehicle weapon system’s Strapdown Inertial Navigation System (SINS) when the exterior sensor is invalid,a new alignment method which aided by vehicle dynamic model is proposed,in contrast to the traditional alignment algorithm,the presented method uses the visual measurement obtained from vehicle dynamic model to provide the aid-information,and the alignment can be achieved,The simulation results show that the azimuth alignment accuracy reaches about 5.86°,the level alignment accuracy are superior to 0.37°and the alignment time is less than 150 s when the exterior sensor is invalid.

  15. 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.

  16. Pyro-Align: Sample-Align based Multiple Alignment system for Pyrosequencing Reads of Large Number

    CERN Document Server

    Saeed, Fahad

    2009-01-01

    Pyro-Align is a multiple alignment program specifically designed for pyrosequencing reads of huge number. Multiple sequence alignment is shown to be NP-hard and heuristics are designed for approximate solutions. Multiple sequence alignment of pyrosequenceing reads is complex mainly because of 2 factors. One being the huge number of reads, making the use of traditional heuristics,that scale very poorly for large number, unsuitable. The second reason is that the alignment cannot be performed arbitrarily, because the position of the reads with respect to the original genome is important and has to be taken into account.In this report we present a short description of the multiple alignment system for pyrosequencing reads.

  17. Dynamics of capillary self-alignment for mesoscopic foil devices

    NARCIS (Netherlands)

    Arutinov, G.; Mastrangeli, M.; Smits, E.C.P.; Schoo, H.F.M.; Brugger, J.; Dietzel, A.H.

    2013-01-01

    We report experimental evidence for three sequential, distinct dynamic regimes in the capillary self-alignment of centimeter-sized foil dies released at large uniaxial offsets from equilibrium. We show that the initial transient wetting regime, along with inertia and wetting properties of the dies,

  18. Image-based temporal alignment of echocardiographic sequences

    Science.gov (United States)

    Danudibroto, Adriyana; Bersvendsen, Jørn; Mirea, Oana; Gerard, Olivier; D'hooge, Jan; Samset, Eigil

    2016-04-01

    Temporal alignment of echocardiographic sequences enables fair comparisons of multiple cardiac sequences by showing corresponding frames at given time points in the cardiac cycle. It is also essential for spatial registration of echo volumes where several acquisitions are combined for enhancement of image quality or forming larger field of view. In this study, three different image-based temporal alignment methods were investigated. First, a method based on dynamic time warping (DTW). Second, a spline-based method that optimized the similarity between temporal characteristic curves of the cardiac cycle using 1D cubic B-spline interpolation. Third, a method based on the spline-based method with piecewise modification. These methods were tested on in-vivo data sets of 19 echo sequences. For each sequence, the mitral valve opening (MVO) time was manually annotated. The results showed that the average MVO timing error for all methods are well under the time resolution of the sequences.

  19. Measuring prosodic alignment in cooperative task-based conversations

    NARCIS (Netherlands)

    Truong, Khiet P.; Heylen, Dirk

    2012-01-01

    In this paper, we investigate prosodic alignment in task-based conversations. We use the HCRC Map Task Corpus and investigate how familiarity affects prosodic alignment and how task success is related to prosodic alignment. A variety of existing alignment measures is used and applied to our data. In

  20. Dynamic Alignment of D2 Enhanced by Two Few-cycle Pulses

    Institute of Scientific and Technical Information of China (English)

    Zeng-qiang Yang; Zhi-rong Guo; Bao-xiang Yin; Mao-zhu Sun

    2008-01-01

    Dynamic alignment of D2 induced by two few-cycle pulses was investigated by solving the time-dependent Schr(o)dinger equation numerically based on a rigid rotor model. The results show that alignment of D2 can be enhanced by two few-cycle pulses compared with the level achievable by a single fewcycle pulse as long as the time delay between two pulses is chosen properly, and the pulse duration of two lasers plays an important role in the aligning process of D2 molecules.

  1. Effect of alignment of easy axes on dynamic magnetization of immobilized magnetic nanoparticles

    Science.gov (United States)

    Yoshida, Takashi; Matsugi, Yuki; Tsujimura, Naotaka; Sasayama, Teruyoshi; Enpuku, Keiji; Viereck, Thilo; Schilling, Meinhard; Ludwig, Frank

    2017-04-01

    In some biomedical applications of magnetic nanoparticles (MNPs), the particles are physically immobilized. In this study, we explore the effect of the alignment of the magnetic easy axes on the dynamic magnetization of immobilized MNPs under an AC excitation field. We prepared three immobilized MNP samples: (1) a sample in which easy axes are randomly oriented, (2) a parallel-aligned sample in which easy axes are parallel to the AC field, and (3) an orthogonally aligned sample in which easy axes are perpendicular to the AC field. First, we show that the parallel-aligned sample has the largest hysteresis in the magnetization curve and the largest harmonic magnetization spectra, followed by the randomly oriented and orthogonally aligned samples. For example, 1.6-fold increase was observed in the area of the hysteresis loop of the parallel-aligned sample compared to that of the randomly oriented sample. To quantitatively discuss the experimental results, we perform a numerical simulation based on a Fokker-Planck equation, in which probability distributions for the directions of the easy axes are taken into account in simulating the prepared MNP samples. We obtained quantitative agreement between experiment and simulation. These results indicate that the dynamic magnetization of immobilized MNPs is significantly affected by the alignment of the easy axes.

  2. An improved Hough transform-based fingerprint alignment approach

    CSIR Research Space (South Africa)

    Mlambo, CS

    2014-11-01

    Full Text Available An improved Hough Transform based fingerprint alignment approach is presented, which improves computing time and memory usage with accurate alignment parameter (rotation and translation) results. This is achieved by studying the strengths...

  3. Capillary self-alignment dynamics for R2R manufacturing of mesoscopic system-in-foil devices

    NARCIS (Netherlands)

    Arutinov, G.; Quintero, A.V.; Smits, E.C.P.; Remoortere, B. van; Brand, J. van den; Schoo, H.F.M.; Briand, D.; Rooij, N.F. de; Dietzel, A.H.

    2012-01-01

    This paper reports a study on the dynamics of foil-based functional component self-alignment onto patterned test substrates and its demonstration when integrating a flexible sensor onto a printed circuitry. We investigate the dependence of alignment time and final precision of stacking of mm- and cm

  4. Effective Electrocardiogram Steganography Based on Coefficient Alignment.

    Science.gov (United States)

    Yang, Ching-Yu; Wang, Wen-Fong

    2016-03-01

    This study presents two types of data hiding methods based on coefficient alignment for electrocardiogram (ECG) signals, namely, lossy and reversible ECG steganographys. The lossy method is divided into high-quality and high-capacity ECG steganography, both of which are capable of hiding confidential patient data in ECG signals. The reversible data hiding method can not only hide secret messages but also completely restore the original ECG signal after bit extraction. Simulations confirmed that the perceived quality generated by the lossy ECG steganography methods was good, while hiding capacity was acceptable. In addition, these methods have a certain degree of robustness, which is rare in conventional ECG stegangraphy schemes. Moreover, the proposed reversible ECG steganography method can not only successfully extract hidden messages but also completely recover the original ECG data.

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

    Science.gov (United States)

    Toh, H

    1997-08-01

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

  6. Anchor-based English-Chinese Bilingual Chunk Alignment Model

    Institute of Scientific and Technical Information of China (English)

    WU We-lin; CHENG Chang-sheng; XU Liang-xian; LU Ru-zhan

    2005-01-01

    Chunk alignment for the bilingual corpus is the base of Example-based Machine Translation. An anchor-based English-Chinese bilingual chunk alignment model and the corresponding algorithm of alignment are presented in this paper. It can effectively overcome the sparse data problem due to the limited size of the bilingual corpus. In this model, the chunk segmentation disambiguation is delayed to the alignment process, and hence the accuracy of chunk segmentation is improved. The experimental results demonstrate the feasibility and viability of this model.

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Farid Amir-Ghiasvand

    2014-01-01

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

  9. Vertically Aligned Carbon Nanofiber based Biosensor Platform for Glucose Sensor

    Energy Technology Data Exchange (ETDEWEB)

    Al Mamun, Khandaker A.; Tulip, Fahmida S.; MacArthur, Kimberly; McFarlane, Nicole; Islam, Syed K.; Hensley, Dale

    2014-03-01

    Vertically aligned carbon nanofibers (VACNFs) have recently become an important tool for biosensor design. Carbon nanofibers (CNF) have excellent conductive and structural properties with many irregularities and defect sites in addition to exposed carboxyl groups throughout their surfaces. These properties allow a better immobilization matrix compared to carbon nanotubes and offer better resolution when compared with the FET-based biosensors. VACNFs can be deterministically grown on silicon substrates allowing optimization of the structures for various biosensor applications. Two VACNF electrode architectures have been employed in this study and a comparison of their performances has been made in terms of sensitivity, sensing limitations, dynamic range, and response time. The usage of VACNF platform as a glucose sensor has been verified in this study by selecting an optimum architecture based on the VACNF forest density. Read More: http://www.worldscientific.com/doi/abs/10.1142/S0129156414500062

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

    Institute of Scientific and Technical Information of China (English)

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

    2013-01-01

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

  11. An Ant-Based Model for Multiple Sequence Alignment

    CERN Document Server

    Guinand, Frédéric

    2008-01-01

    Multiple sequence alignment is a key process in today's biology, and finding a relevant alignment of several sequences is much more challenging than just optimizing some improbable evaluation functions. Our approach for addressing multiple sequence alignment focuses on the building of structures in a new graph model: the factor graph model. This model relies on block-based formulation of the original problem, formulation that seems to be one of the most suitable ways for capturing evolutionary aspects of alignment. The structures are implicitly built by a colony of ants laying down pheromones in the factor graphs, according to relations between blocks belonging to the different sequences.

  12. Research on SINS Alignment Algorithm Based on FIR Filters

    Institute of Scientific and Technical Information of China (English)

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

    2007-01-01

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

  13. Chunk Alignment for Corpus-Based Machine Translation

    Science.gov (United States)

    Kim, Jae Dong

    2011-01-01

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

  14. Comparison of Two Distance Based Alignment Method in Medical Imaging

    Science.gov (United States)

    2001-10-25

    very helpful to register large datasets of contours or surfaces, commonly encountered in medical imaging . They do not require special ordering or...COMPARISON OF TWO DISTANCE BASED ALIGNMENT METHOD IN MEDICAL IMAGING G. Bulan, C. Ozturk Institute of Biomedical Engineering, Bogazici University...Two Distance Based Alignment Method in Medical Imaging Contract Number Grant Number Program Element Number Author(s) Project Number Task Number

  15. Plane alignment design of turnout with the transition curve based on wheel -rail syste m dynamics%基于轮轨动力学的缓和曲线型道岔平面线型设计

    Institute of Scientific and Technical Information of China (English)

    赵卫华; 王平; 曹洋

    2015-01-01

    In order to select proper plane alignments for turnouts with transition curves to meet good running per-formance and improve permissible speed through the diverging track of turnouts,a vehicle -turnout dynamic cou-pling model was established based on the wheel -rail dynamic method.No.42 turnout was taken as an example to calculate wheel /rail dynamic responses of various plane alignments and analyze relationships of evaluation in-dexes and train speeds.Results show the apply of transition curve at the back of the diverging track can ensure the safety and the stability when trains pass at medium or high speed,and adding curve radius or transition curve in the front of the diverging track can reduce the wheel /rail vibration.The higher the speed of train passing through the diverging track,the intenser the wheel /rail system vibration is.When the circular -curve radius of the diverging track of No.42 turnout was increased by 500 m,the permissible speed through the diverging track will increase 10 km /h,and that of the turnout with easement -circular -easement curve can be further in-creased.%为了给缓和曲线型道岔选取合适的平面线型,满足良好的行车性能并提高侧向允许通过速度,基于轮轨动力学建立车辆-道岔动力耦合模型,以42号道岔为例计算不同线型方案下轮轨系统动力响应,且分析各评价指标与列车速度间关系。研究结果表明:道岔侧股后缓和曲线的使用可保证列车中高速通过的安全性和平稳性,增加曲线半径或加设前缓和曲线可降低轮轨系统振动剧烈程度;列车侧向通过速度越高,轮轨系统振动越显著,42号道岔侧股圆曲线半径增加500 m,可使其侧向允许通过速度提高10 km/h,缓圆缓型道岔可进一步提升。

  16. Constructive Alignment for Teaching Model-Based Design for Concurrency

    DEFF Research Database (Denmark)

    Brabrand, Claus

    2007-01-01

    "How can we make sure our students learn what we want them to?" is the number one question in teaching. This paper is intended to provide the reader with: i) a general answer to this question based on the theory of constructive alignment by John Biggs; ii) relevant insights for bringing this answ...... from theory to practice; and iii) specific insights and experiences from using constructive alignment in teaching model-based design for concurrency (as a case study in implementing alignment)......."How can we make sure our students learn what we want them to?" is the number one question in teaching. This paper is intended to provide the reader with: i) a general answer to this question based on the theory of constructive alignment by John Biggs; ii) relevant insights for bringing this answer...

  17. 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

  18. Autonomous Coil Alignment System Using Fuzzy Steering Control for Electric Vehicles with Dynamic Wireless Charging

    Directory of Open Access Journals (Sweden)

    Karam Hwang

    2015-01-01

    Full Text Available An autonomous coil alignment system (ACAS using fuzzy steering control is proposed for vehicles with dynamic wireless charging. The misalignment between the power receiver coil and power transmitter coil is determined based on the voltage difference between two coils installed on the front-left/front-right of the power receiver coil and is corrected through autonomous steering using fuzzy control. The fuzzy control is chosen over other control methods for implementation in ACAS due to the nonlinear characteristic between voltage difference and lateral misalignment distance, as well as the imprecise and constantly varying voltage readings from sensors. The operational validity and feasibility of the ACAS are verified through simulation, where the vehicle equipped with ACAS is able to align with the power transmitter in the road majority of the time during operation, which also implies achieving better wireless power delivery.

  19. A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments

    Directory of Open Access Journals (Sweden)

    McConville Malcolm J

    2007-10-01

    Full Text Available Abstract Background Gas chromatography-mass spectrometry (GC-MS is a robust platform for the profiling of certain classes of small molecules in biological samples. When multiple samples are profiled, including replicates of the same sample and/or different sample states, one needs to account for retention time drifts between experiments. This can be achieved either by the alignment of chromatographic profiles prior to peak detection, or by matching signal peaks after they have been extracted from chromatogram data matrices. Automated retention time correction is particularly important in non-targeted profiling studies. Results A new approach for matching signal peaks based on dynamic programming is presented. The proposed approach relies on both peak retention times and mass spectra. The alignment of more than two peak lists involves three steps: (1 all possible pairs of peak lists are aligned, and similarity of each pair of peak lists is estimated; (2 the guide tree is built based on the similarity between the peak lists; (3 peak lists are progressively aligned starting with the two most similar peak lists, following the guide tree until all peak lists are exhausted. When two or more experiments are performed on different sample states and each consisting of multiple replicates, peak lists within each set of replicate experiments are aligned first (within-state alignment, and subsequently the resulting alignments are aligned themselves (between-state alignment. When more than two sets of replicate experiments are present, the between-state alignment also employs the guide tree. We demonstrate the usefulness of this approach on GC-MS metabolic profiling experiments acquired on wild-type and mutant Leishmania mexicana parasites. Conclusion We propose a progressive method to match signal peaks across multiple GC-MS experiments based on dynamic programming. A sensitive peak similarity function is proposed to balance peak retention time and peak

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

    Institute of Scientific and Technical Information of China (English)

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

    2009-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Thomas Dina

    2005-04-01

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

  2. 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.

  3. mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet.

    Science.gov (United States)

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

    2014-04-01

    The increasing number of available protein structures requires efficient tools for multiple structure comparison. Indeed, multiple structural alignments are essential for the analysis of function, evolution and architecture of protein structures. For this purpose, we proposed a new web server called multiple Protein Block Alignment (mulPBA). This server implements a method based on a structural alphabet to describe the backbone conformation of a protein chain in terms of dihedral angles. This 'sequence-like' representation enables the use of powerful sequence alignment methods for primary structure comparison, followed by an iterative refinement of the structural superposition. This approach yields alignments superior to most of the rigid-body alignment methods and highly comparable with the flexible structure comparison approaches. We implement this method in a web server designed to do multiple structure superimpositions from a set of structures given by the user. Outputs are given as both sequence alignment and superposed 3D structures visualized directly by static images generated by PyMol or through a Jmol applet allowing dynamic interaction. Multiple global quality measures are given. Relatedness between structures is indicated by a distance dendogram. Superimposed structures in PDB format can be also downloaded, and the results are quickly obtained. mulPBA server can be accessed at www.dsimb.inserm.fr/dsimb_tools/mulpba/ .

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

    DEFF Research Database (Denmark)

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

    2007-01-01

    genomes. One main problem with these methods is their computational complexity, and heuristics are therefore employed. Two heuristics are currently very popular: pre-folding and pre-aligning. However, these heuristics are not ideal, as pre-aligning is dependent on sequence similarity that may...... the advantage of providing the constraints dynamically. This has been included in a new implementation of the FOLDALIGN algorithm for pairwise local or global structural alignment of RNA sequences. It is shown that time and memory requirements are dramatically lowered while overall performance is maintained....... Furthermore, a new divide and conquer method is introduced to limit the memory requirement during global alignment and backtrack of local alignment. All branch points in the computed RNA structure are found and used to divide the structure into smaller unbranched segments. Each segment is then realigned...

  5. Dynamic interferometer alignment and its utility in UV Fourier transform spectrometer systems

    Science.gov (United States)

    Dorval, Rick K.; Engel, James R.; Wyntjes, Geert J.

    1993-01-01

    Dynamic alignment has been demonstrated as a practical approach to alignment maintenance for systems in the infrared region of the spectrum. On the basis of work done by OPTRA, this technique was introduced in commercial Fourier transform spectrometer systems in 1982 and in various forms is now available from a number of manufacturers. This paper reports on work by OPTRA to extend the basic technique to systems operating in the ultraviolet. In addition, this paper reports the preliminary results of the development of an alignment system using a laser diode in place of a gas laser normally found in dynamic alignment systems. A unique optical system and spatial heterodyne technique allows for achievement of a metrology system with characteristics that fully satisfy the requirements of an ultraviolet spectrometer system.

  6. Dynamic Programming Used to Align Protein Structures with a Spectrum Is Robust

    Directory of Open Access Journals (Sweden)

    Allen Holder

    2013-11-01

    Full Text Available Several efficient algorithms to conduct pairwise comparisons among large databases of protein structures have emerged in the recent literature. The central theme is the design of a measure between the Cα atoms of two protein chains, from which dynamic programming is used to compute an alignment. The efficiency and efficacy of these algorithms allows large-scale computational studies that would have been previously impractical. The computational study herein shows that the structural alignment algorithm eigen-decomposition alignment with the spectrum (EIGAs is robust against both parametric and structural variation.

  7. Business Alignment: Measurement-Based Alignment of Software Strategies and Business Goals

    Science.gov (United States)

    Münch, Jürgen; Heidrich, Jens; Mandić, Vladimir

    Most of today’s products and services are software-based. Organizations that develop software want to maintain and improve their competitiveness by controlling software-related risks. To do this, they need to align their business goals with software development strategies and translate them into quantitative project management. There is also an increasing need to justify cost and resources for software and system development and other IT services by demonstrating their impact on an organization’s higher-level goals. For both, linking business goals and software-related efforts in an organization is necessary. However, this is a challenging task, and there is a lack of methods addressing this gap.

  8. RM-structure alignment based statistical machine translation model

    Institute of Scientific and Technical Information of China (English)

    Sun Jiadong; Zhao Tiejun

    2008-01-01

    A novel model based on structure alignments is proposed for statistical machine translation in this paper.Meta-structure and sequence of meta-structure for a parse tree are defined.During the translation process, a parse tree is decomposed to deal with the structure divergence and the alignments can be constructed at different levels of recombination of meta-structure (RM).This method can perform the structure mapping across the sub-tree structure between languages.As a result, we get not only the translation for the target language, but sequence of meta-structure of its parse tree at the same time.Experiments show that the model in the framework of log-linear model has better generative ability and significantly outperforms Pharaoh, a phrase-based system.

  9. Robust Non-Frontal Face Alignment with Edge Based Texture

    Institute of Scientific and Technical Information of China (English)

    Hua Li; Shui-Cheng Yan; Li-Zhong Peng

    2005-01-01

    This paper proposes a new algorithm, called Edge-based Texture Driven Shape Model (E-TDSM), for nonfrontal face alignment task. First, the texture is defined as the un-warped edge image contained in the shape rectangle; then,a Bayesian network is constructed to describe the relationship between the shape and texture models; finally, ExpectationMaximization (EM) approach is utilized to infer the optimal texture and position parameters from the observed shape and texture information. Compared with the traditional shape localization algorithms, E-TDSM has the following advantages:1) the un-warped edge-based texture can better predict the shape and is more robust to the illumination and expression variation than the conventional warped gray-level based texture; 2) the presented Bayesian network indicates the logic structure of the face alignment task; and 3) the mutually enhanced shape and texture observations are integrated to infer the optimal parameters of the proposed Bayesian network using EM approach. The extensive experiments on non-frontal face alignment task demonstrate the effectiveness and robustness of the proposed E-TDSM algorithm.

  10. Profile-Based LC-MS data alignment--a Bayesian approach.

    Science.gov (United States)

    Tsai, Tsung-Heng; Tadesse, Mahlet G; Wang, Yue; Ressom, Habtom W

    2013-01-01

    A Bayesian alignment model (BAM) is proposed for alignment of liquid chromatography-mass spectrometry (LC-MS) data. BAM belongs to the category of profile-based approaches, which are composed of two major components: a prototype function and a set of mapping functions. Appropriate estimation of these functions is crucial for good alignment results. BAM uses Markov chain Monte Carlo (MCMC) methods to draw inference on the model parameters and improves on existing MCMC-based alignment methods through 1) the implementation of an efficient MCMC sampler and 2) an adaptive selection of knots. A block Metropolis-Hastings algorithm that mitigates the problem of the MCMC sampler getting stuck at local modes of the posterior distribution is used for the update of the mapping function coefficients. In addition, a stochastic search variable selection (SSVS) methodology is used to determine the number and positions of knots. We applied BAM to a simulated data set, an LC-MS proteomic data set, and two LC-MS metabolomic data sets, and compared its performance with the Bayesian hierarchical curve registration (BHCR) model, the dynamic time-warping (DTW) model, and the continuous profile model (CPM). The advantage of applying appropriate profile-based retention time correction prior to performing a feature-based approach is also demonstrated through the metabolomic data sets.

  11. On the need for system alignment in large water infrastructure. Understanding infrastructure dynamics in Nairobi, Kenya

    Directory of Open Access Journals (Sweden)

    Pär Blomkvist

    2017-06-01

    Full Text Available In this article we contribute to the discussion of infrastructural change in Africa, and explore how a new theoretical perspective may offer a different, more comprehensive and historically informed understanding of the trend towards large water infrastructure in Africa. We examine the socio-technical dynamics of large water infrastructures in Nairobi, Kenya, in a longer historical perspective using two concepts that we call intra-systemic alignment and inter-level alignment. Our theoretical perspective is inspired by Large Technical Systems (LTS and Multi-Level Perspective (MLP. While inter-level alignment focuses on the process of aligning the technological system at the three levels of niche, regime and landscape, intra-systemic alignment deals with how components within the regime are harmonised and standardised to fit with each other. We pay special attention to intrasystemic alignment between the supply side and the demand side, or as we put it, upstream and downstream components of a system. In narrating the history of water supply in Nairobi, we look at both the upstream (largescale supply and downstream activities (distribution and payment, and compare the Nairobi case with European history of large infrastructures. We emphasise that regime actors in Nairobi have dealt with the issues of alignment mainly to facilitate and expand upstream activities, while concerning downstream activities they have remained incapable of expanding service and thus integrating the large segment of low-income consumers. We conclude that the present surge of large-scale water investment in Nairobi is the result of sector reforms that enabled the return to a long tradition – a 'Nairobi style' – of upstream investment mainly benefitting the highincome earners. Our proposition is that much more attention needs to be directed at inter-level alignment at the downstream end of the system, to allow the creation of niches aligned to the regime.

  12. Developmental long trace profiler using optimally aligned mirror based pentaprism

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-07-21

    A low-budget surface slope measuring instrument, the Developmental Long Trace Profiler (DLTP), was recently brought into operation at the Advanced Light Source Optical Metrology Laboratory [Nucl. Instr. and Meth. A 616, 212-223 (2010)]. The instrument is based on a precisely calibrated autocollimator and a movable pentaprism. The capability of the DLTP to achieve sub-microradian surface slope metrology has been verified via cross-comparison measurements with other high-performance slope measuring instruments when measuring the same high-quality test optics. In the present work, a further improvement of the DLTP is achieved by replacing the existing bulk pentaprism with a specially designed mirror based pentaprism. A mirror based pentaprism offers the possibility to eliminate systematic errors introduced by inhomogeneity of the optical material and fabrication imperfections of a bulk pentaprism. We provide the details of the mirror based pentaprism design and describe an original experimental procedure for precision mutual alignment of the mirrors. The algorithm of the alignment procedure and its efficiency are verified with rigorous ray tracing simulations. Results of measurements of a spherically curved test mirror and a flat test mirror using the original bulk pentaprism are compared with measurements using the new mirror based pentaprism, demonstrating the improved performance.

  13. Developmental long trace profiler using optimally aligned mirror based pentaprism

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-12-20

    A low-budget surface slope measuring instrument, the Developmental Long Trace Profiler (DLTP), was recently brought into operation at the Advanced Light Source Optical Metrology Laboratory. The instrument is based on a precisely calibrated autocollimator and a movable pentaprism. The capability of the DLTP to achieve sub-microradian surface slope metrology has been verified via cross-comparison measurements with other high-performance slope measuring instruments when measuring the same high-quality test optics. In the present work, a further improvement of the DLTP is achieved by replacing the existing bulk pentaprism with a specially designed mirror based pentaprism. A mirror based pentaprism offers the possibility to eliminate systematic errors introduced by inhomogeneity of the optical material and fabrication imperfections of a bulk pentaprism. We provide the details of the mirror based pentaprism design and describe an original experimental procedure for precision mutual alignment of the mirrors. The algorithm of the alignment procedure and its efficiency are verified with rigorous ray tracing simulations. Results of measurements of a spherically curved test mirror and a flat test mirror using the original bulk pentaprism are compared with measurements using the new mirror based pentaprism, demonstrating the improved performance.

  14. Dynamics of electric field induced particle alignment in nonpolar polymer matrix

    Science.gov (United States)

    Tai, Xiangyang; Wu, Guozhang; Yui, Hiroshi; Asai, Shigeo; Sumita, Masao

    2003-11-01

    The dynamics of electric field induced particle alignment in nonpolar polymer matrix to build one-dimensional conductive materials was investigated. The influence of electric field on particle alignment was real-time traced by dynamic percolation measurement using carbon black (CB) filled polyethylene as a model system. The activation energy of the continuous CB path formation was calculated and found to be unchanged with CB alignment. The critical percolation concentration at thermodynamic equilibrium state φc* was deduced to characterize the anisotropism of network structure, by which the thermodynamic prerequisite electric field E* for the transition from three-dimensional isotropic network to one-dimensional chain could be easily found out.

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

    Science.gov (United States)

    Khan, Mohammad Ibrahim; Kamal, Md Sarwar

    2015-03-01

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

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

    Science.gov (United States)

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

    2013-06-18

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

  17. Alignment analysis of urban railways based on passenger travel demand

    DEFF Research Database (Denmark)

    Andersen, Jonas Lohmann Elkjær; Landex, Alex

    2010-01-01

    Planning of urban railways like Metro and especially Light Rail Transit often result in multiple alignment alternatives from where it can be difficult to select the best one. Travel demand is a good foundation for evaluating a railway alignment for its ability to attract passengers. Therefore...... and can be applied as decision support in different stages of the urban railway alignment planning....

  18. Alignment dependent ultrafast electron-nuclear dynamics in high-order harmonic generation

    CERN Document Server

    Li, Mu-Zi; Bian, Xue-Bin

    2016-01-01

    We investigated the high-order harmonic generation (HHG) process of diatomic molecular ion $\\mathrm{H}_2^+$ in non-Born-Oppenheimer approximations. The corresponding three-dimensional time-dependent Schr\\"odinger equation is solved with arbitrary alignment angles. It is found that the nuclear motion can lead to spectral modulation of HHG. Redshifts are unique in molecular HHG which decrease with the increase of alignment angles of the molecules and are sensitive to the initial vibrational states. It can be used to extract the ultrafast electron-nuclear dynamics and image molecular structure.

  19. 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...

  20. 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.

  1. Utilizing Time Redundancy for Particle Filter-Based Transfer Alignment

    Science.gov (United States)

    Chattaraj, Suvendu; Mukherjee, Abhik

    2016-07-01

    Signal detection in the presence of high noise is a challenge in natural sciences. From understanding signals emanating out of deep space probes to signals in protein interactions for systems biology, domain specific innovations are needed. The present work is in the domain of transfer alignment (TA), which deals with estimation of the misalignment of deliverable daughter munitions with respect to that of the delivering mother platform. In this domain, the design of noise filtering scheme has to consider a time varying and nonlinear system dynamics at play. The accuracy of conventional particle filter formulation suffers due to deviations from modeled system dynamics. An evolutionary particle filter can overcome this problem by evolving multiple system models through few support points per particle. However, this variant has even higher time complexity for real-time execution. As a result, measurement update gets deferred and the estimation accuracy is compromised. By running these filter algorithms on multiple processors, the execution time can be reduced, to allow frequent measurement updates. Such scheme ensures better system identification so that performance improves in case of simultaneous ejection of multiple daughters and also results in better convergence of TA algorithms for single daughter.

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

    Science.gov (United States)

    Ibarra, Ignacio L; Melo, Francisco

    2010-07-01

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

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

    DEFF Research Database (Denmark)

    Nielsen, Morten; Lund, Ole

    2009-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Claros M Gonzalo

    2010-06-01

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

  5. Similarity Measurement of Web Sessions Based on Sequence Alignment

    Institute of Scientific and Technical Information of China (English)

    LI Chaofeng; LU Yansheng

    2007-01-01

    The task of clustering Web sessions is to group Web sessions based on similarity and consists of maximizing the intra-group similarity while minimizing the inter-group similarity.The first and foremost question needed to be considered in clustering Web sessions is how to measure the similarity between Web sessions. However, there are many shortcomings in traditional measurements. This paper introduces a new method for measuring similarities between Web pages that takes into account not only the URL but also the viewing time of the visited Web page. Then we give a new method to measure the similarity of Web sessions using sequence alignment and the similarity of Web page access in detail.Experiments have proved that our method is valid and efficient.

  6. Space Alignment Based on Regularized Inversion Precoding in Cognitive Transmission

    Directory of Open Access Journals (Sweden)

    R. Yao

    2015-09-01

    Full Text Available For a two-tier Multiple-Input Multiple-Output (MIMO cognitive network with common receiver, the precoding matrix has a compact relationship with the capacity performance in the unlicensed secondary system. To increase the capacity of secondary system, an improved precoder based on the idea of regularized inversion for secondary transmitter is proposed. An iterative space alignment algorithm is also presented to ensure the Quality of Service (QoS for primary system. The simulations reveal that, on the premise of achieving QoS for primary system, our proposed algorithm can get larger capacity in secondary system at low Signal-to-Noise Ratio (SNR, which proves the effectiveness of the algorithm.

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

    Directory of Open Access Journals (Sweden)

    Emanuel Santos

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

  8. A fast and accurate initial alignment method for strapdown inertial navigation system on stationary base

    Institute of Scientific and Technical Information of China (English)

    Xinlong WANG; Gongxun SHEN

    2005-01-01

    In this work,a fast and accurate stationary alignment method for strapdown inertial navigation system (SINS) is proposed.It has been demonstrated that the stationary alignment of SINS can be improved by employing the multiposition technique,but the alignment time of the azimuth error is relatively longer.Over here,the two-position alignment principle is presented.On the basis of this SINS error model,a fast estimation algorithm of the azimuth error for the initial alignment of SINS on stationary base is derived fully from the horizontal velocity outputs and the output rates,and the novel azimuth error estimation algorithm is used for the two-position alignment.Consequently,the speed and accuracy of the SINS's initial alignment is enhanced greatly.The computer simulation results illustrate the efficiency of this alignment method.

  9. 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......' 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...... heuristics. RESULTS: 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...

  10. BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations.

    Science.gov (United States)

    Bahr, A; Thompson, J D; Thierry, J C; Poch, O

    2001-01-01

    BAliBASE is specifically designed to serve as an evaluation resource to address all the problems encountered when aligning complete sequences. The database contains high quality, manually constructed multiple sequence alignments together with detailed annotations. The alignments are all based on three-dimensional structural superpositions, with the exception of the transmembrane sequences. The first release provided sets of reference alignments dealing with the problems of high variability, unequal repartition and large N/C-terminal extensions and internal insertions. Here we describe version 2.0 of the database, which incorporates three new reference sets of alignments containing structural repeats, trans-membrane sequences and circular permutations to evaluate the accuracy of detection/prediction and alignment of these complex sequences. BAliBASE can be viewed at the web site http://www-igbmc.u-strasbg. fr/BioInfo/BAliBASE2/index.html or can be downloaded from ftp://ftp-igbmc.u-strasbg.fr/pub/BAliBASE2 /.

  11. 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.

  12. The cortex-based alignment approach to TMS coil positioning.

    Science.gov (United States)

    Duecker, Felix; Frost, Martin A; de Graaf, Tom A; Graewe, Britta; Jacobs, Christianne; Goebel, Rainer; Sack, Alexander T

    2014-10-01

    TMS allows noninvasive manipulation of brain activity in healthy participants and patients. The effectiveness of TMS experiments critically depends on precise TMS coil positioning, which is best for most brain areas when a frameless stereotactic system is used to target activation foci based on individual fMRI data. From a purely scientific perspective, individual fMRI-guided TMS is thus the method of choice to ensure optimal TMS efficiency. Yet, from a more practical perspective, such individual functional data are not always available, and therefore alternative TMS coil positioning approaches are often applied, for example, based on functional group data reported in Talairach coordinates. We here propose a novel method for TMS coil positioning that is based on functional group data, yet only requires individual anatomical data. We used cortex-based alignment (CBA) to transform individual anatomical data to an atlas brain that includes probabilistic group maps of two functional regions (FEF and hMT+/V5). Then, these functional group maps were back-transformed to the individual brain anatomy, preserving functional-anatomical correspondence. As a proof of principle, the resulting CBA-based functional targets in individual brain space were compared with individual FEF and hMT+/V5 hotspots as conventionally localized with individual fMRI data and with targets based on Talairach coordinates as commonly done in TMS research in case only individual anatomical data are available. The CBA-based approach significantly improved localization of functional brain areas compared with traditional Talairach-based targeting. Given the widespread availability of CBA schemes and preexisting functional group data, the proposed procedure is easy to implement and at no additional measurement costs. However, the accuracy of individual fMRI-guided TMS remains unparalleled, and the CBA-based approach should only be the method of choice when individual functional data cannot be obtained or

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

    Directory of Open Access Journals (Sweden)

    Jakob H Havgaard

    2007-10-01

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

  14. Simulation of beamline alignment operations

    Energy Technology Data Exchange (ETDEWEB)

    Annese, C; Miller, M G

    1999-02-02

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

  15. zPicture: Dynamic Alignment and Visualization Tool for Analyzing Conservation Profiles

    Energy Technology Data Exchange (ETDEWEB)

    Ovcharenko, I. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Energy, Environment and Institutional Computing; Genome Biology Division; Loots, G. G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Genome Biology Division; Hardison, R. C. [Pennsylvania State Univ., Univ. Park, PA (United States). Dept. of Computer Science and Engineering; Miller., W. [Pennsylvania State Univ., Univ. Park, PA (United States). Dept. of Computer Science and Engineering; Dept. of Biology; Stubbs, L. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Genome Biology Division

    2004-03-01

    Comparative sequence analysis has evolved as an essential technique for identifying functional coding and noncoding elements conserved throughout evolution. Here we introduce zPicture (http://zpicture.dcode.org), an interactive web-based sequence alignment and visualization tool for dynamically generating conservation profiles and identifying evolutionary conserved regions (ECRs). zPicture is highly flexible because critical parameters can be modified interactively, allowing users to differentially predict ECRs in comparisons of sequences of different phylogenetic distances and evolutionary rates. We demonstrate the application of this module to identify a known regulatory element in the HOXD locus, where functional ECRs are difficult to discern against the highly conserved genomic background. zPicture also facilitates transcription factor binding site analysis via the rVISTA tool portal. We present an example of the HBB complex when zPicture/rVista combination specifically pinpoints to two ECRs containing GATA- 1, NF-E2 and TAL1/E47 binding sites that were previously identified as transcriptional enhancers. In addition, zPicture is linked to the UCSC Genome Browser allowing users to automatically extract sequences and gene annotations for any recorded locus. Finally, we describe how this tool can be efficiently applied to the analysis of nonvertebrate genomes including those of microbial organisms.

  16. Quality measures for HRR alignment based ISAR imaging algorithms

    CSIR Research Space (South Africa)

    Janse van Rensburg, V

    2013-05-01

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

  17. Error Analysis and Compensation of Gyrocompass Alignment for SINS on Moving Base

    Directory of Open Access Journals (Sweden)

    Bo Xu

    2014-01-01

    Full Text Available An improved method of gyrocompass alignment for strap-down inertial navigation system (SINS on moving base assisted with Doppler velocity log (DVL is proposed in this paper. After analyzing the classical gyrocompass alignment principle on static base, implementation of compass alignment on moving base is given in detail. Furthermore, based on analysis of velocity error, latitude error, and acceleration error on moving base, two improvements are introduced to ensure alignment accuracy and speed: (1 the system parameters are redesigned to decrease the acceleration interference and (2 a data repeated calculation algorithm is used in order to shorten the prolonged alignment time caused by changes in parameters. Simulation and test results indicate that the improved method can realize the alignment on moving base quickly and effectively.

  18. Beam based alignment of the SSRF storage ring

    Institute of Scientific and Technical Information of China (English)

    ZHANG Man-Zhou; LI Hao-Hu; JIANG Bo-Cheng; LIU Gui-Min; LI De-Ming

    2009-01-01

    There are 140 beam position monitors (BPMs) in the Shanghai Synchrotron Radiation Facility (SSRF) storage ring used for measuring the closed orbit. As the BPM pickup electrodes are assembled directly on the vacuum chamber, it is important to calibrate the electrical center offset of the BPM to an adjacent quadrupole magnetic center. A beam based alignment (BBA) method which varies individual quadrupole magnet strength and observes its effects on the orbit is used to measure the BPM offsets in both the horizontal and vertical planes. It is a completely automated technique with various data processing methods. There are several parameters such as the strength change of the correctors and the quadrupoles which should be chosen carefully in real measurement. After several rounds of BBA measurement and closed orbit correction, these offsets are set to an accuracy better than 10 μm. In this paper we present the method of beam based calibration of BPMs, the experimental results of the SSRF storage ring, and the error analysis.

  19. Analysis of chimpanzee history based on genome sequence alignments.

    Directory of Open Access Journals (Sweden)

    Jennifer L Caswell

    2008-04-01

    Full Text Available Population geneticists often study small numbers of carefully chosen loci, but it has become possible to obtain orders of magnitude for more data from overlaps of genome sequences. Here, we generate tens of millions of base pairs of multiple sequence alignments from combinations of three western chimpanzees, three central chimpanzees, an eastern chimpanzee, a bonobo, a human, an orangutan, and a macaque. Analysis provides a more precise understanding of demographic history than was previously available. We show that bonobos and common chimpanzees were separated approximately 1,290,000 years ago, western and other common chimpanzees approximately 510,000 years ago, and eastern and central chimpanzees at least 50,000 years ago. We infer that the central chimpanzee population size increased by at least a factor of 4 since its separation from western chimpanzees, while the western chimpanzee effective population size decreased. Surprisingly, in about one percent of the genome, the genetic relationships between humans, chimpanzees, and bonobos appear to be different from the species relationships. We used PCR-based resequencing to confirm 11 regions where chimpanzees and bonobos are not most closely related. Study of such loci should provide information about the period of time 5-7 million years ago when the ancestors of humans separated from those of the chimpanzees.

  20. Codebook-based interference alignment for uplink MIMO interference channels

    KAUST Repository

    Lee, Hyun Ho

    2014-02-01

    In this paper, we propose a codebook-based interference alignment (IA) scheme in the constant multiple-input multipleoutput (MIMO) interference channel especially for the uplink scenario. In our proposed scheme, we assume cooperation among base stations (BSs) through reliable backhaul links so that global channel knowledge is available for all BSs, which enables BS to compute the transmit precoder and inform its quantized index to the associated user via limited rate feedback link.We present an upper bound on the rate loss of the proposed scheme and derive the scaling law of the feedback load tomaintain a constant rate loss relative to IA with perfect channel knowledge. Considering the impact of overhead due to training, cooperation, and feedback, we address the effective degrees of freedom (DOF) of the proposed scheme and derive the maximization of the effective DOF. From simulation results, we verify our analysis on the scaling law to preserve the multiplexing gain and confirm that the proposed scheme is more effective than the conventional IA scheme in terms of the effective DOF. © 2014 KICS.

  1. 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.

  2. Dynamic-template-directed multiscale assembly for large-area coating of highly-aligned conjugated polymer thin films

    Science.gov (United States)

    Mohammadi, Erfan; Zhao, Chuankai; Meng, Yifei; Qu, Ge; Zhang, Fengjiao; Zhao, Xikang; Mei, Jianguo; Zuo, Jian-Min; Shukla, Diwakar; Diao, Ying

    2017-07-01

    Solution processable semiconducting polymers have been under intense investigations due to their diverse applications from printed electronics to biomedical devices. However, controlling the macromolecular assembly across length scales during solution coating remains a key challenge, largely due to the disparity in timescales of polymer assembly and high-throughput printing/coating. Herein we propose the concept of dynamic templating to expedite polymer nucleation and the ensuing assembly process, inspired by biomineralization templates capable of surface reconfiguration. Molecular dynamic simulations reveal that surface reconfigurability is key to promoting template-polymer interactions, thereby lowering polymer nucleation barrier. Employing ionic-liquid-based dynamic template during meniscus-guided coating results in highly aligned, highly crystalline donor-acceptor polymer thin films over large area (>1 cm2) and promoted charge transport along both the polymer backbone and the π-π stacking direction in field-effect transistors. We further demonstrate that the charge transport anisotropy can be reversed by tuning the degree of polymer backbone alignment.

  3. Beam based alignment and its relevance in Indus-2

    Energy Technology Data Exchange (ETDEWEB)

    Jena, Saroj Kumar; Husain, Riyasat; Gandhi, M. L.; Agrawal, R. K.; Yadav, S.; Ghodke, A. D. [Raja Ramanna Centre for Advanced Technology, Indore (India)

    2015-09-15

    Initially in the Indus-2 storage ring, the closed orbit distortion (COD) could be best corrected to 1.3 mm rms in the horizontal and 0.43 mm rms in the vertical plane. The strength of the corrector magnets required high values for COD correction. This revealed that offsets in COD readout by the beam position monitors (BPMs) played a role in not achieving a rms COD lower than the above value. Thus, the offset between the electrical center of BPMs and the magnetic center of the nearest quadrupole magnet could be estimated using the beam based alignment (BBA) method. It prefers that the quadrupole magnet is able to be controlled individually and active shunt power supply (ASPS) system was designed for this purpose that works efficiently. This paper describes the methodology of BBA, topology of ASPS and its performance, and COD minimization using the measured BPM offsets. After BBA, the COD could be reduced to 0.45 mm rms and 0.2 mm rms in horizontal and vertical planes, respectively.

  4. C-GRAAL: common-neighbors-based global GRAph ALignment of biological networks.

    Science.gov (United States)

    Memišević, Vesna; Pržulj, Nataša

    2012-07-01

    Networks are an invaluable framework for modeling biological systems. Analyzing protein-protein interaction (PPI) networks can provide insight into underlying cellular processes. It is expected that comparison and alignment of biological networks will have a similar impact on our understanding of evolution, biological function, and disease as did sequence comparison and alignment. Here, we introduce a novel pairwise global alignment algorithm called Common-neighbors based GRAph ALigner (C-GRAAL) that uses heuristics for maximizing the number of aligned edges between two networks and is based solely on network topology. As such, it can be applied to any type of network, such as social, transportation, or electrical networks. We apply C-GRAAL to align PPI networks of eukaryotic and prokaryotic species, as well as inter-species PPI networks, and we demonstrate that the resulting alignments expose large connected and functionally topologically aligned regions. We use the resulting alignments to transfer biological knowledge across species, successfully validating many of the predictions. Moreover, we show that C-GRAAL can be used to align human-pathogen inter-species PPI networks and that it can identify patterns of pathogen interactions with host proteins solely from network topology.

  5. A parallelogram-based compliant remote-center-of-motion stage for active parallel alignment

    Science.gov (United States)

    Qu, Jianliang; Chen, Weihai; Zhang, Jianbin

    2014-09-01

    Parallel alignment stage with remote-center-of-motion (RCM) is of key importance in precision out-of-plane aligning since it can eliminate the harmful lateral displacement generated at the output platform. This paper presents the development of a parallelogram-based compliant RCM stage for active parallel alignment. Different from conventional parallelogram-based RCM mechanism, the proposed stage is designed with compliant mechanisms, which endows the stage with many attractive merits when used in precision micro-/nanomanipulations. A symmetric double-parallelogram mechanism (SDPM) based on flexure hinges is developed as the rotary guiding component to realize desired RCM function. Due to the geometrical constraint of the SDPM, the operating space of the stage can be easily adjusted by bending the input links without loss of rotational precision. The stage is driven by a piezoelectric actuator and its output motion is measured by non-contact displacement sensors. Based on pseudo-rigid-body simplification method, the analytical models predicting kinematics, statics, and dynamics of the RCM stage have been established. Besides, the dimensional optimization is conducted in order to maximize the first resonance frequency of the stage. After that, finite element analysis is conducted to validate the established models and the prototype of the stage is fabricated for performance tests. The experimental results show that the developed RCM stage has a rotational range of 1.45 mrad while the maximum center shift of the RCM point is as low as 1 μm, which validate the effectiveness of the proposed scheme.

  6. Active network alignment: a matching-based approach

    CERN Document Server

    Malmi, Eric; Gionis, Aristides

    2016-01-01

    Network alignment is the problem of matching the nodes of two graphs, maximizing the similarity of the matched nodes and the edges between them. This problem is encountered in a wide array of applications - from biological networks to social networks to ontologies - where multiple networked data sources need to be integrated. Due to the difficulty of the task, an accurate alignment can rarely be found without human assistance. Thus, it is of great practical importance to develop network alignment algorithms that can optimally leverage experts who are able to provide the correct alignment for a small number of nodes. Yet, only a handful of existing works address this active network alignment setting. The majority of the existing active methods focus on absolute queries ("are nodes $a$ and $b$ the same or not?"), whereas we argue that it is generally easier for a human expert to answer relative queries ("which node in the set $\\{b_1, \\ldots, b_n\\}$ is the most similar to node $a$?"). This paper introduces a nov...

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

    CSIR Research Space (South Africa)

    Mlambo, CS

    2015-01-01

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

  8. 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.

  9. Seeing the song: left auditory structures may track auditory-visual dynamic alignment.

    Directory of Open Access Journals (Sweden)

    Julia A Mossbridge

    Full Text Available Auditory and visual signals generated by a single source tend to be temporally correlated, such as the synchronous sounds of footsteps and the limb movements of a walker. Continuous tracking and comparison of the dynamics of auditory-visual streams is thus useful for the perceptual binding of information arising from a common source. Although language-related mechanisms have been implicated in the tracking of speech-related auditory-visual signals (e.g., speech sounds and lip movements, it is not well known what sensory mechanisms generally track ongoing auditory-visual synchrony for non-speech signals in a complex auditory-visual environment. To begin to address this question, we used music and visual displays that varied in the dynamics of multiple features (e.g., auditory loudness and pitch; visual luminance, color, size, motion, and organization across multiple time scales. Auditory activity (monitored using auditory steady-state responses, ASSR was selectively reduced in the left hemisphere when the music and dynamic visual displays were temporally misaligned. Importantly, ASSR was not affected when attentional engagement with the music was reduced, or when visual displays presented dynamics clearly dissimilar to the music. These results appear to suggest that left-lateralized auditory mechanisms are sensitive to auditory-visual temporal alignment, but perhaps only when the dynamics of auditory and visual streams are similar. These mechanisms may contribute to correct auditory-visual binding in a busy sensory environment.

  10. Association between hip abductor function, rear-foot dynamic alignment, and dynamic knee valgus during single-leg squats and drop landings

    Directory of Open Access Journals (Sweden)

    Yoshinori Kagaya

    2015-06-01

    Conclusion: Dynamic hip mal-alignment might be associated with both greater KID and HOD, whereas rear-foot eversion is associated only with greater KID. Hip abductor and rear-foot dysfunction are important factors for dynamic knee valgus and thus evaluating DTT and HFT will help to prevent dynamic knee valgus.

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

    Science.gov (United States)

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

    2014-12-10

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

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

    Directory of Open Access Journals (Sweden)

    Zengke Li

    2014-12-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-04-02

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

  14. Self-aligning LED-based optical link

    Science.gov (United States)

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

    2016-09-01

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

  15. Towards a pivotal-based approach for business process alignment

    OpenAIRE

    Ulmer, Jean-Stéphane; Belaud, Jean-Pierre; Le Lann, Jean-Marc

    2011-01-01

    This article focuses on business process engineering, especially on alignment between business analysis and implementation. Through a business process management approach, different transformations interfere with process models in order to make them executable. To keep the consistency of process model from business model to IT model, we propose a pivotal metamodel-centric methodology. It aims at keeping or giving all requisite structural and semantic data needed to perform such transformation...

  16. An Investigation of the Sampling-Based Alignment Method and its Contributions

    Directory of Open Access Journals (Sweden)

    Juan Luo

    2013-07-01

    Full Text Available By investigating the distribution of phrase pairs in phrase translation tables, the work in this paperdescribes an approach to increase the number of n-gram alignments in phrase translation tables outputbya sampling-based alignment method. This approach consists in enforcing the alignment of n-grams indistinct translation subtables so as to increase the number of n-grams. Standard normal distribution is usedto allot alignment time among translation subtables, which results in adjustment of the distribution of n-grams. This leads to better evaluation results on statistical machine translation tasks than the originalsampling-based alignment approach. Furthermore, thetranslation quality obtained by merging phrasetranslation tables computed from the sampling-basedalignment method and from MGIZA++ is examined

  17. Alignment and integration of complex networks by hypergraph-based spectral clustering

    CERN Document Server

    Michoel, Tom

    2012-01-01

    Complex networks possess a rich, multi-scale structure reflecting the dynamical and functional organization of the systems they model. Often there is a need to analyze multiple networks simultaneously, to model a system by more than one type of interaction or to go beyond simple pairwise interactions, but currently there is a lack of theoretical and computational methods to address such problems. Here we introduce a framework for multi-network analysis based on hypergraph representations. Our main result is a generalization of the Perron-Frobenius theorem from which we derive spectral clustering algorithms for directed and undirected hypergraphs. We illustrate our approach with applications for tripartite community detection in folksonomies, for local and global alignment of protein-protein interaction networks between multiple species and for detecting clusters of overlapping regulatory pathways in directed networks.

  18. Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments

    Directory of Open Access Journals (Sweden)

    Tcherepanov Vasily

    2004-07-01

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

  19. Automation of beam based alignment for the PAL-XFEL undulator line

    Energy Technology Data Exchange (ETDEWEB)

    Parc, Yong Woon; Hwang, Ilmoon [Pohang Accelerator Laboratory, Pohang 790-784 (Korea, Republic of); Han, Jang-Hui, E-mail: janghui_han@postech.ac.kr [Pohang Accelerator Laboratory, Pohang 790-784 (Korea, Republic of); Ko, In Soo [Pohang University of Science and Technology, Pohang 790-784 (Korea, Republic of)

    2015-05-11

    An automated method of quadrupole beam based alignment in an X-ray free electron laser (XFEL) undulator line is proposed. To realize the automatic beam based alignment (BBA) independently of operator's skill and efforts, the procedure is simplified. Simulation results on the BBA technique using two alignment stages for the Pohang Accelerator Laboratory XFEL's (PAL-XFEL) undulator line is carried out. After a standard mechanical alignment the quadrupoles are expected to be aligned to 100 μm rms from our previous experience. A rough alignment method in this study is able to align the quadrupoles to about 40 μm rms without any pre-handling of electron beam orbit or quadrupoles position. At the second stage, the singular value decomposition (SVD) method is applied to perform a fine alignment in which the trajectory of an electron beam is controlled within 5 μm rms to the ideal orbit. All procedures are programmable to perform the BBA automatically.

  20. Prokaryotic Phylogeny Based on Complete Genomes Without Sequence Alignment

    Science.gov (United States)

    Hao, Bailin; Qi, Ji; Wang, Bin

    2003-04-01

    This is a brief review of a series of on-going work on bacterial phylogeny. We have proposed a new method to infer relatedness of prokaryotes from their complete genome data without using sequence alignment. It has led to results comparable with the bacteriologists' systematics as reflected in the latest 2001 edition of the Bergey's Manual of Systematic Bacteriology1. In what follows we only touch on the mathematical aspects of the method. The biological implications of our results will be published elsewhere.

  1. An Autonomous Coil Alignment System for the Dynamic Wireless Charging of Electric Vehicles to Minimize Lateral Misalignment

    Directory of Open Access Journals (Sweden)

    Karam Hwang

    2017-03-01

    Full Text Available This paper proposes an autonomous coil alignment system (ACAS for electric vehicles (EVs with dynamic wireless charging (DWC to mitigate the reduction in received power caused by lateral misalignment between the source and load coils. The key component of the ACAS is a novel sensor coil design, which can detect the load coil’s left or right position relative to the source coil by observing the change in voltage phase. This allows the lateral misalignment to be estimated through the wireless power transfer (WPT system alone, which is a novel tracking method for vehicular applications. Once misalignment is detected, the vehicle’s lateral position is self-adjusted by an autonomous steering function. The feasibility of the overall operation of the ACAS was verified through simulation and experiments. In addition, an analysis based on experimental results was conducted, demonstrating that 26% more energy can be transferred during DWC with the ACAS, just by keeping the vehicle’s load coil aligned with the source coil.

  2. Dynamics of capillary infiltration of liquids into a highly aligned multi-walled carbon nanotube film.

    Science.gov (United States)

    Boncel, Sławomir; Walczak, Krzysztof Z; Koziol, Krzysztof K K

    2011-01-01

    The physical compatibility of a highly aligned carbon nanotube (HACNT) film with liquids was established using a fast and convenient experimental protocol. Two parameters were found to be decisive for the infiltration process. For a given density of nanotube packing, the thermodynamics of the infiltration process (wettability) were described by the contact angle between the nanotube wall and a liquid meniscus (θ). Once the wettability criterion (θ capillarity for a steady process (Lucas-Washburn law), where the nanoscale capillary force, here supported by gravity, is compensated by viscous drag. This most general theory of capillarity can be applied in a prediction of both wettability of HACNT films and the dynamics of capillary rise in the intertube space in various technological applications.

  3. High-harmonic probing of electronic coherence in dynamically aligned molecules

    CERN Document Server

    Kraus, P M; Gijsbertsen, A; Lucchese, R R; Rohringer, N; Wörner, H J

    2013-01-01

    We introduce and demonstrate a new approach to measuring coherent electron wave packets using high-harmonic spectroscopy. By preparing a molecule in a coherent superposition of electronic states, we show that electronic coherence opens previously unobserved high-harmonic-generation channels that connect distinct but coherently related electronic states. Performing the measurements in dynamically aligned nitric oxide (NO) molecules we observe the complex temporal evolution of the electronic coherence under coupling to nuclear motion. Choosing a weakly allowed transition to prepare the wave packet, we demonstrate an unprecedented sensitivity that arises from optical interference between coherent and incoherent pathways. This mechanism converts a 0.1 $%$ excitation fraction into a $\\sim$20 $%$ signal modulation.

  4. Improving alignment in Tract-based spatial statistics: Evaluation and optimization of image registration

    NARCIS (Netherlands)

    De Groot, M.; Vernooij, M.W.; Klein, S.; Arfan Ikram, M.; Vos, F.M.; Smith, S.M.; Niessen, W.J.; Andersson, J.L.R.

    2013-01-01

    Anatomical alignment in neuroimaging studies is of such importance that considerable effort is put into improving the registration used to establish spatial correspondence. Tract-based spatial statistics (TBSS) is a popular method for comparing diffusion characteristics across subjects. TBSS

  5. Ancient Maya Cultivation in a Dynamic Wetland Environment: Insights into the Functions of Anthropogenic Rock Alignments at El Edén Ecological Reserve, Quintana Roo, Mexico

    OpenAIRE

    Chmilar, Jennifer Andrea

    2013-01-01

    Cultivation has taken many forms throughout the Maya lowlands. In the Yalahau region of the northern Maya lowlands, a series of wetlands produce a dynamic environment of wet, dry, and intermediate areas depending on fluctuations of the annual hydrologic cycle. Within these wetlands, anthropogenic rock alignments suggest human use and manipulation of the environment dating to the late Preclassic period. The dissertation is based on research at a single wetland at El Edén Ecological Reserve, Q...

  6. 测量船用捷联惯导动基座快速粗对准技术%Dynamic rapid course alignment for measurement ship SINS

    Institute of Scientific and Technical Information of China (English)

    孙伟; 车莉娜

    2013-01-01

    According to the problem that it is difficult to achieve the coarse alignment when the measure-ment ship is on a swing base. The essential distinction and applicability between the analytic coarse alignment and the inertial coarse alignment are analyzed contrastively. Based on the nature of the inertial coarse alignment is a dynamic process, the inertial coarse alignment is quoted in the strapdown inertial navigation system (SINS) , the theoretical derivation and the mathematical analysis are also presented. The process of coarse alignment is analysed on the typical three-axial swing, and the results are compared with the situation of tradi-tional course alignment. The mooring experiment is used to validate the feasibility of the inertial alignment method. The results show that when the measurement ship is on the swing state, the strapdown matrix can be built exactly. Compared with the traditional analytical inertial alignment, the inertial alignment has a better sta-bilization.%针对测量船用捷联惯导系统(strapdown inertial navigation system,SINS)粗对准问题,对比分析了传统解析法和惯性系粗对准法的本质区别与适用范围,利用惯性系对准过程是动态过程的性质,提出在SINS中引入惯性系粗对准法并进行理论推导与分析.模拟测量船典型三轴摇摆状态下对SINS惯性系粗对准过程进行仿真分析,并与传统解析粗对准结果比对.选取测量船的系泊状态建立试验环境并得到实验结果:惯性系对准方法可建立更为准确的捷联矩阵,惯性系对准结果具有更好的稳定性.

  7. A Research on Bilingual Dictionary Based Sentence Alignment for Chinese English Parallel Corpus

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Parallel corpus is of great importance to machine translation, and automatic sentence alignment is the first step towards its processing. This paper puts forward a bilingual dictionary based sentence alignment method for Chinese English parallel corpus, which differs from previous length based algorithm in its knowledge-rich approach. Experimental result shows that this method produces over 93% accuracy with usual English-Chinese dictionaries whose translations cover 31.88%~47.90% of the corpus.

  8. DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment

    Directory of Open Access Journals (Sweden)

    Morgenstern Burkhard

    2008-05-01

    Full Text Available Abstract Background DIALIGN-T is a reimplementation of the multiple-alignment program DIALIGN. Due to several algorithmic improvements, it produces significantly better alignments on locally and globally related sequence sets than previous versions of DIALIGN. However, like the original implementation of the program, DIALIGN-T uses a a straight-forward greedy approach to assemble multiple alignments from local pairwise sequence similarities. Such greedy approaches may be vulnerable to spurious random similarities and can therefore lead to suboptimal results. In this paper, we present DIALIGN-TX, a substantial improvement of DIALIGN-T that combines our previous greedy algorithm with a progressive alignment approach. Results Our new heuristic produces significantly better alignments, especially on globally related sequences, without increasing the CPU time and memory consumption exceedingly. The new method is based on a guide tree; to detect possible spurious sequence similarities, it employs a vertex-cover approximation on a conflict graph. We performed benchmarking tests on a large set of nucleic acid and protein sequences For protein benchmarks we used the benchmark database BALIBASE 3 and an updated release of the database IRMBASE 2 for assessing the quality on globally and locally related sequences, respectively. For alignment of nucleic acid sequences, we used BRAliBase II for global alignment and a newly developed database of locally related sequences called DIRM-BASE 1. IRMBASE 2 and DIRMBASE 1 are constructed by implanting highly conserved motives at random positions in long unalignable sequences. Conclusion On BALIBASE3, our new program performs significantly better than the previous program DIALIGN-T and outperforms the popular global aligner CLUSTAL W, though it is still outperformed by programs that focus on global alignment like MAFFT, MUSCLE and T-COFFEE. On the locally related test sets in IRMBASE 2 and DIRM-BASE 1, our method

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

    Directory of Open Access Journals (Sweden)

    Hoffmann Nils

    2012-08-01

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

  10. A New Pre-alignment Approach Based on Four-Quadrant-Photo-Detector for IC Mask

    Institute of Scientific and Technical Information of China (English)

    Yun Liu; De Xu; Min Tan

    2007-01-01

    In this paper, a new pre-alignment approach based on Four-Quadrant-Photo-Detector (FQPD) for IC mask is presented.The voltage outputs from FQPDs are the functions of alignment mark's position offsets with respect to FQPDs. The functions are obtained with least squares error (LSE)-based polynomial fitting after the normalization of experimental data. As the acquired functions are not monotonic about their variables, the alignment mark's position offset cannot be given by direct inverse operation on the obtained functions. However, the piecewise polynomial fitting gives the inverse function, with which the alignment mark's position offset can be predicted according to the voltage outputs of FQPDs. On the basis of prediction, a pre-alignment control strategy is proposed.The feasibility and robustness of the pre-alignment approach is shown by experiments. Furthermore, the results demonstrate that the maximum error of mask's position offset in the X- and Y- directions is less than 15 μm after coarse pre-alignment.

  11. Shape-based discriminative analysis of combined bilateral hippocampi using multiple object alignment

    Science.gov (United States)

    Shen, Li; Makedon, Fillia; Saykin, Andrew

    2004-05-01

    Shape analysis of hippocampi in schizophrenia has been preformed previously using the spherical harmonic SPHARM description. In these studies, the left and right hippocampi are aligned independently and the spatial relation between them is not explored. This paper presents a new SPHARM-based technique which examines not only the individual shape information of the two hippocampi but also the spatial relation between them. The left and right hippocampi are treated as a single shape configuration. A ploy-shape alignment algorithm is developed for aligning configurations of multiple SPHARM surfaces as follows: (1) the total volume is normalized; (2) the parameter space is aligned for creating the surface correspondence; (3) landmarks are created by a uniform sampling of multiple surfaces for each configuration; (4) a quaternion-based algorithm is employed to align each landmark representation to the mean configuration through the least square rotation and translation iteratively until the mean converges. After applying the poly-shape alignment algorithm, a point distribution model is applied to aligned landmarks for feature extraction. Classification is performed using Fisher's linear discriminant with an effective feature selection scheme. Applying the above procedure to our hippocampal data (14 controls versus 25 schizophrenics, all right-handed males), we achieve the best cross-validation accuracy of 92%, supporting the idea that the whole shape configuration of the two hippocampi provides valuable information in detecting schizophrenia. The results of an ROC analysis and a visualization of discriminative patterns are also included.

  12. BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark.

    Science.gov (United States)

    Thompson, Julie D; Koehl, Patrice; Ripp, Raymond; Poch, Olivier

    2005-10-01

    Multiple sequence alignment is one of the cornerstones of modern molecular biology. It is used to identify conserved motifs, to determine protein domains, in 2D/3D structure prediction by homology and in evolutionary studies. Recently, high-throughput technologies such as genome sequencing and structural proteomics have lead to an explosion in the amount of sequence and structure information available. In response, several new multiple alignment methods have been developed that improve both the efficiency and the quality of protein alignments. Consequently, the benchmarks used to evaluate and compare these methods must also evolve. We present here the latest release of the most widely used multiple alignment benchmark, BAliBASE, which provides high quality, manually refined, reference alignments based on 3D structural superpositions. Version 3.0 of BAliBASE includes new, more challenging test cases, representing the real problems encountered when aligning large sets of complex sequences. Using a novel, semiautomatic update protocol, the number of protein families in the benchmark has been increased and representative test cases are now available that cover most of the protein fold space. The total number of proteins in BAliBASE has also been significantly increased from 1444 to 6255 sequences. In addition, full-length sequences are now provided for all test cases, which represent difficult cases for both global and local alignment programs. Finally, the BAliBASE Web site (http://www-bio3d-igbmc.u-strasbg.fr/balibase) has been completely redesigned to provide a more user-friendly, interactive interface for the visualization of the BAliBASE reference alignments and the associated annotations.

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

    Directory of Open Access Journals (Sweden)

    Kaufmann Michael

    2005-03-01

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

  14. 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.

  15. 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.

  16. Dynamics of capillary infiltration of liquids into a highly aligned multi-walled carbon nanotube film

    Directory of Open Access Journals (Sweden)

    Sławomir Boncel

    2011-06-01

    Full Text Available The physical compatibility of a highly aligned carbon nanotube (HACNT film with liquids was established using a fast and convenient experimental protocol. Two parameters were found to be decisive for the infiltration process. For a given density of nanotube packing, the thermodynamics of the infiltration process (wettability were described by the contact angle between the nanotube wall and a liquid meniscus (θ. Once the wettability criterion (θ < 90° was met, the HACNT film (of free volume equal to 91% was penetrated gradually by the liquid in a rate that can be linearly correlated to dynamic viscosity of the liquid (η. The experimental results follow the classical theory of capillarity for a steady process (Lucas–Washburn law, where the nanoscale capillary force, here supported by gravity, is compensated by viscous drag. This most general theory of capillarity can be applied in a prediction of both wettability of HACNT films and the dynamics of capillary rise in the intertube space in various technological applications.

  17. Photoconductive study and carrier dynamics of vertically aligned GaAs nanowires

    Institute of Scientific and Technical Information of China (English)

    Hui Xia; Bimu Yao; Zhenyu Lu; Pingping Chen; Tianxin Li

    2013-01-01

    Single wire devices are generally fabricated to study the electrical and photoelectric behaviors of semiconductor nanowires (NWs);however detriment or contamination can hardly be avoided during manipulation of NWs under focused ion and electron beams. This could not be a trivial factor for III-V NWs which are candidates for high efficiency solar energy harvesting and sensitive photodetection. In this study an alternative way to probe the photoconductive property of individual epitaxial GaAs NWs is presented. For the sample preparation, a uniform spin-coated layer of polymer was selected to be the supporting medium for the vertically aligned NWs structure;then the adequate thinning and polishing of the sample exposed the NW tip and also achieved the required height of NW. An external power adjustable laser was introduced as the excitation source, and the dark and photoconductive current-voltage properties of individual NW were measured by the conductive atomic force microscopy. The typical Schottky style photoconductive behavior was observed in the vertically aligned GaAs NW, and its photoresponsivity has been found to be much higher than that of the reported for single NW photodetector. Finally, a numerical model based on the experimental setup was established to simulate the photoelectric behavior of individual NW. The minority hole lifetime has been found to dominate the photoconductive current-voltage properties of NW under the positive sample bias, and can be derived from the quantitative fitting of experimental photo-IV curves.

  18. Membrane based Deformable Mirror: Intrinsic aberrations and alignment issues

    CERN Document Server

    Bayanna, A Raja; Chatterjee, S; Mathew, Shibu K; Venkatakrishnan, P

    2015-01-01

    A Deformable Mirror (DM) is an important component of an Adaptive Optics system. It is known that an on-axis spherical/parabolic optical component, placed at an angle to the incident beam introduces defocus as well as astigmatism in the image plane. Although the former can be compensated by changing the focal plane position, the latter cannot be removed by mere optical re-alignment. Since the DM is to be used to compensate a turbulence-induced curvature term in addition to other aberrations, it is necessary to determine the aberrations induced by such (curved DM surface) an optical element when placed at an angle (other than 0 degree) of incidence in the optical path. To this effect, we estimate to a first order, the aberrations introduced by a DM as a function of the incidence angle and deformation of the DM surface. We record images using a simple setup in which the incident beam is reflected by a 37 channel Micro-machined Membrane Deformable Mirror for various angles of incidence. It is observed that astig...

  19. Complementary characterization data in support of uniaxially aligned electrospun nanocomposites based on a model PVOH-epoxy system.

    Science.gov (United States)

    Karimi, Samaneh; Staiger, Mark P; Buunk, Neil; Fessard, Alison; Tucker, Nick

    2016-06-01

    This paper presents complementary data corresponding to characterization tests done for our research article entitled "Uniaxially aligned electrospun fibers for advanced nanocomposites based on a model PVOH-epoxy system" (Karimi et al., 2016) [1]. Poly(vinyl alcohol) and epoxy resin were selected as a model system and the effect of electrospun fiber loading on polymer properties was examined in conjunction with two manufacturing methods. A novel electrospinning technology for production of uniaxially aligned nanofiber arrays was used. A conventional wet lay-up fabrication method is compared against a novel, hybrid electrospinning-electrospraying approach. The structure and thermomechanical properties of resulting composite materials were examined using scanning electron microscopy, dynamic mechanical analysis, thermogravimetric analysis, differential scanning calorimetry, Fourier transform infrared spectroscopy, and tensile testing. For discussion of obtained results please refer to the research paper (Karimi et al., 2016) [1].

  20. Complementary characterization data in support of uniaxially aligned electrospun nanocomposites based on a model PVOH-epoxy system

    Directory of Open Access Journals (Sweden)

    Samaneh Karimi

    2016-06-01

    Full Text Available This paper presents complementary data corresponding to characterization tests done for our research article entitled “Uniaxially aligned electrospun fibers for advanced nanocomposites based on a model PVOH-epoxy system” (Karimi et al., 2016 [1]. Poly(vinyl alcohol and epoxy resin were selected as a model system and the effect of electrospun fiber loading on polymer properties was examined in conjunction with two manufacturing methods. A novel electrospinning technology for production of uniaxially aligned nanofiber arrays was used. A conventional wet lay-up fabrication method is compared against a novel, hybrid electrospinning–electrospraying approach. The structure and thermomechanical properties of resulting composite materials were examined using scanning electron microscopy, dynamic mechanical analysis, thermogravimetric analysis, differential scanning calorimetry, Fourier transform infrared spectroscopy, and tensile testing. For discussion of obtained results please refer to the research paper (Karimi et al., 2016 [1].

  1. Complementary characterization data in support of uniaxially aligned electrospun nanocomposites based on a model PVOH-epoxy system

    Science.gov (United States)

    Karimi, Samaneh; Staiger, Mark P.; Buunk, Neil; Fessard, Alison; Tucker, Nick

    2016-01-01

    This paper presents complementary data corresponding to characterization tests done for our research article entitled “Uniaxially aligned electrospun fibers for advanced nanocomposites based on a model PVOH-epoxy system” (Karimi et al., 2016) [1]. Poly(vinyl alcohol) and epoxy resin were selected as a model system and the effect of electrospun fiber loading on polymer properties was examined in conjunction with two manufacturing methods. A novel electrospinning technology for production of uniaxially aligned nanofiber arrays was used. A conventional wet lay-up fabrication method is compared against a novel, hybrid electrospinning–electrospraying approach. The structure and thermomechanical properties of resulting composite materials were examined using scanning electron microscopy, dynamic mechanical analysis, thermogravimetric analysis, differential scanning calorimetry, Fourier transform infrared spectroscopy, and tensile testing. For discussion of obtained results please refer to the research paper (Karimi et al., 2016) [1]. PMID:26977430

  2. Measurement of word frequencies in genomic DNA sequences based on partial alignment and fuzzy set.

    Science.gov (United States)

    Shida, Fumiya; Mizuta, Satoshi

    2014-08-01

    Accompanied with the rapid increase of the amount of data registered in the databases of biological sequences, the need for a fast method of sequence comparison applicable to sequences of large size is also increasing. In general, alignment is used for sequence comparison. However, the alignment may not be appropriate for comparison of sequences of large size such as whole genome sequences due to its large time complexity. In this article, we propose a semi alignment-free method of sequence comparison based on word frequency distributions, in which we partially use the alignment to measure word frequencies along with the idea of fuzzy set theory. Experiments with ten bacterial genome sequences demonstrated that the fuzzy measurements has the effect that facilitates discrimination between close relatives and distant relatives.

  3. SOAP3: ultra-fast GPU-based parallel alignment tool for short reads.

    Science.gov (United States)

    Liu, Chi-Man; Wong, Thomas; Wu, Edward; Luo, Ruibang; Yiu, Siu-Ming; Li, Yingrui; Wang, Bingqiang; Yu, Chang; Chu, Xiaowen; Zhao, Kaiyong; Li, Ruiqiang; Lam, Tak-Wah

    2012-03-15

    SOAP3 is the first short read alignment tool that leverages the multi-processors in a graphic processing unit (GPU) to achieve a drastic improvement in speed. We adapted the compressed full-text index (BWT) used by SOAP2 in view of the advantages and disadvantages of GPU. When tested with millions of Illumina Hiseq 2000 length-100 bp reads, SOAP3 takes < 30 s to align a million read pairs onto the human reference genome and is at least 7.5 and 20 times faster than BWA and Bowtie, respectively. For aligning reads with up to four mismatches, SOAP3 aligns slightly more reads than BWA and Bowtie; this is because SOAP3, unlike BWA and Bowtie, is not heuristic-based and always reports all answers.

  4. Alignment and temperature effects in liquid-crystal-based active polarimetry.

    Science.gov (United States)

    Gladish, James C; Duncan, Donald D

    2014-06-20

    It is well known that in liquid crystal (LC)-based active polarimetry, alignment and temperature effects impact polarimeter performance. Practically speaking, when constructing a polarimetric measurement system from LC variable retarders (LCVRs), unavoidable alignment and temperature uncertainties will occur, leading to systematic error that propagates to the Mueller matrix. Typical calibration methods use only a single metric to assess polarimeter performance (the condition number) and often ignore the relationship between systematic error and specific Mueller matrix elements. Here we explore alignment and temperature effects in a Stokes generator and polarimeter, each consisting of two LCVRs, through a series of simulations to calibrate the polarimeter and measure the Mueller matrix of air. We achieve this by modifying an existing LCVR model to incorporate alignment and temperature effects. This new approach offers insight into employing LCVRs individually and associating particular Mueller matrix element error with specific LCVR effects.

  5. 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.

  6. 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.

  7. Study of High Precision Dynamic Initial Alignment Technology for Inertial Navigation System%惯导系统高精度动态对准技术研究

    Institute of Scientific and Technical Information of China (English)

    先治文; 胡小平; 练军想; 李冠南

    2013-01-01

    惯性导航初始对准技术是惯性导航的关键技术之一,而动态对准技术可以增强惯导系统的环境适应性.就GPS位置信息辅助下的惯性导航系统高精度动态对准技术进行研究.首先构建了15状态的Kalman滤波器,分析验证了Kalman滤波参数对于对准精度和对准速度的影响,在一定范围内,适当调整滤波参数,可以较好地改善滤波性能;然后在对准过程中使用了两位置转动观测增强的方法,提高了系统可观性,正确地估计比传感器件的零偏误差,并在纯惯导中加以补偿;最后通过跑车实验进行行车动态对准,达到了对准后24h纯惯导定位误差优于1 nmil的精度.%Inertial navigation is a process of integration, the main task of initial alignment of inertial navigation is determine the initial values of the integration and gyro drift errors and accelerometer biases. The initial alignment is one of the key technique of inertial navigation , in which dynamic initial alignment can improve the application of inertial navigation. In the paper, a high precision dynamic initial alignment technique is proposed for the GPS aided inertial navigation system (INS) on the moving base. This paper proposes the Kalman filter of 15 states, analyzes the effects of the Kalman parameters on the alignment accuracy and speed, showes that it will improve the performace of the filter that changing the Kalman paramaters properly. On the other hand, this paper uses the two-position a-lignment to improve the observability of the system, estimated the sensor-errores correctly then compensated them in the process of inertial navigation. Finally, the field-test used the high precision dynamic initial alignment technique, and the position error of navigation o-vermatch 1 nmile for 24 hours navigation.

  8. Measurement of process dynamics through coaxially aligned high speed near-infrared imaging in laser powder bed fusion additive manufacturing

    Science.gov (United States)

    Fox, Jason C.; Lane, Brandon M.; Yeung, Ho

    2017-05-01

    For process stability in laser powder bed fusion (LPBF) additive manufacturing (AM), control of melt pool dimensions is imperative. In order to control melt pool dimensions in real time, sampling frequencies in excess of 10 kHz may be required, which presents a challenge for many thermal and optical monitoring systems. The National Institute of Standards and Technology (NIST) is currently developing the Additive Manufacturing Metrology Testbed (AMMT), which replicates a metal based laser powder bed fusion AM process while providing open architecture for control, sensing, and calibration sources. The system is outfitted with a coaxially aligned, near-infrared (NIR) high speed melt pool monitoring (MPM) system. Similar monitoring systems are incorporated into LPBF research testbeds, and appearing on commercial machines, but at lower available frame rates, which may limit observation of higher frequency events such as spatter or size fluctuations. This paper presents an investigation of the coaxial imaging systems of the AMMT to capture the process dynamics, and quantify the effects of dynamic fluctuations on melt pool size measurements. Analysis is carried out on a baseline experiment with no powder material added, melt pool size measurements collected in-situ are compared to ex-situ measurements, and results are discussed in terms of temporal bandwidth. Findings will show that, even at the frame rate and resolution presented, challenges in relating in-situ video signals to the ex-situ measurement analysis remain.

  9. CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding.

    Directory of Open Access Journals (Sweden)

    Yongchao Liu

    Full Text Available The majority of next-generation sequencing short-reads can be properly aligned by leading aligners at high speed. However, the alignment quality can still be further improved, since usually not all reads can be correctly aligned to large genomes, such as the human genome, even for simulated data. Moreover, even slight improvements in this area are important but challenging, and usually require significantly more computational endeavor. In this paper, we present CUSHAW3, an open-source parallelized, sensitive and accurate short-read aligner for both base-space and color-space sequences. In this aligner, we have investigated a hybrid seeding approach to improve alignment quality, which incorporates three different seed types, i.e. maximal exact match seeds, exact-match k-mer seeds and variable-length seeds, into the alignment pipeline. Furthermore, three techniques: weighted seed-pairing heuristic, paired-end alignment pair ranking and read mate rescuing have been conceived to facilitate accurate paired-end alignment. For base-space alignment, we have compared CUSHAW3 to Novoalign, CUSHAW2, BWA-MEM, Bowtie2 and GEM, by aligning both simulated and real reads to the human genome. The results show that CUSHAW3 consistently outperforms CUSHAW2, BWA-MEM, Bowtie2 and GEM in terms of single-end and paired-end alignment. Furthermore, our aligner has demonstrated better paired-end alignment performance than Novoalign for short-reads with high error rates. For color-space alignment, CUSHAW3 is consistently one of the best aligners compared to SHRiMP2 and BFAST. The source code of CUSHAW3 and all simulated data are available at http://cushaw3.sourceforge.net.

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

    Science.gov (United States)

    He, Xin; Ling, Xu; Sinha, Saurabh

    2009-03-01

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

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

    Directory of Open Access Journals (Sweden)

    Xin He

    2009-03-01

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

  12. 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

  13. 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.

  14. An anti-disturbance high-precision alignment for distributed POS based on inertial reference frame

    Science.gov (United States)

    Bai, Lijian; Wang, Yue

    2017-03-01

    The distributed POS is playing an important role in the ultra-high resolution aerial survey and remote sensing system, and can accurately provide time-spatial reference information for various imaging sensors. However, the distributed POS faces a special problem that the flexible arms used to connect the inertial measurement units (IMUs) would deteriorate the phenomenon that external disturbance leads to serious alignment errors. In order to improve the alignment precision of distributed POS in external disturbance, an anti-disturbance coarse alignment based on inertial reference frame is proposed. This method is developed mainly based on the structure of non-collinear vectors, which are constructed by a velocity vector determined by gravity vector integration. The disturbed acceleration and rotation is decreased a lot by the integral operation in the proposed method. Finally, the experiments were carried out and verified the validity of the proposed method.

  15. 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.

  16. Image-based quantification of fiber alignment within electrospun tissue engineering scaffolds is related to mechanical anisotropy.

    Science.gov (United States)

    Fee, Timothy; Downs, Crawford; Eberhardt, Alan; Zhou, Yong; Berry, Joel

    2016-07-01

    It is well documented that electrospun tissue engineering scaffolds can be fabricated with variable degrees of fiber alignment to produce scaffolds with anisotropic mechanical properties. Several attempts have been made to quantify the degree of fiber alignment within an electrospun scaffold using image-based methods. However, these methods are limited by the inability to produce a quantitative measure of alignment that can be used to make comparisons across publications. Therefore, we have developed a new approach to quantifying the alignment present within a scaffold from scanning electron microscopic (SEM) images. The alignment is determined by using the Sobel approximation of the image gradient to determine the distribution of gradient angles with an image. This data was fit to a Von Mises distribution to find the dispersion parameter κ, which was used as a quantitative measure of fiber alignment. We fabricated four groups of electrospun polycaprolactone (PCL) + Gelatin scaffolds with alignments ranging from κ = 1.9 (aligned) to κ = 0.25 (random) and tested our alignment quantification method on these scaffolds. It was found that our alignment quantification method could distinguish between scaffolds of different alignments more accurately than two other published methods. Additionally, the alignment parameter κ was found to be a good predictor the mechanical anisotropy of our electrospun scaffolds. The ability to quantify fiber alignment within and make direct comparisons of scaffold fiber alignment across publications can reduce ambiguity between published results where cells are cultured on "highly aligned" fibrous scaffolds. This could have important implications for characterizing mechanics and cellular behavior on aligned tissue engineering scaffolds. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1680-1686, 2016.

  17. Dynamic and static knee alignment at baseline predict structural abnormalities on MRI associated with medial compartment knee osteoarthritis after 2 years.

    Science.gov (United States)

    Mahmoudian, Armaghan; van Dieёn, Jaap H; Bruijn, Sjoerd M; Baert, Isabel A C; Faber, Gert S; Luyten, Frank P; Verschueren, Sabine M P

    2017-09-01

    Dynamic and static varus alignment, both, have been reported as risk factors associated with structural progression of knee osteoarthritis. However the association of none of the static and dynamic alignment with structural, clinical, and functional progression associated with knee osteoarthritis has not been assessed yet in a longitudinal study. Forty-seven women with early and established medial knee osteoarthritis were evaluated. Static and dynamic alignment as well as MRI detected structural features, clinical, and functional characteristics of patients were assessed at baseline and at 2 years follow-up. Associations between baseline static and dynamic alignment with structural, functional, and clinical characteristics at the time of entry, as well as the changes over 2 years were evaluated. Both static and dynamic varus alignment at baseline were significantly associated with osteoarthritis related tibio-femoral joint structural abnormalities detected on MRI, at the time of entry. Only the magnitude of varus thrust at baseline was predictive of the changes in the presence of meniscal maceration over two years. None of the static or dynamic measures of knee joint alignment were associated with clinical characteristics associated with medial knee osteoarthritis. The key finding of this study is that both frontal plane dynamic and static alignment, are associated with structural abnormalities in patients with medial knee osteoarthritis. Copyright © 2017. Published by Elsevier B.V.

  18. A study of Hough Transform-based fingerprint alignment algorithms

    CSIR Research Space (South Africa)

    Mlambo, CS

    2014-10-01

    Full Text Available array. In 2013 Paulino et al [10] applied Ratha et al’s [2] approach in latent fingerprint matching to present a descriptor-based Hough transform. This involved the use of orientation field and minutiae information to accumulate evidence into accumulator... and improves on the early work presented in the 1990’s, as presented in [5], [14], [8], [17], [11], [10], and [12]. As a result, the memory requirements, computing time and performance on different conditions of minutiae points has not been presented...

  19. Alignment of global supply networks based on strategic groups of supply chains

    Directory of Open Access Journals (Sweden)

    Nikos G. Moraitakis

    2017-09-01

    Full Text Available Background: From a supply chain perspective, often big differences exist between global raw material suppliers’ approaches to supply their respective local markets. The progressing complexity of large centrally managed global supply networks and their often-unknown upstream ramifications increase the likelihood of undetected bottlenecks and inefficiencies. It is therefore necessary to develop an approach to strategically master the upstream complexity of such networks from a holistic supply chain perspective in order to align regional competitive priorities and supply chain structures. The objective of this research is hence to develop an approach for the supply-chain-based alignment of complex global supply networks. Method: We review existing literature from the fields of supply chain and network management, strategic sourcing, and strategic management. Based on the literature review and theoretical and practical considerations we deduce a conceptual approach to consider upstream supply chain structures in supply network alignment initiatives. Results: On the basis of these considerations and current empirical literature we transfer strategic group theory to the supply network management context. The proposed approach introduces strategic groups of supply chains as a segmentation criterion for complex global supply networks which enables the network-wide alignment of competitive priorities. Conclusion: Supply-chain-based segmentation of global supply network structures can effectively reduce the complexity, firms face when aiming to strategically align their supply chains on a holistic level. The results of this research are applicable for certain types of global supply networks and can be used for network alignment and strategy development. The approach can furthermore generate insights useable for negotiation support with suppliers.

  20. Investigating Conversational Dynamics: Interactive Alignment, Interpersonal Synergy, and Collective Task Performance.

    Science.gov (United States)

    Fusaroli, Riccardo; Tylén, Kristian

    2016-01-01

    This study investigates interpersonal processes underlying dialog by comparing two approaches, interactive alignment and interpersonal synergy, and assesses how they predict collective performance in a joint task. While the interactive alignment approach highlights imitative patterns between interlocutors, the synergy approach points to structural organization at the level of the interaction-such as complementary patterns straddling speech turns and interlocutors. We develop a general, quantitative method to assess lexical, prosodic, and speech/pause patterns related to the two approaches and their impact on collective performance in a corpus of task-oriented conversations. The results show statistical presence of patterns relevant for both approaches. However, synergetic aspects of dialog provide the best statistical predictors of collective performance and adding aspects of the alignment approach does not improve the model. This suggests that structural organization at the level of the interaction plays a crucial role in task-oriented conversations, possibly constraining and integrating processes related to alignment.

  1. SOAP3-dp: fast, accurate and sensitive GPU-based short read aligner.

    Directory of Open Access Journals (Sweden)

    Ruibang Luo

    Full Text Available To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS, most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, CUSHAW2, GEM and GPU-based aligners BarraCUDA and CUSHAW, SOAP3-dp was found to be two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR on Illumina reads with different lengths. Transcending its predecessor SOAP3, which does not allow gapped alignment, SOAP3-dp by default tolerates alignment similarity as low as 60%. Real data evaluation using human genome demonstrates SOAP3-dp's power to enable more authentic variants and longer Indels to be discovered. Fosmid sequencing shows a 9.1% FDR on newly discovered deletions. SOAP3-dp natively supports BAM file format and provides the same scoring scheme as BWA, which enables it to be integrated into existing analysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and Tianhe-1A.

  2. 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.

  3. 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.

  4. Two-Stream Transformer Networks for Video-based Face Alignment.

    Science.gov (United States)

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

    2017-08-01

    In this paper, we propose a two-stream transformer networks (TSTN) approach for video-based face alignment. Unlike conventional image-based face alignment approaches which cannot explicitly model the temporal dependency in videos and motivated by the fact that consistent movements of facial landmarks usually occur across consecutive frames, our TSTN aims to capture the complementary information of both the spatial appearance on still frames and the temporal consistency information across frames. To achieve this, we develop a two-stream architecture, which decomposes the video-based face alignment into spatial and temporal streams accordingly. Specifically, the spatial stream aims to transform the facial image to the landmark positions by preserving the holistic facial shape structure. Accordingly, the temporal stream encodes the video input as active appearance codes, where the temporal consistency information across frames is captured to help shape refinements. Experimental results on the benchmarking video-based face alignment datasets show very competitive performance of our method in comparisons to the state-of-the-arts.

  5. DOPA: GPU-based protein alignment using database and memory access optimizations

    NARCIS (Netherlands)

    Hasan, L.; Kentie, M.; Al-Ars, Z.

    2011-01-01

    Background Smith-Waterman (S-W) algorithm is an optimal sequence alignment method for biological databases, but its computational complexity makes it too slow for practical purposes. Heuristics based approximate methods like FASTA and BLAST provide faster solutions but at the cost of reduced accurac

  6. DOPA: GPU-based protein alignment using database and memory access optimizations

    NARCIS (Netherlands)

    Hasan, L.; Kentie, M.; Al-Ars, Z.

    2011-01-01

    Background Smith-Waterman (S-W) algorithm is an optimal sequence alignment method for biological databases, but its computational complexity makes it too slow for practical purposes. Heuristics based approximate methods like FASTA and BLAST provide faster solutions but at the cost of reduced accurac

  7. Photographer Paths: Sequence Alignment of Geotagged Photos for Exploration-based Route Planning

    NARCIS (Netherlands)

    el Ali, A.; van Sas, S.N.A.; Nack, F.

    2013-01-01

    Urban mobility analysis of geotagged photos can unlock mobility patterns of users who took these photos, which can be used for exploration-based city route planners. Applying sequence alignment techniques on 5 years of geotagged Flickr photos in Amsterdam (The Netherlands) allowed creating walkable

  8. Dynamics of a ±1/2 defect pair in a confined geometry:A thin hybrid aligned nematic cell

    Institute of Scientific and Technical Information of China (English)

    路丽霞; 张志东

    2015-01-01

    Confined geometry can change defect structure and properties. In this paper, we investigate numerically the dynamics of a dipole of ±1/2 parallel wedge disclination lines in a confined geometry: a thin hybrid aligned nematic (HAN) cell, based on Landau–de Gennes theory. When the cell gap d is larger than a critical value of 12ξ (whereξ is the characteristic length for order-parameter change), the pair annihilates. A pure HAN configuration without defect is formed in an equi-librium state. In the confined geometry of d≤12ξ, the diffusion process is discovered for the first time and an eigenvalue exchange configuration is formed in an equilibrium state. The eigenvalue exchange configuration is induced by different essential reasons. When 10ξ

  9. Predicting three-dimensional patellofemoral kinematics from static imaging-based alignment measures.

    Science.gov (United States)

    Freedman, Benjamin R; Sheehan, Frances T

    2013-03-01

    Patellofemoral pain syndrome causes significant discomfort and disability among much of the general population. Despite recent breakthroughs in dynamic three-dimensional imaging technologies to assess pathological patellofemoral motion, such tools remain costly for clinical diagnostics applications. Thus, this study investigated whether three-dimensional patellofemoral kinematics could be predicted from routine two-dimensional static measures of patellofemoral joint alignment quantified from magnetic resonance imaging (MRI) data acquired in full knee extension. Twenty-six volunteers clinically diagnosed with patellofemoral pain (19 F/7 M, 25.9 ± 11.1 years) and 26 control subjects (19 F/7 M, 25.3 ± 7.7 years) were included in this IRB-approved study. Static three-dimensional sagittal T1-weighted gradient recall echo and dynamic MRI scans were acquired. For the dynamic image acquisition, subjects cyclically flexed and extended their knee (at 30 cycles/min) while a full cine-phase contrast MRI set (24 time frames of anatomic images and x-, y-, and z-velocity images) was acquired. From these data, static measures of patellofemoral alignment and three-dimensional patellofemoral kinematics were derived. Single and multiple regressions between static and kinematic variables were evaluated. Although shown reliable, the static MRI measures could only partially predict patellofemoral kinematics, with r(2) -values ranging from 16% to 77%. This makes it imperitave that the current precise, accurate, 3D, dynamic imaging techniques be translated into clinical tools.

  10. FtsZ rings and helices: physical mechanisms for the dynamic alignment of biopolymers in rod-shaped bacteria

    Science.gov (United States)

    Fischer-Friedrich, Elisabeth; Friedrich, Benjamin M.; Gov, Nir S.

    2012-02-01

    In many bacterial species, the protein FtsZ forms a cytoskeletal ring that marks the future division site and scaffolds the division machinery. In rod-shaped bacteria, most frequently membrane-attached FtsZ rings or ring fragments are reported and occasionally helices. By contrast, axial FtsZ clusters have never been reported. In this paper, we investigate theoretically how dynamic FtsZ aggregates align in rod-shaped bacteria. We study systematically different physical mechanisms that affect the alignment of FtsZ polymers using a computational model that relies on autocatalytic aggregation of FtsZ filaments at the membrane. Our study identifies a general tool kit of physical and geometrical mechanisms by which rod-shaped cells align biopolymer aggregates. Our analysis compares the relative impact of each mechanism on the circumferential alignment of FtsZ as observed in rod-shaped bacteria. We determine spontaneous curvature of FtsZ polymers and axial confinement of FtsZ on the membrane as the strongest factors. Including Min oscillations in our model, we find that these stabilize axial and helical clusters on short time scales, but promote the formation of an FtsZ ring at the cell middle at longer times. This effect could provide an explanation to the long standing puzzle of transiently observed oscillating FtsZ helices in Escherichia coli cells prior to cell division.

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

    Institute of Scientific and Technical Information of China (English)

    郭宁; 冯萍; 康继昌

    2011-01-01

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

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

    Science.gov (United States)

    Rani, R Ranjani; Ramyachitra, D

    2016-12-01

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

  13. Investigating conversational dynamics: Interactive alignment, Interpersonal synergy, and collective task performance

    DEFF Research Database (Denmark)

    Fusaroli, Riccardo; Tylén, Kristian

    2016-01-01

    interlocutors, the synergy approach points to structural organization at the level of the interaction - such as complementary patterns straddling speech-turns and interlocutors. We develop a general, quantitative method to assess lexical, prosodic and speech/pause patterns related to the two approaches......This study investigates interpersonal processes underlying dialog by comparing two approaches, interactive alignment and interpersonal synergy, and assesses how they predict collective performance in a joint task. While the interactive alignment approach highlights imitative patterns between...... and their impact on collective performance in a corpus of task-oriented conversations. The results show statistical presence of patterns relevant for both approaches. However, synergetic aspects of dialog provide the best statistical predictors of collective performance and adding aspects of the alignment approach...

  14. Method for automatization of the alignment of a laboratory based x-ray phase contrast edge illumination system.

    Science.gov (United States)

    Millard, T P; Endrizzi, M; Ignatyev, K; Hagen, C K; Munro, P R T; Speller, R D; Olivo, A

    2013-08-01

    Here we present a general alignment algorithm for an edge illumination x-ray phase contrast imaging system, which is used with the laboratory systems developed at UCL. It has the flexibility to be used with all current mask designs, and could also be applied to future synchrotron based systems. The algorithm has proved to be robust experimentally, and can be used for the automatization of future commercial systems through automatic alignment and alignment correction.

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

    Energy Technology Data Exchange (ETDEWEB)

    Draeger, Jula

    2011-08-15

    In order to fully exploit the discovery potential of the CMS detector for new physics beyond the Standard Model at the high luminosity and centre-of-mass energy provided by the Large Hadron Collider, a careful calibration of the detector and profound understanding of its impact on physics performance are necessary to provide realistic uncertainties for the measurements of physics processes. This thesis describes the track-based alignment of the inner tracking system of CMS with the Millepede II algorithm. Using the combined information of tracks from cosmic rays and collisions taken in 2010, a remarkable local alignment precision has been reached that meets the design specification for most regions of the detector and takes into account instabilities of the detector geometry over time. In addition, the impact of the alignment of b tagging or the Z boson resonance are investigated. The latter is studied to investigate the impact of correlated detector distortions which hardly influence the overall solution of the minimisation problem but introduce biases in the track parameters and thus the derived physics quantities. The determination and constraint of these weak modes present the future challenge of the alignment task at CMS. (orig.)

  16. Extended particle-based simulation for magnetic-aligned compaction of hard magnetic particles

    Energy Technology Data Exchange (ETDEWEB)

    Soda, Rikio; Takagi, Kenta; Ozaki, Kimihiro, E-mail: r-soda@aist.go.jp

    2015-12-15

    In order to understand the magnetic-aligned compaction process, we develop a three-dimensional (3D) discrete element method for simulating the motion of hard magnetic particles subjected to strong compression and magnetic fields. The proposed simulation model also considers the exact magnetic force involved via the calculation of the magnetic moment. First, to validate the simulation model, single-action compaction in the absence of a magnetic field was calculated. The calculated compaction curves are in good quantitative agreement with experimental ones. Based on this simulation model, the alignment behavior of Nd–Fe–B particles during compression under the application of a static magnetic field. The developed simulation model enables the visualization of particle behavior including the misorientation of the magnetization easy axis, which provided the quantitative relationships between applied pressure and particle misorientation. - Highlights: • A practical 3D DEM simulation technique for magnetic-aligned compaction was developed. • An extended simulation model was introduced for hard magnetic particles. • Magnetic-aligned compaction was simulated using the developed simulation model.

  17. Comparison of LHC collimator beam-based alignment to BPM-Interpolated centers

    CERN Document Server

    Valentino, G; Assmann, R W; Bruce, R; Muller, G J; Redaelli, S; Rossi, A; Lari, L

    2012-01-01

    The beam centers at the Large Hadron Collider collimators are determined by beam-based alignment, where both jaws of a collimator are moved in separately until a loss spike is detected on a Beam LossMonitor downstream. Orbit drifts of more than a few hundred micrometers cannot be tolerated, as they would compromise the performance of the collimation system. Beam Position Monitors (BPMs) are installed at various locations around the LHC ring, and a linear interpolation of the orbit can be obtained at the collimator positions. In this paper, the results obtained from beam-based alignment are compared with the orbit interpolated from the BPM data throughout the 2011 and 2012 LHC proton runs.

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

    Directory of Open Access Journals (Sweden)

    Guofeng Tong

    2014-04-01

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

  19. On the Feasibility of Precoding-Based Network Alignment for Three Unicast Sessions

    CERN Document Server

    Meng, Chun; Markopoulou, Athina; Jafar, Syed Ali

    2012-01-01

    We consider the problem of network coding across three unicast sessions over a directed acyclic graph, when each session has min-cut one. Previous work by Das et al. adapted a precoding-based interference alignment technique, originally developed for the wireless interference channel, specifically to this problem. We refer to this approach as precoding-based network alignment (PBNA). Similar to the wireless setting, PBNA asymptotically achieves half the minimum cut; different from the wireless setting, its feasibility depends on the graph structure. Das et al. provided a set of feasibility conditions for PBNA with respect to a particular precoding matrix. However, the set consisted of an infinite number of conditions, which is impossible to check in practice. Furthermore, the conditions were purely algebraic, without interpretation with regards to the graph structure. In this paper, we first prove that the set of conditions provided by Das. et al are also necessary for the feasibility of PBNA with respect to ...

  20. Shafting Alignment Calculation Based on APDL%基于APDL的轴系校中计算

    Institute of Scientific and Technical Information of China (English)

    张兴涛; 蒋岚岚

    2012-01-01

    本文介绍了轴系合理校中的必要性以及基于APDL的校中计算方法,并通过对比计算结果,说明该计算方法是完全适用的。%This paper introduces the necessity of shafting alignment and the calculation method based on APDL. By comparing the calculation results, it is proved that the method is completely applicable.

  1. Are institutional missions aligned with journal-based or document-based disciplinary structures?

    Energy Technology Data Exchange (ETDEWEB)

    Klavans, R.; Boyack, K.W.

    2016-07-01

    Missions represent the underlying purpose of an institution. These missions can be focused (finding a cure for cancer) or diverse (providing all health services to a local population). They might be aimed at basic research (finding new sub-atomic particles) or very applied (forecasting tomorrow’s weather). Missions can be extremely practical (building i-phones) or abstract (creating maps of scientific inquiry). Our primary focus is on those institutions that are also contributing to society’s knowledge about scientific and technical phenomena. The publications of these institutions are, to some degree, an implicit statement of their mission. Institutions focusing on a cure for cancer will publish articles associated with cancer, while hospitals will publish in a diverse set of medical specialties. Institutions focused on subatomic particles publish in specialized physics journals. While the publication profile of an institution is obviously not the same as an institution’s mission, it is typically consistent with its mission. In this study we analyze the publication profiles of over 4400 institutions using Scopus data to determine if their institutional missions are best explained using a journal-based classification system or a document-based classification system. The structure of this article is as follows. The background section places this work in the context of two streams of research – the accuracies of different document classification systems, and the effect of different national contexts (specifically wealth, health and democracy) on science systems and their impact. We then describe our data and methods before addressing two questions: Do the missions of certain types of institutions align with journal-based or article-based disciplines, and does this vary with national context (wealth, health and democracy). We conclude with a discussion of limitations and possible areas for further investigation. (Author)

  2. Alignment dynamics of slow light diffusion in ultracold atomic $^{85}$Rb

    CERN Document Server

    Balik, S; Sukenik, C I; Havey, M D; Datsyuk, V M; Sokolov, I M; Kupriyanov, D V

    2014-01-01

    A combined experimental and theoretical investigation of time- and alignment-dependent propagation of light in an ultracold atomic gas of atomic $^{85}$Rb is reported. Coherences among the scattering amplitudes for light scattering off excited hyperfine levels produce strong variations of the light polarization in the vicinity of atomic resonance. Measurements are in excellent agreement with Monte-Carlo simulations of the multiple scattering process.

  3. Value-based insurance design: aligning incentives and evidence in pulmonary medicine.

    Science.gov (United States)

    Fendrick, A Mark; Zank, Daniel C

    2013-11-01

    When consumers are required to pay the same out-of-pocket amount for pulmonary services for which clinical benefits depend on patient characteristics, clinical indication, and provider choice, there is an enormous potential for both underutilization and overutilization. Unlike most current one-size-fits-all health plan designs, value-based insurance design (V-BID) explicitly acknowledges clinical heterogeneity across the continuum of care. By adding clinical nuance to benefit design, V-BID seeks to align consumer and provider incentives with value, encouraging the use of high-value services and discouraging the use of low-value interventions. This article describes the concept of V-BID; creates a framework for its development in pulmonary medicine; and outlines how this concept aligns with research, care delivery, and payment reform initiatives.

  4. Beam-based alignment at the KEK-ATF damping ring

    Energy Technology Data Exchange (ETDEWEB)

    Woodley, Mark D.; Nelson, Janice; Ross, Marc; Turner, James; Wolski, A.; Kubo, Kiyoshi

    2004-06-30

    The damping rings of a future linear collider will have demanding alignment and stability requirements in order to achieve the low vertical emittance necessary for high luminosity. The Accelerator Test Facility (ATF) at KEK has successfully demonstrated the vertical emittance below 5 pm that is specified for the GLC/NLC Main Damping Rings. One contribution to this accomplishment has been the use of Beam Based Alignment (BBA) techniques. The mode of operation of the ATF presents particular challenges for BBA, and we describe here how we have deduced the offsets of the BPMs with respect to the quadrupoles. We also discuss a technique that allows for direct measurements of the beam-to-quad offsets.

  5. Weighted measures based on maximizing deviation for alignment-free sequence comparison

    Science.gov (United States)

    Qian, Kun; Luan, Yihui

    2017-09-01

    Alignment-free sequence comparison is becoming fairly popular in many fields of computational biology due to less requirements for sequence itself and computational efficiency for a large scale of sequence data sets. Especially, the approaches based on k-tuple like D2, D2S and D2∗ are used widely and effectively. However, these measures treat each k-tuple equally without accounting for the potential importance differences among all k-tuples. In this paper, we take advantage of maximizing deviation method proposed in multiple attribute decision making to evaluate the weights of different k-tuples. We modify D2, D2S and D2∗ with weights and test them by similarity search and evaluation on functionally related regulatory sequences. The results demonstrate that the newly proposed measures are more efficient and robust compared to existing alignment-free methods.

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

    Directory of Open Access Journals (Sweden)

    Chen-Sheng Chen

    2016-03-01

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

  7. Vibrating wire alignment technique

    CERN Document Server

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

    2013-01-01

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

  8. Field application of moment-based wavefront sensing to in-situ alignment and image quality assessment of astronomical spectrographs: results and analysis of aligning VIRUS unit spectrographs

    Science.gov (United States)

    Lee, Hanshin; Hill, Gary J.; Tuttle, Sarah E.; Noyola, Eva; Peterson, Trent; Vattiat, Brian L.

    2014-07-01

    Teague introduced a phase retrieval method that uses the image shape moments. More recently, an independent study arrived at a similar technique, which was then applied to in-situ full-field image-quality evaluation of spectroscopic systems. This moment-based wavefront sensing (MWFS) method relies on the geometric relation between the image shape moments and the geometric wavefront modal coefficients. The MWFS method allows a non-iterative determination of the modal coefficients from focus-modulated images at arbitrary spatial resolutions. The determination of image moments is a direct extension of routine centroid and image size calculation, making its implementation easy. Previous studies showed that the MWFS works well in capturing large low-order modes, and is quite suitable for in-situ alignment diagnostics. At the Astronomical Instrumentation conference in 2012, we presented initial results of the application of the moment-based wavefront sensing to a fiber-fed astronomical spectrograph, called VIRUS (a set of replicated 150 identical integral-field unit spectrographs contained in 75 unit pairs). This initial result shows that the MWFS can provide accurate full-field image-quality assessment for efficiently aligning these 150 spectrographs. Since then, we have assembled more than 24 unit pairs using this technique. In this paper, we detail the technical update/progress made so far for the moment-based wavefront sensing method and the statistical estimates of the before/after alignment aberrations, image-quality, and various efficiency indicators of the unit spectrograph alignment process.

  9. Functionally informed cortex based alignment: an integrated approach for whole-cortex macro-anatomical and ROI-based functional alignment.

    Science.gov (United States)

    Frost, Martin A; Goebel, Rainer

    2013-12-01

    Due to anatomical variability across subjects many brain mapping experiments have analysis focused on a few particular regions of interest so as to circumvent the problem of sub-optimal statistics resulting from the lack of anatomical correspondence across subjects. Since the topographic distribution of experimental effects across the cortex is also often of interest, two separate analyses are often conducted, one on the regions of interest alone, as well as a separate 'whole brain' analysis with sub-optimal spatial correspondence across brains. In this paper we present a new group alignment procedure which incorporates, from each subject, both macro-anatomical (curvature) information and functional information from standard localizer experiments. After specifying appropriate parameters to weight anatomical and functional alignment forces, we were able to create a group cortical reconstruction which was well aligned in terms of both anatomical and functional areas. We observed an increase in the overlap of functional areas as well as an improvement in group statistics following this integrated alignment procedure. We propose that, using this alignment scheme, two separate analyses may not be necessary as both analyses can be integrated into a single procedure. After an integrated structural and functional alignment one is able to carry out a whole brain analysis with improved statistical sensitivity due to the reduction in spatial variation in the location of functional regions of interest which fCBA accomplishes. Furthermore, regions in the vicinity of localised and aligned regions-of-interest will also benefit from the integrated alignment.

  10. 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 ...

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

    Institute of Scientific and Technical Information of China (English)

    Li Jiao; Jing Zhongliang; He Jiaona; Wang An

    2005-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-01-29

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

  13. CLIC main beam quadrupole active pre-alignment based on cam movers

    CERN Document Server

    Kemppinen, J; Leuxe, R; Mainaud Durand, H; Sandomierski, J; Sosin, M

    2012-01-01

    Compact Linear Collider (CLIC) is a study for a future 48 km long linear electron-positron collider in the multi TeV range. Its target luminosity can only be reached if the main beam quadrupoles (MB quads) are actively pre-aligned within 17 µm in sliding windows of 200 m with respect to a straight reference line. In addition to the positioning requirement, the pre-alignment system has to provide a rigid support for the nano-stabilization system to ensure that the first eigenfrequency is above 100 Hz. Re-adjustment based on cam movers was chosen for detailed studies to meet the stringent pre-alignment requirements. There are four different types of MB quads in CLIC. Their lengths and masses vary so that at least two types of cam movers have to be developed. The validation of the cams with less stringent space restrictions has proceeded to a test setup in 5 degrees of freedom (DOF). Prototypes of the more demanding, smaller cams have been manufactured and they are under tests in 1 DOF. This paper describes the...

  14. Improvement of the CMS Muon Reconstruction Performance due to Precise Track-based Alignment

    Science.gov (United States)

    Brown, Malachi

    2017-01-01

    The performance of the CMS muon system depends on a precise knowledge of the positions and orientations of all its elements. The muon tracks reconstructed in proton-proton collision data at the LHC are used to align the individual muon detectors with respect to the inner silicon tracker. The alignment procedure measures these positions and provides geometries of the muon system that must be validated to ensure the performance of the detectors. In this report we present a set of sophisticated validation tools, developed to test the accuracy of a given muon system geometry with data from collisions. The validation procedure uses events with pairs of muons from Z-boson decays and events with very high pT muons, in order to quantify the reconstruction performance of the muon system for a given geometry. Kinematic properties of muons reconstructed using information from the muon system are compared to the properties of muons built using information from the tracker. We demonstrate improvements of the muon reconstruction performance after track-based alignment procedures are performed with 2016 data.

  15. A scheme for multiple sequence alignment optimization--an improvement based on family representative mechanics features.

    Science.gov (United States)

    Liu, Xin; Zhao, Ya-Pu

    2009-12-21

    As a basic tool of modern biology, sequence alignment can provide us useful information in fold, function, and active site of protein. For many cases, the increased quality of sequence alignment means a better performance. The motivation of present work is to increase ability of the existing scoring scheme/algorithm by considering residue-residue correlations better. Based on a coarse-grained approach, the hydrophobic force between each pair of residues is written out from protein sequence. It results in the construction of an intramolecular hydrophobic force network that describes the whole residue-residue interactions of each protein molecule, and characterizes protein's biological properties in the hydrophobic aspect. A former work has suggested that such network can characterize the top weighted feature regarding hydrophobicity. Moreover, for each homologous protein of a family, the corresponding network shares some common and representative family characters that eventually govern the conservation of biological properties during protein evolution. In present work, we score such family representative characters of a protein by the deviation of its intramolecular hydrophobic force network from that of background. Such score can assist the existing scoring schemes/algorithms, and boost up the ability of multiple sequences alignment, e.g. achieving a prominent increase (approximately 50%) in searching the structurally alike residue segments at a low identity level. As the theoretical basis is different, the present scheme can assist most existing algorithms, and improve their efficiency remarkably.

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

    Directory of Open Access Journals (Sweden)

    Inês Soares

    2012-01-01

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

  17. 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...

  18. Thalamocortical dynamics of the McCollough effect: boundary-surface alignment through perceptual learning.

    Science.gov (United States)

    Grossberg, Stephen; Hwang, Seungwoo; Mingolla, Ennio

    2002-05-01

    This article further develops the FACADE neural model of 3-D vision and figure-ground perception to quantitatively explain properties of the McCollough effect (ME). The model proposes that many ME data result from visual system mechanisms whose primary function is to adaptively align, through learning, boundary and surface representations that are positionally shifted due to the process of binocular fusion. For example, binocular boundary representations are shifted by binocular fusion relative to monocular surface representations, yet the boundaries must become positionally aligned with the surfaces to control binocular surface capture and filling-in. The model also includes perceptual reset mechanisms that use habituative transmitters in opponent processing circuits. Thus the model shows how ME data may arise from a combination of mechanisms that have a clear functional role in biological vision. Simulation results with a single set of parameters quantitatively fit data from 13 experiments that probe the nature of achromatic/chromatic and monocular/binocular interactions during induction of the ME. The model proposes how perceptual learning, opponent processing, and habituation at both monocular and binocular surface representations are involved, including early thalamocortical sites. In particular, it explains the anomalous ME utilizing these multiple processing sites. Alternative models of the ME are also summarized and compared with the present model.

  19. 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.

  20. Multi-classification of cell deformation based on object alignment and run length statistic.

    Science.gov (United States)

    Li, Heng; Liu, Zhiwen; An, Xing; Shi, Yonggang

    2014-01-01

    Cellular morphology is widely applied in digital pathology and is essential for improving our understanding of the basic physiological processes of organisms. One of the main issues of application is to develop efficient methods for cell deformation measurement. We propose an innovative indirect approach to analyze dynamic cell morphology in image sequences. The proposed approach considers both the cellular shape change and cytoplasm variation, and takes each frame in the image sequence into account. The cell deformation is measured by the minimum energy function of object alignment, which is invariant to object pose. Then an indirect analysis strategy is employed to overcome the limitation of gradual deformation by run length statistic. We demonstrate the power of the proposed approach with one application: multi-classification of cell deformation. Experimental results show that the proposed method is sensitive to the morphology variation and performs better than standard shape representation methods.

  1. Correction of static axial alignment in children with knee varus or valgus deformities through guided growth: Does it also correct dynamic frontal plane moments during walking?

    Science.gov (United States)

    Böhm, Harald; Stief, Felix; Sander, Klaus; Hösl, Matthias; Döderlein, Leonhard

    2015-09-01

    Malaligned knees are predisposed to the development and progression of unicompartmental degenerations because of the excessive load placed on one side of the knee. Therefore, guided growth in skeletally immature patients is recommended. Indication for correction of varus/valgus deformities are based on static weight bearing radiographs. However, the dynamic knee abduction moment during walking showed only a weak correlation to malalignment determined by static radiographs. Therefore, the aim of the study was to measure the effects of guided growth on the normalization of frontal plane knee joint moments during walking. 15 legs of 8 patients (11-15 years) with idiopathic axial varus or valgus malalignment were analyzed. 16 typically developed peers served as controls. Instrumented gait analysis and clinical assessment were performed the day before implantation and explantation of eight-plates. Correlation between static mechanical tibiofemoral axis angle (MAA) and dynamic frontal plane knee joint moments and their change by guided growth were performed. The changes in dynamic knee moment in the frontal plane following guided growth showed high and significant correlation to the changes in static MAA (R=0.97, pknee moment before treatment showed a more pathological one after treatment. In conclusion, the changes in the dynamic load situation during walking can be predicted from the changes in static alignment. If pre-surgical gait analysis reveals a natural load situation, despite a static varus or valgus deformity, the intervention must be critically discussed.

  2. Experimental study of new laser-based alignment system at the KEK B-factory injector linear accelerator

    Energy Technology Data Exchange (ETDEWEB)

    Suwada, T.; Satoh, M.; Kadokura, E. [Accelerator Laboratory, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan)

    2010-12-15

    A new laser-based alignment system for the precise alignment of accelerator components along an ideal straight line at the KEK B-factory injector linear accelerator (linac) is under development. This system is strongly required in the next generation of B-factories for the stable acceleration of high-brightness electron and positron beams with high bunch charges and also for maintaining the stability of injection beams with high quality. A new laser optics for the generation of a so-called Airy beam has been developed for the laser-based alignment system. The laser propagation characteristics both in vacuum and at atmospheric pressure have been systematically investigated in an 82-m-long straight section of the injector linac. The laser-based alignment measurements based on the new laser optics have been carried out with a measurement resolution of {+-}0.1 mm level by using an existing laser detection electronics. The horizontal and vertical displacements from a reference laser line measured using this system are in good agreement with those measured using a standard telescope-based optical alignment technique. In this report, we describe the experimental study in detail along with the basic designs and the recent developments in the new laser-based alignment system.

  3. A dynamic knowledge base based search engine

    Institute of Scientific and Technical Information of China (English)

    WANG Hui-jin; HU Hua; LI Qing

    2005-01-01

    Search engines have greatly helped us to find thedesired information from the Intemet. Most search engines use keywords matching technique. This paper discusses a Dynamic Knowledge Base based Search Engine (DKBSE), which can expand the user's query using the keywords' concept or meaning. To do this, the DKBSE needs to construct and maintain the knowledge base dynamically via the system's searching results and the user's feedback information. The DKBSE expands the user's initial query using the knowledge base, and returns the searched information after the expanded query.

  4. 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.

  5. 考虑动态挠曲变形时的传递对准方法研究%Study on Transfer Alignment with Dynamic Flexure Deformation

    Institute of Scientific and Technical Information of China (English)

    董亮; 陈帅

    2015-01-01

    针对传递对准过程中存在的动态挠曲变形的问题,本文提出了一种“量测失准角+速度”匹配的快速传递对准方法。通过将动态挠曲变形模型的相关变量引入到传递对准状态方程中,从而降低动态挠曲变形对传递对准精度的影响。仿真结果表明,该方法有效降低了动态挠曲变形对传递对准精度的影响,满足传递对准的高精度和快速性要求。%In view of the problem that dynamic flexure deformation exists in the process of transfer a-lignment, a new “measurement misalignment angle +velocity” matching method is proposed in this pa-per .By adding the related variables of dynamic flexure deformation model to the transfer alignment equa -tion of state , the influence of dynamic flexure deformation on the transfer alignment accuracy can be re-duced.The simulation results show that the proposed method effectively reduces the influence of dynamic flexure deformation on the transfer alignment accuracy , and can meet the requirements of accuracy and fastness on the transfer alignment .

  6. 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...

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

    Science.gov (United States)

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

    2015-08-01

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

  8. Reliability of lower limb alignment measures using an established landmark-based method with a customized computer software program.

    Science.gov (United States)

    Sled, Elizabeth A; Sheehy, Lisa M; Felson, David T; Costigan, Patrick A; Lam, Miu; Cooke, T Derek V

    2011-01-01

    The objective of the study was to evaluate the reliability of frontal plane lower limb alignment measures using a landmark-based method by (1) comparing inter- and intra-reader reliability between measurements of alignment obtained manually with those using a computer program, and (2) determining inter- and intra-reader reliability of computer-assisted alignment measures from full-limb radiographs. An established method for measuring alignment was used, involving selection of 10 femoral and tibial bone landmarks. (1) To compare manual and computer methods, we used digital images and matching paper copies of five alignment patterns simulating healthy and malaligned limbs drawn using AutoCAD. Seven readers were trained in each system. Paper copies were measured manually and repeat measurements were performed daily for 3 days, followed by a similar routine with the digital images using the computer. (2) To examine the reliability of computer-assisted measures from full-limb radiographs, 100 images (200 limbs) were selected as a random sample from 1,500 full-limb digital radiographs which were part of the Multicenter Osteoarthritis Study. Three trained readers used the software program to measure alignment twice from the batch of 100 images, with two or more weeks between batch handling. Manual and computer measures of alignment showed excellent agreement (intraclass correlations [ICCs] 0.977-0.999 for computer analysis; 0.820-0.995 for manual measures). The computer program applied to full-limb radiographs produced alignment measurements with high inter- and intra-reader reliability (ICCs 0.839-0.998). In conclusion, alignment measures using a bone landmark-based approach and a computer program were highly reliable between multiple readers.

  9. A novel twisted nematic alignment and its effects on the electro-optical dynamics of nanoscale liquid crystalline films

    Science.gov (United States)

    Rauzan, Brittany; Lee, Lay Min; Nuzzo, Ralph

    2015-03-01

    Vibrational spectroscopic studies of a surface induced, twisted alignment of the nematic liquid crystal, 4-n-pentyl-4'-cyanobiphenyl (5CB) and its temperature-dependent electro-optical (EO) dynamics were studied near the crystalline-nematic and nematic-isotropic transition temperatures, and at a median temperature in the nematic phase. A 50 nm thick film of 5CB was confined in nanocavities defined by the dimensions of a gold interdigitated electrode array patterned on a unidirectionally polished ZnSe substrate. The film was assembled between two polished substrates bearing extended nanometer-scaled grooves that are oriented orthogonally to one another. The results show that with this anchoring scheme, the molecular director of the LC film undergoes a ninety-degree twist. Step-scan time resolved spectroscopy (TRS) measurements were made to determine the rate constants for the temperature-dependent EO dynamics of both the electric field-induced orientation and thermal relaxation processes of the LC film. The work rationalizes the impacts of organizational anisotropy and illustrates how it can be exploited as a design principle to effectively influence the electric field-induced dynamics of LC systems.

  10. Rotation-invariant texture retrieval via signature alignment based on steerable sub-Gaussian modeling.

    Science.gov (United States)

    Tzagkarakis, George; Beferull-Lozano, Baltasar; Tsakalides, Panagiotis

    2008-07-01

    This paper addresses the construction of a novel efficient rotation-invariant texture retrieval method that is based on the alignment in angle of signatures obtained via a steerable sub-Gaussian model. In our proposed scheme, we first construct a steerable multivariate sub-Gaussian model, where the fractional lower-order moments of a given image are associated with those of its rotated versions. The feature extraction step consists of estimating the so-called covariations between the orientation subbands of the corresponding steerable pyramid at the same or at adjacent decomposition levels and building an appropriate signature that can be rotated directly without the need of rotating the image and recalculating the signature. The similarity measurement between two images is performed using a matrix-based norm that includes a signature alignment in angle between the images being compared, achieving in this way the desired rotation-invariance property. Our experimental results show how this retrieval scheme achieves a lower average retrieval error, as compared to previously proposed methods having a similar computational complexity, while at the same time being competitive with the best currently known state-of-the-art retrieval system. In conclusion, our retrieval method provides the best compromise between complexity and average retrieval performance.

  11. Image-based overlay (IBO) target segment design on self-aligned patterning process

    Science.gov (United States)

    Ye, Lei; Hu, Huayong; He, Weiming

    2016-03-01

    Self-Aligned Double Patterning (SADP) is widely applied in advanced sub-4X patterning technology, especially for the 1D resolution shrinkage of memory technology. As the application of SADP makes lithography minimum pitch down to half of design pitch with the remaining spacer aside core, its alignment mark and overlay (OVL) mark have to be well-segmented to ensure enough mark contrast. In this paper, we designed two types of image-based overlay (IBO) bar in bar (BIB) OVL target: bar-segmentation and background-segmentation with different duty ratio. Based on these two designed types of marks, we focus on the OVL of 2nd photo layer to 1st SADP layer with the core removed (which means spacer grating structure remained). We studied the effect of the overlay target segmentation on the precision and robustness of wafer-level overlay performance. Different lithography processes were also studied, including single layer lithography and tri-layer lithography with planarized spacer grating structures. We found there are strong correlations between overlay measurement accuracy and background segmentation rules. The results of our study will be presented and discussed in this paper.

  12. A Dirichlet Process Mixture Based Name Origin Clustering and Alignment Model for Transliteration

    Directory of Open Access Journals (Sweden)

    Chunyue Zhang

    2015-01-01

    Full Text Available In machine transliteration, it is common that the transliterated names in the target language come from multiple language origins. A conventional maximum likelihood based single model can not deal with this issue very well and often suffers from overfitting. In this paper, we exploit a coupled Dirichlet process mixture model (cDPMM to address overfitting and names multiorigin cluster issues simultaneously in the transliteration sequence alignment step over the name pairs. After the alignment step, the cDPMM clusters name pairs into many groups according to their origin information automatically. In the decoding step, in order to use the learned origin information sufficiently, we use a cluster combination method (CCM to build clustering-specific transliteration models by combining small clusters into large ones based on the perplexities of name language and transliteration model, which makes sure each origin cluster has enough data for training a transliteration model. On the three different Western-Chinese multiorigin names corpora, the cDPMM outperforms two state-of-the-art baseline models in terms of both the top-1 accuracy and mean F-score, and furthermore the CCM significantly improves the cDPMM.

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

    Science.gov (United States)

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

    2015-07-08

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

  14. CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform.

    Science.gov (United States)

    Liu, Yongchao; Schmidt, Bertil; Maskell, Douglas L

    2012-07-15

    New high-throughput sequencing technologies have promoted the production of short reads with dramatically low unit cost. The explosive growth of short read datasets poses a challenge to the mapping of short reads to reference genomes, such as the human genome, in terms of alignment quality and execution speed. We present CUSHAW, a parallelized short read aligner based on the compute unified device architecture (CUDA) parallel programming model. We exploit CUDA-compatible graphics hardware as accelerators to achieve fast speed. Our algorithm uses a quality-aware bounded search approach based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini index to reduce the search space and achieve high alignment quality. Performance evaluation, using simulated as well as real short read datasets, reveals that our algorithm running on one or two graphics processing units achieves significant speedups in terms of execution time, while yielding comparable or even better alignment quality for paired-end alignments compared with three popular BWT-based aligners: Bowtie, BWA and SOAP2. CUSHAW also delivers competitive performance in terms of single-nucleotide polymorphism calling for an Escherichia coli test dataset. http://cushaw.sourceforge.net

  15. Dynamic analysis of double-row self-aligning ball bearings due to applied loads, internal clearance, surface waviness and number of balls

    Science.gov (United States)

    Zhuo, Yaobin; Zhou, Xiaojun; Yang, Chenlong

    2014-11-01

    In this paper, a three degrees of freedom (dof) model was established for a double-row self-aligning ball bearing (SABB) system, and was applied to study the dynamic behavior of the system during starting process and constant speed rotating process. A mathematical model was developed concerning stiffness and damping characteristics of the bearing, as well as three-dimensional applied load, rotor centrifugal force, etc. Balls and races were all considered as nonlinear springs, and the contact force between ball and race was calculated based on classic Hertzian elastic contact deformation theory and deformation compatibility theory. The changes of each ball's contact force and loaded angle of each row were taken into account. In order to solve the nonlinear dynamical equilibrium equations of the system, these equations were rewritten as differential equations and the fourth order Runge-Kutta method was used to solve the equations iteratively. In order to verify accuracy of the dynamical model and correctness of the numerical solution method, a kind of SABB-BRF30 was chosen for case studies. The effects of several important governing parameters, such as radial and axial applied loads, normal internal, inner and outer races waviness, and number of balls were investigated. These parametric studies led to a complete characterization of the shaft-bearing system vibration transmission. The research provided a theoretical reference for new type bearing design, shaft-bearing system kinetic analysis, optimal design, etc.

  16. Dynamic states of swimming bacteria in a nematic liquid crystal cell with homeotropic alignment

    Science.gov (United States)

    Zhou, Shuang; Tovkach, Oleh; Golovaty, Dmitry; Sokolov, Andrey; Aranson, Igor S.; Lavrentovich, Oleg D.

    2017-05-01

    Flagellated bacteria such as Escherichia coli and Bacillus subtilis exhibit effective mechanisms for swimming in fluids and exploring the surrounding environment. In isotropic fluids such as water, the bacteria change swimming direction through the run-and-tumble process. Lyotropic chromonic liquid crystals (LCLCs) have been introduced recently as an anisotropic environment in which the direction of preferred orientation, the director, guides the bacterial trajectories. In this work, we describe the behavior of bacteria B. subtilis in a homeotropic LCLC geometry, in which the director is perpendicular to the bounding plates of a shallow cell. We demonstrate that the bacteria are capable of overcoming the stabilizing elastic forces of the LCLC and swim perpendicularly to the imposed director (and parallel to the bounding plates). The effect is explained by a finite surface anchoring of the director at the bacterial body; the role of surface anchoring is analyzed by numerical simulations of a rod realigning in an otherwise uniform director field. Shear flows produced by a swimming bacterium cause director distortions around its body, as evidenced both by experiments and numerical simulations. These distortions contribute to a repulsive force that keeps the swimming bacterium at a distance of a few micrometers away from the bounding plates. The homeotropic alignment of the director imposes two different scenarios of bacterial tumbling: one with an 180° reversal of the horizontal velocity and the other with the realignment of the bacterium by two consecutive 90° turns. In the second case, the angle between the bacterial body and the imposed director changes from 90° to 0° and then back to 90° the new direction of swimming does not correlate with the previous swimming direction.

  17. 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, ...

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

    Science.gov (United States)

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

    2008-01-01

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

  19. 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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2004-09-30

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

  1. Accurate alignment of functional EPI data to anatomical MRI using a physics-based distortion model.

    Science.gov (United States)

    Studholme, C; Constable, R T; Duncan, J S

    2000-11-01

    Mapping of functional magnetic resonance imaging (fMRI) to conventional anatomical MRI is a valuable step in the interpretation of fMRI activations. One of the main limits on the accuracy of this alignment arises from differences in the geometric distortion induced by magnetic field inhomogeneity. This paper describes an approach to the registration of echo planar image (EPI) data to conventional anatomical images which takes into account this difference in geometric distortion. We make use of an additional spin echo EPI image and use the known signal conservation in spin echo distortion to derive a specialized multimodality nonrigid registration algorithm. We also examine a plausible modification using log-intensity evaluation of the criterion to provide increased sensitivity in areas of low EPI signal. A phantom-based imaging experiment is used to evaluate the behavior of the different criteria, comparing nonrigid displacement estimates to those provided by a imagnetic field mapping acquisition. The algorithm is then applied to a range of nine brain imaging studies illustrating global and local improvement in the anatomical alignment and localization of fMRI activations.

  2. Aligned carbon nanotube based ultrasonic microtransducers for durability monitoring in civil engineering

    Energy Technology Data Exchange (ETDEWEB)

    Lebental, B [Universite Paris-Est, IFSTTAR, 58 boulevard Lefebvre, 75732 Paris Cedex 15 (France); Chainais, P [INRIA Lille-Nord Europe (SEQUEL), 40 avenue Halley, 59650 Villeneuve d' Ascq (France); Chenevier, P [SPEC, IRAMIS, CEA/Saclay, Gif-sur-Yvette (France); Chevalier, N; Delevoye, E; Fabbri, J-M; Nicoletti, S; Renaux, P; Ghis, A, E-mail: berengere.lebental@ifsttar.fr [CEA, LETI, MINATEC Campus, F-38054 Grenoble (France)

    2011-09-30

    Structural health monitoring of porous materials such as concrete is becoming a major component in our resource-limited economy, as it conditions durable exploitation of existing facilities. Durability in porous materials depends on nanoscale features which need to be monitored in situ with nanometric resolution. To address this problem, we put forward an approach based on the development of a new nanosensor, namely a capacitive micrometric ultrasonic transducer whose vibrating membrane is made of aligned single-walled carbon nanotubes (SWNT). Such sensors are meant to be embedded in large numbers within a porous material in order to provide information on its durability by monitoring in situ neighboring individual micropores. In the present paper, we report on the feasibility of the key building block of the proposed sensor: we have fabricated well-aligned, ultra-thin, dense SWNT membranes that show above-nanometer amplitudes of vibration over a large range of frequencies spanning from 100 kHz to 5 MHz.

  3. Aligned carbon nanotube based ultrasonic microtransducers for durability monitoring in civil engineering.

    Science.gov (United States)

    Lebental, B; Chainais, P; Chenevier, P; Chevalier, N; Delevoye, E; Fabbri, J-M; Nicoletti, S; Renaux, P; Ghis, A

    2011-09-30

    Structural health monitoring of porous materials such as concrete is becoming a major component in our resource-limited economy, as it conditions durable exploitation of existing facilities. Durability in porous materials depends on nanoscale features which need to be monitored in situ with nanometric resolution. To address this problem, we put forward an approach based on the development of a new nanosensor, namely a capacitive micrometric ultrasonic transducer whose vibrating membrane is made of aligned single-walled carbon nanotubes (SWNT). Such sensors are meant to be embedded in large numbers within a porous material in order to provide information on its durability by monitoring in situ neighboring individual micropores. In the present paper, we report on the feasibility of the key building block of the proposed sensor: we have fabricated well-aligned, ultra-thin, dense SWNT membranes that show above-nanometer amplitudes of vibration over a large range of frequencies spanning from 100 kHz to 5 MHz.

  4. Radiological Outcomes and Operative Time following Total Knee Arthroplasty using Accelerometer-based, Portable Navigation versus Conventional Inter-Medullary Alignment Guides

    Science.gov (United States)

    MacDessi, Samuel; Solayar, GN; Thatcher, N; Chen, Darren B

    2016-01-01

    Objectives: Accelerometer-based, portable navigation instrumentation is a new method of achieving desired resection alignments in total knee arthroplasty (TKA). Methods: After randomisation and the application of exclusion criteria, 79 knees were analysed. 42 patients which underwent TKA using conventional intra-medullary (IM) alignment guides were compared to 37 patients with the use of accelerometer-based, portable navigation device (KneeAlign; OrthoAlign Inc, Aliso Viejo, California). Radiographic results were obtained from post-operative computer-tomography following the CT Perth Protocol. Results: In the IM cohort, 81.0% of patients had a coronal alignment within 3° of a neutral mechanical axis (vs 83.8% with KneeAlign, p=0.74), 81.0% had a femoral coronal alignment within 2° of perpendicular to the femoral mechanical axis (vs 89.2% with KneeAlign, p=0.31), and 92.9% had a tibial coronal alignment within 2° of perpendicular to the tibial mechanical axis (vs 81.1% with KneeAlign, p=0.12). Regarding sagittal alignment, the IM cohort had 90.5% of patients with femoral component alignment within 2° of optimum (vs 91.9% with KneeAlign, p=0.83) and 92.9% had a tibial component alignment within 2° of the optimal tibial slope (vs 89.2% with KneeAlign, p=0.57). The mean tourniquet time (from incision to completion of coronal bone resections) in the IM cohort was 16.5± 8.9 minutes vs 22.2 ± 7.6 minutes in the KneeAlign cohort (p<0.003). Conclusion: Accelerometer-based, portable navigation has a statistically similar outcome in alignment following TKA as IM guides. It is noted that using the portable navigation device does prolong surgical time compared to conventional IM surgery and this may be due to the learning curve.

  5. Innovation, improvement and operations: an exploration of the management of alignment

    NARCIS (Netherlands)

    de Leede, Jan; Looise, Jan C.; Alders, B.C.M.; Alders, Ben C.M.

    2002-01-01

    Based on the assumption that the three functions of operations, improvement and innovation within companies need to be aligned to improve company performance, this article addresses two internal alignment mechanisms structural and social-dynamic alignment. A survey of 267 companies confirms that suc

  6. Innovation, improvement and operations: an exploration of the management of alignment

    NARCIS (Netherlands)

    de Leede, Jan; Looise, Jan C.; Alders, B.C.M.; Alders, Ben C.M.

    2002-01-01

    Based on the assumption that the three functions of operations, improvement and innovation within companies need to be aligned to improve company performance, this article addresses two internal alignment mechanisms structural and social-dynamic alignment. A survey of 267 companies confirms that

  7. Quantitative conformational analysis of the core region of N-glycans using residual dipolar couplings, aqueous molecular dynamics, and steric alignment

    Energy Technology Data Exchange (ETDEWEB)

    Almond, Andrew; Duus, Jens O. [Carlsberg Laboratory (Denmark)

    2001-08-15

    A method is described for quantitatively investigating the dynamic conformation of small oligosaccharides containing an {alpha}(1{sup {yields}}6) linkage. It was applied to the oligosaccharide Man-{alpha}(1{sup {yields}}3) {l_brace}Man-{alpha} (1{sup {yields}}6){r_brace}Man-{alpha}-O-Me, which is a core region frequently observed in N-linked glycans. The approach tests an aqueous molecular dynamics simulation, capable of predicting microscopic dynamics, against experimental residual dipolar couplings, by assuming that alignment is caused purely by steric hindrance. The experimental constraints were heteronuclear and homonuclear residual dipolar couplings, and in particular those within the {alpha}(1{sup {yields}}6) linkage itself. Powerful spin-state-selective pulse sequences and editing schemes were used to obtain the most relevant couplings for testing the model. Molecular dynamics simulations in water over a period of 50 ns were not able to predict the correct rotamer population at the {alpha}(1{sup {yields}}6) linkage to agree with the experimental data. However, this sampling problem could be corrected using a simple maximum likelihood optimisation, indicating that the simulation was modelling local dynamics correctly. The maximum likelihood prediction of the residual dipolar couplings was found to be an almost equal population of the gg and gt rotamer conformations at the {alpha}(1{sup {yields}}6) linkage, and the tg conformation was predicted to be unstable and unpopulated in aqueous solution. In this case all twelve measured residual dipolar couplings could be satisfied. This conformer population could also be used to make predictions of scalar couplings with the use of a previously derived empirical equation, and is qualitatively in agreement with previous predictions based on NMR, X-ray crystallography and optical data.

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

    DEFF Research Database (Denmark)

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

    2007-01-01

    not be present and pre-folding ignores the comparative information. Here, pruning of the dynamical programming matrix is presented as an alternative novel heuristic constraint. All subalignments that do not exceed a length-dependent minimum score are discarded as the matrix is filled out, thus giving...... and backtracked in a normal fashion. Finally, the FOLDALIGN algorithm has also been updated with a better memory implementation and an improved energy model. With these improvements in the algorithm, the FOLDALIGN software package provides the molecular biologist with an efficient and user-friendly tool...

  9. A note on the dynamics of two aligned bubbles perpendicular to and above a thin membrane

    Energy Technology Data Exchange (ETDEWEB)

    Aghdam, A Hajizadeh [Department of Mechanical Engineering, Arak University of Technology, Arak 3818141167 (Iran, Islamic Republic of); Khoo, B C, E-mail: Hajizadeh@arakut.ac.ir [Department of Mechanical Engineering, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260 (Singapore)

    2015-06-15

    The interaction of two perpendicular bubbles of a similar size (upper bubble and lower bubble) and the thin elastic membrane beneath them is studied experimentally. The dynamical behavior of the lower bubble (Bubble1), which is placed between the membrane and upper bubble (Bubble2), is rather complex. Observed phenomena such as the splitting of Bubble1 into the ‘mushroom shape’ and ‘masher shape’, the bubble-collapse induced jetting toward Bubble2 and even the coalescence effect are found and systematically categorized by the stated dimensionless parameters. (paper)

  10. Spindle alignment regulates the dynamic association of checkpoint proteins with yeast spindle pole bodies.

    Science.gov (United States)

    Caydasi, Ayse Koca; Pereira, Gislene

    2009-01-01

    In many polarized cells, the accuracy of chromosome segregation depends on the correct positioning of the mitotic spindle. In budding yeast, the spindle positioning checkpoint (SPOC) delays mitotic exit when the anaphase spindle fails to extend toward the mother-daughter axis. However it remains to be established how spindle orientation is translated to SPOC components at the yeast spindle pole bodies (SPB). Here, we used photobleaching techniques to show that the dynamics with which Bub2-Bfa1 turned over at SPBs significantly increased upon SPOC activation. A version of Bfa1 that was stably associated with SPBs rendered the cells SPOC deficient without affecting other Bub2-Bfa1 functions, demonstrating the functional importance of regulating the dynamics of Bfa1 SPB association. In addition, we established that the SPOC kinase Kin4 is the major regulator of Bfa1 residence time at SPBs. We suggest that upon SPOC activation Bfa1-Bub2 spreads throughout the cytoplasm, thereby inhibiting mitotic exit.

  11. Dynamic mechanical analysis and high strain-rate energy absorption characteristics of vertically aligned carbon nanotube reinforced woven fiber-glass composites

    Science.gov (United States)

    The dynamic mechanical behavior and energy absorption characteristics of nano-enhanced functionally graded composites, consisting of 3 layers of vertically aligned carbon nanotube (VACNT) forests grown on woven fiber-glass (FG) layer and embedded within 10 layers of woven FG, with polyester (PE) and...

  12. 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.

  13. Highly uniform hole spacing micro brushes based on aligned carbon nanotube arrays

    Science.gov (United States)

    Yang, Zhi; Zhu, Xingzhong; Huang, Xiaolu; Cheng, Yingwu; Liu, Yun; Geng, Huijuan; Wu, Yue; Su, Yanjie; Wei, Hao; Zhang, Yafei

    2013-11-01

    Highly uniform hole spacing micro brushes were fabricated based on aligned carbon nanotube (CNT) arrays synthesized by chemical vapor deposition method with the assistance of anodic aluminum oxide (AAO) template. Different micro brushes from CNT arrays were constructed on silicon, glass, and polyimide substrates, respectively. The micro brushes had highly uniform hole spacing originating from the regularly periodic pore structure of AAO template. The CNT arrays, serving as bristles, were firmly grafted on the substrates. The brushes can easily clean particles with scale of micrometer on the surface of silicon wafer and from the narrow spaces between the electrodes in a series of cleaning experiments. The results show the potential application of the CNT micro brushes as a cleaning tool in microelectronics manufacture field.

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

    Science.gov (United States)

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

    2014-02-01

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

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

    Science.gov (United States)

    Taylor, Jaime; Rakoczy, John; Steincamp, James

    2003-01-01

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

  16. Alternate transmission relaying based on interference alignment in 3-relay half-duplex MIMO systems

    KAUST Repository

    Park, Seongho

    2012-09-01

    In a half-duplex relaying, the capacity pre-log factor 1/2 is a major drawback in spectral efficiency. This paper proposes a linear precoding/decoding scheme and an alternate relaying protocol in a dual-hop half-duplex system where three relays help the communication between the source and the destination. In our proposed scheme, we consider a phase incoherent method in relays in which the source alternately transmits message signals to the different relays. In addition, we propose a linear interference alignment scheme which can suppress the inter-relay interference resulting from the phase incoherence of relaying. Based on our analysis of degrees of freedom and our simulation results, we show that our proposed scheme achieves additional degrees of freedom compared to the conventional half-duplex relaying. © 2012 IEEE.

  17. GaAs-based self-aligned stripe superluminescent diodes processed normal to the cleaved facet

    Science.gov (United States)

    Ghazal, O. M. S.; Lei, D.; Childs, D. T.; Stevens, B. J.; Babazadeh, N.; Hogg, R. A.; Groom, K. M.

    2016-03-01

    We demonstrate GaAs-based superluminescent diodes (SLDs) incorporating a window-like back facet in a self-aligned stripe. SLDs are realised with low spectral modulation depth (SMD) at high power spectral density, without application of anti-reflection coatings. Such application of a window-like facet reduces effective facet reflectivity in a broadband manner. We demonstrate 30mW output power in a narrow bandwidth with only 5% SMD, outline the design criteria for high power and low SMD, and describe the deviation from a linear dependence of SMD on output power as a result of Joule heating in SLDs under continuous wave current injection. Furthermore, SLDs processed normal to the facet demonstrate output powers as high as 20mW, offering improvements in beam quality, ease of packaging and use of real estate.

  18. Bright single photon source based on self-aligned quantum dot–cavity systems

    DEFF Research Database (Denmark)

    Maier, Sebastian; Gold, Peter; Forchel, Alfred

    2014-01-01

    We report on a quasi-planar quantum-dot-based single-photon source that shows an unprecedented high extraction efficiency of 42% without complex photonic resonator geometries or post-growth nanofabrication. This very high efficiency originates from the coupling of the photons emitted by a quantum...... avenue for efficient (up to 42% demonstrated) and pure (g2(0) value of 0.023) single-photon emission....... dot to a Gaussian shaped nanohill defect that naturally arises during epitaxial growth in a self-aligned manner. We investigate the morphology of these defects and characterize the photonic operation mechanism. Our results show that these naturally arising coupled quantum dot-defects provide a new...

  19. Evaluation of an image-based tracking workflow with Kalman filtering for automatic image plane alignment in interventional MRI.

    Science.gov (United States)

    Neumann, M; Cuvillon, L; Breton, E; de Matheli, M

    2013-01-01

    Recently, a workflow for magnetic resonance (MR) image plane alignment based on tracking in real-time MR images was introduced. The workflow is based on a tracking device composed of 2 resonant micro-coils and a passive marker, and allows for tracking of the passive marker in clinical real-time images and automatic (re-)initialization using the microcoils. As the Kalman filter has proven its benefit as an estimator and predictor, it is well suited for use in tracking applications. In this paper, a Kalman filter is integrated in the previously developed workflow in order to predict position and orientation of the tracking device. Measurement noise covariances of the Kalman filter are dynamically changed in order to take into account that, according to the image plane orientation, only a subset of the 3D pose components is available. The improved tracking performance of the Kalman extended workflow could be quantified in simulation results. Also, a first experiment in the MRI scanner was performed but without quantitative results yet.

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

    Directory of Open Access Journals (Sweden)

    Yun Li

    2016-12-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  2. High performance flexible pH sensor based on carboxyl-functionalized and DEP aligned SWNTs

    Science.gov (United States)

    Liu, Lu; Shao, Jinyou; Li, Xiangming; Zhao, Qiang; Nie, Bangbang; Xu, Chuan; Ding, Haitao

    2016-11-01

    The detection and control of the pH is very important in many biomedical and chemical reaction processes. A miniaturized flexible pH sensor that is light weight, robust, and conformable is very important in many applications, such as multifunctional lab-on-a-chip systems or wearable biomedical devices. In this work, we demonstrate a flexible chemiresistive pH sensor based on dielectrophoresis (DEP) aligned carboxyl-functionalized single-walled carbon nanotubes (SWNTs). Decorated carboxyl groups can react with hydrogen (H+) and hydroxide (OH-) ions, enabling the sensor to be capable of sensing the pH. DEP is used to deposit well-organized and highly aligned SWNTs in desired locations, which improves the metal-nanotube interface and highly rapid detection of the pH, resulting in better overall device performance. When pH buffer solutions are dropped onto such SWNTs, the H+ and OH- ions caninteract with the carboxyl groups and affect the generation of holes and electrons in the SWNTs, leading to resistance variations in the SWNTs. The results shows that the relative resistance variations of the sensor increases linearly with increasing the pH values in the range from 5 to 9 and the response time ranges from 0.2 s to 22.6 s. The pH sensor also shows high performance in mechanical bendability, which benefited from the combination of flexible PET substrates and SWNTs. The SWNT-based flexible pH sensor demonstrates great potential in a wide range of areas due to its simple structure, excellent performance, low power consumption, and compatibility with integrated circuits.

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

    Science.gov (United States)

    Nair, Pradeep S; John, Eugene B

    2007-01-01

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

  4. A simple method to control over-alignment in the MAFFT multiple sequence alignment program.

    Science.gov (United States)

    Katoh, Kazutaka; Standley, Daron M

    2016-07-01

    We present a new feature of the MAFFT multiple alignment program for suppressing over-alignment (aligning unrelated segments). Conventional MAFFT is highly sensitive in aligning conserved regions in remote homologs, but the risk of over-alignment is recently becoming greater, as low-quality or noisy sequences are increasing in protein sequence databases, due, for example, to sequencing errors and difficulty in gene prediction. The proposed method utilizes a variable scoring matrix for different pairs of sequences (or groups) in a single multiple sequence alignment, based on the global similarity of each pair. This method significantly increases the correctly gapped sites in real examples and in simulations under various conditions. Regarding sensitivity, the effect of the proposed method is slightly negative in real protein-based benchmarks, and mostly neutral in simulation-based benchmarks. This approach is based on natural biological reasoning and should be compatible with many methods based on dynamic programming for multiple sequence alignment. The new feature is available in MAFFT versions 7.263 and higher. http://mafft.cbrc.jp/alignment/software/ katoh@ifrec.osaka-u.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  5. 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.

  6. Ontology alignment with OLA

    OpenAIRE

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

    2004-01-01

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

  7. Photoresponsive carbohydrate-based giant surfactants: automatic vertical alignment of nematic liquid crystal for the remote-controllable optical device.

    Science.gov (United States)

    Kim, Dae-Yoon; Lee, Sang-A; Kang, Dong-Gue; Park, Minwook; Choi, Yu-Jin; Jeong, Kwang-Un

    2015-03-25

    Photoresponsive carbohydrate-based giant surfactants (abbreviated as CELAnD-OH) were specifically designed and synthesized for the automatic vertical alignment (VA) layer of nematic (N) liquid crystal (LC), which can be applied for the fabrication of remote-controllable optical devices. Without the conventional polymer-based LC alignment process, a perfect VA layer was automatically constructed by directly adding the 0.1 wt % CELA1D-OH in the N-LC media. The programmed CELA1D-OH giant surfactants in the N-LC media gradually diffused onto the substrates of LC cell and self-assembled to the expanded monolayer structure, which can provide enough empty spaces for N-LC molecules to crawl into the empty zones for the construction of VA layer. On the other hand, the CELA3D-OH giant surfactants forming the condensed monolayer structure on the substrates exhibited a planar alignment (PA) rather than a VA. Upon tuning the wavelength of light, the N-LC alignments were reversibly switched between VA and PA in the remote-controllable LC optical devices. Based on the experimental results, it was realized that understanding the interactions between N-LC molecules and amphiphilic giant surfactants is critical to design the suitable materials for the automatic LC alignment.

  8. Consensus-Based Course Design and Implementation of Constructive Alignment Theory in a Power System Analysis Course

    Science.gov (United States)

    Vanfretti, Luigi; Farrokhabadi, Mostafa

    2015-01-01

    This article presents the implementation of the constructive alignment theory (CAT) in a power system analysis course through a consensus-based course design process. The consensus-based design process involves both the instructor and graduate-level students and it aims to develop the CAT framework in a holistic manner with the goal of including…

  9. NEW METHOD FOR SHAPE RECOGNITION BASED ON DYNAMIC PROGRAMMING

    Directory of Open Access Journals (Sweden)

    NOREDINNE GHERABI

    2011-02-01

    Full Text Available In this paper we present a new method for shape recognition based on dynamic programming. First, each contour of shape is represented by a set of points. After alignment and matching between two shapes, the outline of the shape is divided into parts according to N angular and M radial sectors , Each Sector contains a portion of the contour; thisportion is divided at the inflexion points into convex and concave sections, and the information about sections are extracted in order to provide a semantic content to the outline shape, then this information are coded and transformed into a string of symbols. Finally we find the best alignment of two complete strings and compute the optimal cost of similarity. The algorithm has been tested on a large set of shape databases and real images (MPEG-7, natural silhouette database.

  10. Dynamical image-charge effect in molecular tunnel junctions: Beyond energy level alignment

    Science.gov (United States)

    Jin, Chengjun; Thygesen, Kristian S.

    2014-01-01

    When an electron tunnels between two metal contacts it temporarily induces an image charge (IC) in the electrodes which acts back on the tunneling electron. It is usually assumed that the IC forms instantaneously such that a static model for the image potential applies. Here we investigate how the finite IC formation time affects charge transport through a molecule suspended between two electrodes. For a single-level model, an analytical treatment shows that the conductance is suppressed by a factor Z2, where Z is the quasiparticle renormalization factor, compared to the static IC approximation. We show that Z can be expressed either in terms of the plasma frequency of the electrode or as the overlap between electrode wave functions corresponding to an empty and filled level, respectively. First-principles GW calculations for benzene-diamine connected to gold electrodes show that the dynamical corrections can reduce the conductance by more than a factor of two when compared to static GW or density functional theory where the molecular energy levels have been shifted to match the exact quasiparticle levels.

  11. Design of a novel 5-DOF flexure-based compound alignment stage for Roll-to-Roll Printed Electronics

    Science.gov (United States)

    Chen, Weihai; Yang, Shang; Liu, Jingmeng; Chen, Wenjie; Jin, Yan

    2017-02-01

    Alignment stage is a pivotal component for Roll-to-Roll Printed Electronic (R2RPE), especially for Roll-to-Roll inkjet printing. This paper presents the design, modeling, and testing of a new flexure-based compound alignment stage for R2RPE. In this design, the alignment stage has 5-DOF (Degree of Freedom) motions for compensating the alignment errors and only the rotation motion about the y-axis is redundant. The stage is constructed in series by four key parts and adopts a compounded flexure structure to achieve a great performance. Each part is driven by a piezoelectric actuator or voice coil motor actuator to obtain one or two DOF motion. In order to enlarge the travel range of the alignment stage, a Scott-Russell mechanism and a lever mechanism are arranged in series for forming a two-grade displacement amplifier to overcome the small displacement of the actuator. Based on the pseudo-rigid-body simplification method, alignment models are developed. Kinematic and static analyses are conducted to evaluate the performance of the stage in terms of travel range and input stiffness. Finite element simulation is carried out to examine the mechanical performance and the theoretical models. A prototype is fabricated and experiments are conducted. Results show that the proposed alignment stage possesses an error compensation workspace of 148.11 μ m ×149.73 μ m × 813.61 μ m × 1.558 mrad × 3.501 mrad with output coupling errors of 0.693% and 0.637% between the x- and y-axis, which meets the requirements of Roll-to-Roll inkjet printing.

  12. An Analysis of Strategies for Teaching Standards-Based Lesson Plan Alignment to Preservice Teachers

    Science.gov (United States)

    Drost, Bryan R.; Levine, Anita C.

    2015-01-01

    Research consistently shows that well-aligned lesson plans lead to better student learning outcomes. The development of these plans challenges both preservice teachers and the teacher educators who instruct them. This exploratory study examined strategies for teaching lesson plan alignment utilized by 87 teacher educators in the United States.…

  13. Vertical Alignment: Ensuring Opportunity to Learn in a Standards-Based System. Issue Brief

    Science.gov (United States)

    Center for Comprehensive School Reform and Improvement, 2009

    2009-01-01

    In response to requirements in the No Child Left Behind Act (NCLB), state policymakers have made concerted efforts to align state standards with state accountability assessments. When strongly aligned and articulated, state standards and assessments can provide a clear and coherent set of expectations for students and educators. How do districts…

  14. Development of an Eccentric CAM Based Active Pre-Alignment System for the CLIC Main Beam Quadrupole Magnet

    CERN Document Server

    Lackner, F; Collette, C; Mainaud Durand, H; Hauviller, C; Kemppinen, J; Leuxe, R

    2010-01-01

    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 of today's particle accelerators. The demanding transverse and vertical beam sizes and emittance specifications are resulting in stringent alignment and a nanometre stability requirement. In the current feasibility study, the main beam quadrupole magnets have to be actively pre-aligned with a precision of 1 µm in 5 degrees of freedom (d.o.f.) before being mechanically stabilized to the nm scale above 1 Hz. This contribution describes the approach of performing this active pre-alignment based on an eccentric cam system. In order to limit the amplification of the vibration sources at resonant frequencies a sufficiently high Eigenfrequency is required. Therefore the contact region between cam and support was optimized for adequate stiffness based on the Hertzian theory. Furthermore, practical tests performed on a single degree of freedom mock-up wil...

  15. An electrical bio-chip to transfer and detect electromagnetic stimulation on the cells based on vertically aligned carbon nanotubes.

    Science.gov (United States)

    Rafizadeh-Tafti, Saeed; Haqiqatkhah, Mohammad Hossein; Saviz, Mehrdad; Janmaleki, Mohsen; Faraji Dana, Reza; Zanganeh, Somayeh; Abdolahad, Mohammad

    2017-01-01

    A highly sensitive impedimetric bio-chip based on vertically aligned multiwall carbon nanotubes (VAMWCNTs), was applied in direct interaction with lung cancer cells. Our tool provided both inducing and monitoring the bioelectrical changes in the cells initiated by electromagnetic (EM) wave stimulation. EM wave of 940MHz frequency with different intensities was used. Here, wave ablation might accumulate electrical charge on the tips of nanotubes penetrated into cell's membrane. The charge might induce ionic exchanges into the cell and cause alterations in electrical states of the membrane. Transmembrane electrostatic/dynamic states would be strongly affected due to such exchanges. Our novel modality was that, the cells' vitality changes caused by charge inductions were electrically detected with the same nanotubes in the architecture of electrodes for impedance measurement. The responses of the sensor were confirmed by electron and florescent microscopy images as well as biological assays. In summation, our method provided an effective biochip for enhancing and detecting external EM stimulation on the cells useful for future diagnostic and therapeutic applications, such as wave-guided drug-resistance breakage.

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

    Science.gov (United States)

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

    2010-02-01

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

  17. Real time radiation dosimeters based on vertically aligned multiwall carbon nanotubes and graphene

    Science.gov (United States)

    Funaro, Maria; Sarno, Maria; Ciambelli, Paolo; Altavilla, Claudia; Proto, Antonio

    2013-02-01

    Measurements of the absorbed dose and quality assurance programs play an important role in radiotherapy. Ionization chambers (CIs) are considered the most important dosimeters for their high accuracy, practicality and reliability, allowing absolute dose measurements. However, they have a relative large physical size, which limits their spatial resolution, and require a high bias voltage to achieve an acceptable collection of charges, excluding their use for in vivo dosimetry. In this paper, we propose new real time radiation detectors with electrodes based on graphene or vertically aligned multiwall carbon nanotubes (MWCNTs). We have investigated their charge collection efficiency and compared their performance with electrodes made of a conventional material. Moreover, in order to highlight the effect of nanocarbons, reference radiation detectors were also tested. The proposed dosimeters display an excellent linear response to dose and collect more charge than reference ones at a standard bias voltage, permitting the construction of miniaturized CIs. Moreover, an MWCNT based CI gives the best charge collection efficiency and it enables working also to lower bias voltages and zero volts, allowing in vivo applications. Graphene based CIs show better performance with respect to reference dosimeters at a standard bias voltage. However, at decreasing bias voltage the charge collection efficiency becomes worse if compared to a reference detector, likely due to graphene’s semiconducting behavior.

  18. Enhanced photocurrent and dynamic response in vertically aligned In₂S₃/Ag core/shell nanorod array photoconductive devices.

    Science.gov (United States)

    Cansizoglu, Hilal; Cansizoglu, Mehmet F; Watanabe, Fumiya; Karabacak, Tansel

    2014-06-11

    Enhanced photocurrent values were achieved through a semiconductor-core/metal-shell nanorod array photoconductive device geometry. Vertically aligned indium sulfide (In2S3) nanorods were formed as the core by using glancing angle deposition technique (GLAD). A thin silver (Ag) layer is conformally coated around nanorods as the metallic shell through a high pressure sputter deposition method. This was followed by capping the nanorods with a metallic blanket layer of Ag film by utilizing a new small angle deposition technique combined with GLAD. Radial interface that was formed by the core/shell geometry provided an efficient charge carrier collection by shortening carrier transit times, which led to a superior photocurrent and gain. Thin metal shells around nanorods acted as a passivation layer to decrease surface states that cause prolonged carrier lifetimes and slow recovery of the photocurrent in nanorods. A combination of efficient carrier collection with surface passivation resulted in enhanced photocurrent and dynamic response at the same time in one device structure. In2S3 nanorod devices without the metal shell and with relatively thicker metal shell were also fabricated and characterized for comparison. In2S3 nanorods with thin metal shell showed the highest photosensitivity (photocurrent/dark current) response compared to two other designs. Microstructural, morphological, and electronic properties of the core/shell nanorods were used to explain the results observed.

  19. High performance flexible pH sensor based on carboxyl-functionalized and DEP aligned SWNTs

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Lu; Shao, Jinyou, E-mail: jyshao@mail.xjtu.edu.cn; Li, Xiangming; Zhao, Qiang; Nie, Bangbang; Xu, Chuan; Ding, Haitao

    2016-11-15

    Highlights: • The flexible chemiresistive pH sensor based on two-terminal microsensors eliminating the need for a reference electrode, is simple in structure and can be fabricated on a variety of substrates such as PET, PI and PVC. • SWNTs as an ideal one dimensional material are carboxyl-functionalized to make the pH sensor show high sensitivity and outstanding flexibility for practical applications. • DEP technique is used to manipulate and position SWNTs into appropriate locations and desired formations to improve the metal-nanotube interface and highly rapid detection of pH value, resulting in better overall device performance. • Mechanical bendability of the pH sensor, which arises from the combination of flexible PET substrates and SWNTs, offer a significant improvement for applications that are difficult or impossible to achieve with traditional sensors on rigid substrates. - Abstract: The detection and control of the pH is very important in many biomedical and chemical reaction processes. A miniaturized flexible pH sensor that is light weight, robust, and conformable is very important in many applications, such as multifunctional lab-on-a-chip systems or wearable biomedical devices. In this work, we demonstrate a flexible chemiresistive pH sensor based on dielectrophoresis (DEP) aligned carboxyl-functionalized single-walled carbon nanotubes (SWNTs). Decorated carboxyl groups can react with hydrogen (H{sup +}) and hydroxide (OH{sup −}) ions, enabling the sensor to be capable of sensing the pH. DEP is used to deposit well-organized and highly aligned SWNTs in desired locations, which improves the metal-nanotube interface and highly rapid detection of the pH, resulting in better overall device performance. When pH buffer solutions are dropped onto such SWNTs, the H{sup +} and OH{sup −} ions caninteract with the carboxyl groups and affect the generation of holes and electrons in the SWNTs, leading to resistance variations in the SWNTs. The results

  20. Robust Nanogenerator Based on Vertically Aligned ZnO Nanorods Using Copper Substrate

    Directory of Open Access Journals (Sweden)

    Naveed Sheikh

    2013-01-01

    Full Text Available We report the growth of well-aligned ZnO nanorods that were successfully synthesized on copper (Cu substrate by using a simple hydrothermal method at low temperature leading to a robust large area nanogenerator (NG based on cost effective Cu electrode which could enable energy harvest from the walking motions. First, the seed layer of gold (Au has been deposited by plasma sputtering. Then, the growth process of nanorods was carried out in a sealed chemical bath. The lengths of nanorods 5-6 μm were achieved. The longer and bigger nanorods produced a surface with larger contact area and higher roughness. The larger contact area improves the absorption rate of incident light and the rougher surface strengthens the scattering effect. The surfaces were characterized by X-ray diffraction (XRD, scanning electron microscope (SEM, and energy dispersive X-ray spectroscopy (EDX. Then, Cu substrate was used for the development of high-output NG. Twenty-seven NGs were developed with maximum output voltage that exceeded to 1.8 V and maximum output current that exceeded to 148 nA. The structural simulation of nanorod has also been performed in ANSYS. The Cu substrate-based NG provides a feasible technique for effectively converting mechanical energies to electrical energy from external force.

  1. A Toolbox of Metrology-Based Techniques for Optical System Alignment

    Science.gov (United States)

    Coulter, Phillip; Ohl, Raymond G.; Blake, Peter N.; Bos, Brent J.; Eichhorn, William L.; Gum, Jeffrey S.; Hadjimichael, Theodore J.; Hagopian, John G.; Hayden, Joseph E.; Hetherington, Samuel E.; Kubalak, David A.; McLean, Kyle F.; McMann, Joseph; Redman, Kevin W.; Sampler, Henry P.; Wenzel, Greg W.; Young, Jerrod L.

    2016-01-01

    The NASA Goddard Space Flight Center (GSFC) and its partners have broad experience in the alignment of flight optical instruments and spacecraft structures. Over decades, GSFC developed alignment capabilities and techniques for a variety of optical and aerospace applications. In this paper, we provide an overview of a subset of the capabilities and techniques used on several recent projects in a "toolbox" format. We discuss a range of applications, from small-scale optical alignment of sensors to mirror and bench examples that make use of various large-volume metrology techniques. We also discuss instruments and analytical tools.

  2. A toolbox of metrology-based techniques for optical system alignment

    Science.gov (United States)

    Coulter, Phillip; Ohl, Raymond G.; Blake, Peter N.; Bos, Brent J.; Chambers, Victor J.; Eichhorn, William L.; Gum, Jeffrey S.; Hadjimichael, Theodore J.; Hagopian, John G.; Hayden, Joseph E.; Hetherington, Samuel E.; Kubalak, David A.; Mclean, Kyle F.; McMann, Joseph C.; Redman, Kevin W.; Sampler, Henry P.; Wenzel, Greg W.; Young, Jerrod L.

    2016-10-01

    The NASA Goddard Space Flight Center (GSFC) and its partners have broad experience in the alignment of flight optical instruments and spacecraft structures. Over decades, GSFC developed alignment capabilities and techniques for a variety of optical and aerospace applications. In this paper, we provide an overview of a subset of the capabilities and techniques used on several recent projects in a "toolbox" format. We discuss a range of applications, from small-scale optical alignment of sensors to mirror and bench examples that make use of various large-volume metrology techniques. We also discuss instruments and analytical tools.

  3. Novel methods in track-based alignment to correct for time-dependent distortions of the ATLAS Inner Detector

    CERN Document Server

    Estrada Pastor, Oscar; The ATLAS collaboration

    2017-01-01

    ATLAS is a multipurpose experiment at the LHC proton-proton collider. Its physics goals require high resolution, unbiased measurement of all charged particle kinematic parameters. These critically depend on the layout and performance of the tracking system and the quality of its offline alignment. For the LHC Run II, the system has been upgraded with the installation of a new pixel layer, the Insertable B-layer (IBL). Offline track alignment of the ATLAS tracking system has to deal with about 700,000 degrees of freedom (DoF) defining its geometrical parameters, representing a considerable numerical challenge in terms of both CPU time and precision. An outline of the track based alignment approach and its implementation within the ATLAS software will be presented. Special attention will be paid to describe the techniques allowing to pinpoint and eliminate track parameters biases due to alignment. During Run-II, ATLAS Inner Detector Alignment framework has been adapted and upgraded to correct very short time sc...

  4. Strategic Alignment of Business Intelligence

    OpenAIRE

    Cederberg, Niclas

    2010-01-01

    This thesis is about the concept of strategic alignment of business intelligence. It is based on a theoretical foundation that is used to define and explain business intelligence, data warehousing and strategic alignment. By combining a number of different methods for strategic alignment a framework for alignment of business intelligence is suggested. This framework addresses all different aspects of business intelligence identified as relevant for strategic alignment of business intelligence...

  5. 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.

  6. A LabVIEW based user-friendly nano-CT image alignment and 3D reconstruction platform

    CERN Document Server

    Wang, Shenghao; Wang, Zhili; Gao, Kun; Wu, Zhao; Zhu, Peiping; Wu, Ziyu

    2014-01-01

    X-ray nanometer computed tomography (nano-CT) offers applications and opportunities in many scientific researches and industrial areas. Here we present a user-friendly and fast LabVIEW based package running, after acquisition of the raw projection images, a procedure to obtain the inner structure of the sample under analysis. At first, a reliable image alignment procedure fixes possible misalignments among image series due to mechanical errors, thermal expansion and other external contributions, then a novel fast parallel beam 3D reconstruction performs the tomographic reconstruction. The remarkable improved reconstruction after the image calibration confirms the fundamental role of the image alignment procedure. It minimizes blurring and additional streaking artifacts present in a reconstructed slice that cause loss of information and faked structures in the observed material. The nano-CT image alignment and 3D reconstruction LabVIEW package significantly reducing the data process, makes faster and easier th...

  7. An empirical test of the treatment of indels during optimization alignment based on the phylogeny of the genus Secale (Poaceae)

    DEFF Research Database (Denmark)

    Petersen, Gitte; Seberg, Ole; Aagesen, Lone

    2004-01-01

    The ability of the program POY, implementing optimization alignment, to deal with major indels is explored and discussed in connection with a phylogenetic analysis of the genus Secale based on partial Adhl sequences. The Adhl sequences used span exon 2-4. Nearly all variation is found in intron 2...

  8. A Fuzzy Logic Based Controller for the Automated Alignment of a Laser-beam-smoothing Spatial Filter

    Science.gov (United States)

    Krasowski, M. J.; Dickens, D. E.

    1992-01-01

    A fuzzy logic based controller for a laser-beam-smoothing spatial filter is described. It is demonstrated that a human operator's alignment actions can easily be described by a system of fuzzy rules of inference. The final configuration uses inexpensive, off-the-shelf hardware and allows for a compact, readily implemented embedded control system.

  9. Fast comparison of genomic and meta-genomic reads with alignment-free measures based on quality values.

    Science.gov (United States)

    Comin, Matteo; Schimd, Michele

    2016-08-12

    Sequencing technologies are generating enormous amounts of read data, however assembly of genomes and metagenomes remain among the most challenging tasks. In this paper we study the comparison of genomes and metagenomes only based on read data, using word counts statistics called alignment-free thus not requiring reference genomes or assemblies. Quality scores produced by sequencing platforms are fundamental for various analyses, moreover future-generation sequencing platforms, will produce longer reads but with error rate around 15 %. In this context it will be fundamental to exploit quality values information within the framework of alignment-free measures. In this paper we present a family of alignment-free measures, called d (q) -type, that are based on k-mer counts and quality values. These statistics can be used to compare genomes and metagenomes based on their read sets. Results show that the evolutionary relationship of genomes can be reconstructed based on the direct comparison of theirs reads sets. The use of quality values on average improves the classification accuracy, and its contribution increases when the reads are more noisy. Also the comparison of metagenomic microbial communities can be performed efficiently. Similar metagenomes are quickly detected, just by processing their read data, without the need of costly alignments.

  10. Nonlinear dynamics based digital logic and circuits.

    Science.gov (United States)

    Kia, Behnam; Lindner, John F; Ditto, William L

    2015-01-01

    We discuss the role and importance of dynamics in the brain and biological neural networks and argue that dynamics is one of the main missing elements in conventional Boolean logic and circuits. We summarize a simple dynamics based computing method, and categorize different techniques that we have introduced to realize logic, functionality, and programmability. We discuss the role and importance of coupled dynamics in networks of biological excitable cells, and then review our simple coupled dynamics based method for computing. In this paper, for the first time, we show how dynamics can be used and programmed to implement computation in any given base, including but not limited to base two.

  11. Beam-Based Alignment of the NuMI Target Station Components at FNAL

    Energy Technology Data Exchange (ETDEWEB)

    Zwaska, R.; /Argonne; Bishai, M.; Childress, S.; Drake, G.; Escobar, C.; Gouffon, P.; Harris, D.A.; Hylen, J.; Indurthy, D.; Koizumi, G.; Kopp, S.; /Argonne /Brookhaven

    2006-09-01

    The Neutrinos at the Main Injector (NuMI) facility is a conventional horn-focused neutrino beam which produces muon neutrinos from a beam of mesons directed into a long evacuated decay volume. The relative alignment of the primary proton beam, target, and focusing horns affects the neutrino energy spectrum delivered to experiments. This paper describes a check of the alignment of these components using the proton beam.

  12. 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.

  13. Prostate lesion detection and localization based on locality alignment discriminant analysis

    Science.gov (United States)

    Lin, Mingquan; Chen, Weifu; Zhao, Mingbo; Gibson, Eli; Bastian-Jordan, Matthew; Cool, Derek W.; Kassam, Zahra; Chow, Tommy W. S.; Ward, Aaron; Chiu, Bernard

    2017-03-01

    Prostatic adenocarcinoma is one of the most commonly occurring cancers among men in the world, and it also the most curable cancer when it is detected early. Multiparametric MRI (mpMRI) combines anatomic and functional prostate imaging techniques, which have been shown to produce high sensitivity and specificity in cancer localization, which is important in planning biopsies and focal therapies. However, in previous investigations, lesion localization was achieved mainly by manual segmentation, which is time-consuming and prone to observer variability. Here, we developed an algorithm based on locality alignment discriminant analysis (LADA) technique, which can be considered as a version of linear discriminant analysis (LDA) localized to patches in the feature space. Sensitivity, specificity and accuracy generated by the proposed algorithm in five prostates by LADA were 52.2%, 89.1% and 85.1% respectively, compared to 31.3%, 85.3% and 80.9% generated by LDA. The delineation accuracy attainable by this tool has a potential in increasing the cancer detection rate in biopsies and in minimizing collateral damage of surrounding tissues in focal therapies.

  14. Alignment tolerant expanded beam connector based on a gapless fiber-lens interface.

    Science.gov (United States)

    Lee, Yong-Geon; Park, Chang-Hyun; Back, Seon-Woo; Kim, Haeng-Jeong; Lee, Sang-Shin

    2016-01-10

    An expanded beam connector (EBC) has been proposed and realized, where a single-mode fiber is seamlessly integrated with a ball lens exhibiting a near-zero back focal length (BFL) so that the incoming small mode exiting the fiber translates into an enlarged collimated beam via the lens. The structural tolerance for the fiber-optic connector is primarily relaxed by relieving the restrictions imposed on the meticulous control of the gap between the lens and the fiber. The EBC has been designed through rigorous ray-optic simulations and then constructed based on a ball lens in LASF35 (n=∼1.98 at λ=1.3  μm), exhibiting an ultrashort BFL of ∼13  μm. It was practically confirmed that an input mode of a ∼10  μm spot relating to the single-mode fiber could be efficiently converted into a highly collimated beam of a ∼350  μm spot that emanates from the ball lens, leading to a 35-fold beam expansion. The alignment tolerance for the fiber as well as the connector unit was scrutinized with respect to the angular tilt and transverse displacement. The measured insertion loss for the EBC, allowing for no separation between the fiber and ball lens, was slightly over 0.8 dB.

  15. A GaAs-based self-aligned stripe distributed feedback laser

    Science.gov (United States)

    Lei, H.; Stevens, B. J.; Fry, P. W.; Babazadeh, N.; Ternent, G.; Childs, D. T.; Groom, K. M.

    2016-08-01

    We demonstrate operation of a GaAs-based self-aligned stripe (SAS) distributed feedback (DFB) laser. In this structure, a first order GaInP/GaAs index-coupled DFB grating is built within the p-doped AlGaAs layer between the active region and the n-doped GaInP opto-electronic confinement layer of a SAS laser structure. In this process no Al-containing layers are exposed to atmosphere prior to overgrowth. The use of AlGaAs cladding affords the luxury of full flexibility in upper cladding design, which proved necessary due to limitations imposed by the grating infill and overgrowth with the GaInP current block layer. Resultant devices exhibit single-mode lasing with high side-mode-suppression of >40 dB over the temperature range 20 °C-70 °C. The experimentally determined optical profile and grating confinement correlate well with those simulated using Fimmwave.

  16. Centered Kernel Alignment Enhancing Neural Network Pretraining for MRI-Based Dementia Diagnosis

    Directory of Open Access Journals (Sweden)

    David Cárdenas-Peña

    2016-01-01

    Full Text Available Dementia is a growing problem that affects elderly people worldwide. More accurate evaluation of dementia diagnosis can help during the medical examination. Several methods for computer-aided dementia diagnosis have been proposed using resonance imaging scans to discriminate between patients with Alzheimer’s disease (AD or mild cognitive impairment (MCI and healthy controls (NC. Nonetheless, the computer-aided diagnosis is especially challenging because of the heterogeneous and intermediate nature of MCI. We address the automated dementia diagnosis by introducing a novel supervised pretraining approach that takes advantage of the artificial neural network (ANN for complex classification tasks. The proposal initializes an ANN based on linear projections to achieve more discriminating spaces. Such projections are estimated by maximizing the centered kernel alignment criterion that assesses the affinity between the resonance imaging data kernel matrix and the label target matrix. As a result, the performed linear embedding allows accounting for features that contribute the most to the MCI class discrimination. We compare the supervised pretraining approach to two unsupervised initialization methods (autoencoders and Principal Component Analysis and against the best four performing classification methods of the 2014 CADDementia challenge. As a result, our proposal outperforms all the baselines (7% of classification accuracy and area under the receiver-operating-characteristic curve at the time it reduces the class biasing.

  17. Markov Random Field Based Automatic Image Alignment for ElectronTomography

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-11-30

    Cryo electron tomography (cryo-ET) is the primary method for obtaining 3D reconstructions of intact bacteria, viruses, and complex molecular machines ([7],[2]). It first flash freezes a specimen in a thin layer of ice, and then rotates the ice sheet in a transmission electron microscope (TEM) recording images of different projections through the sample. The resulting images are aligned and then back projected to form the desired 3-D model. The typical resolution of biological electron microscope is on the order of 1 nm per pixel which means that small imprecision in the microscope's stage or lenses can cause large alignment errors. To enable a high precision alignment, biologists add a small number of spherical gold beads to the sample before it is frozen. These beads generate high contrast dots in the image that can be tracked across projections. Each gold bead can be seen as a marker with a fixed location in 3D, which provides the reference points to bring all the images to a common frame as in the classical structure from motion problem. A high accuracy alignment is critical to obtain a high resolution tomogram (usually on the order of 5-15nm resolution). While some methods try to automate the task of tracking markers and aligning the images ([8],[4]), they require user intervention if the SNR of the image becomes too low. Unfortunately, cryogenic electron tomography (or cryo-ET) often has poor SNR, since the samples are relatively thick (for TEM) and the restricted electron dose usually results in projections with SNR under 0 dB. This paper shows that formulating this problem as a most-likely estimation task yields an approach that is able to automatically align with high precision cryo-ET datasets using inference in graphical models. This approach has been packaged into a publicly available software called RAPTOR-Robust Alignment and Projection estimation for Tomographic Reconstruction.

  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. 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...

  20. 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...

  1. CTSS: a robust and efficient method for protein structure alignment based on local geometrical and biological features.

    Science.gov (United States)

    Can, Tolga; Wang, Yuan-Fang

    2003-01-01

    We present a new method for conducting protein structure similarity searches, which improves on the accuracy, robustness, and efficiency of some existing techniques. Our method is grounded in the theory of differential geometry on 3D space curve matching. We generate shape signatures for proteins that are invariant, localized, robust, compact, and biologically meaningful. To improve matching accuracy, we smooth the noisy raw atomic coordinate data with spline fitting. To improve matching efficiency, we adopt a hierarchical coarse-to-fine strategy. We use an efficient hashing-based technique to screen out unlikely candidates and perform detailed pairwise alignments only for a small number of candidates that survive the screening process. Contrary to other hashing based techniques, our technique employs domain specific information (not just geometric information) in constructing the hash key, and hence, is more tuned to the domain of biology. Furthermore, the invariancy, localization, and compactness of the shape signatures allow us to utilize a well-known local sequence alignment algorithm for aligning two protein structures. One measure of the efficacy of the proposed technique is that we were able to discover new, meaningful motifs that were not reported by other structure alignment methods.

  2. Relationships between static foot alignment and dynamic plantar loads in runners with acute and chronic stages of plantar fasciitis: a cross-sectional study

    Directory of Open Access Journals (Sweden)

    Ana P. Ribeiro

    2016-02-01

    Full Text Available BACKGROUND: The risk factors for the development of plantar fasciitis (PF have been associated with the medial longitudinal arch (MLA, rearfoot alignment and calcaneal overload. However, the relationships between the biomechanical variables have yet to be determined. OBJECTIVE: The goal of this study was to investigate the relationships between the MLA, rearfoot alignment, and dynamic plantar loads in runners with unilateral PF in acute and chronic phases. METHOD: Cross-sectional study which thirty-five runners with unilateral PF were evaluated: 20 in the acute phase (with pain and 15 with previous chronic PF (without pain. The MLA index and rearfoot alignment were calculated using digital images. The contact area, maximum force, peak pressure, and force-time integral over three plantar areas were acquired with Pedar X insoles while running at 12 km/h, and the loading rates were calculated from the vertical forces. RESULTS: The multiple regression analyses indicated that both the force-time integral (R2=0.15 for acute phase PF; R2=0.17 for chronic PF and maximum force (R2=0.35 for chronic PF over the forefoot were predicted by an elevated MLA index. The rearfoot valgus alignment predicted the maximum force over the rearfoot in both PF groups: acute (R2=0.18 and chronic (R2=0.45. The rearfoot valgus alignment also predicted higher loading rates in the PF groups: acute (R2=0.19 and chronic (R2=0.40. CONCLUSION: The MLA index and the rearfoot alignment were good predictors of plantar loads over the forefoot and rearfoot areas in runners with PF. However, rearfoot valgus was demonstrated to be an important clinical measure, since it was able to predict the maximum force and both loading rates over the rearfoot.

  3. Relationships between static foot alignment and dynamic plantar loads in runners with acute and chronic stages of plantar fasciitis: a cross-sectional study

    Science.gov (United States)

    Ribeiro, Ana P.; Sacco, Isabel C. N.; Dinato, Roberto C.; João, Silvia M. A.

    2016-01-01

    BACKGROUND: The risk factors for the development of plantar fasciitis (PF) have been associated with the medial longitudinal arch (MLA), rearfoot alignment and calcaneal overload. However, the relationships between the biomechanical variables have yet to be determined. OBJECTIVE: The goal of this study was to investigate the relationships between the MLA, rearfoot alignment, and dynamic plantar loads in runners with unilateral PF in acute and chronic phases. METHOD: Cross-sectional study which thirty-five runners with unilateral PF were evaluated: 20 in the acute phase (with pain) and 15 with previous chronic PF (without pain). The MLA index and rearfoot alignment were calculated using digital images. The contact area, maximum force, peak pressure, and force-time integral over three plantar areas were acquired with Pedar X insoles while running at 12 km/h, and the loading rates were calculated from the vertical forces. RESULTS: The multiple regression analyses indicated that both the force-time integral (R 2=0.15 for acute phase PF; R 2=0.17 for chronic PF) and maximum force (R 2=0.35 for chronic PF) over the forefoot were predicted by an elevated MLA index. The rearfoot valgus alignment predicted the maximum force over the rearfoot in both PF groups: acute (R 2=0.18) and chronic (R 2=0.45). The rearfoot valgus alignment also predicted higher loading rates in the PF groups: acute (R 2=0.19) and chronic (R 2=0.40). CONCLUSION: The MLA index and the rearfoot alignment were good predictors of plantar loads over the forefoot and rearfoot areas in runners with PF. However, rearfoot valgus was demonstrated to be an important clinical measure, since it was able to predict the maximum force and both loading rates over the rearfoot. PMID:26786073

  4. Tidal alignment of galaxies

    Energy Technology Data Exchange (ETDEWEB)

    Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš

    2015-08-01

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

  5. Dynamic Antenna Alignment Control in Microwave Air-Bridging for Sky-Net Mobile Communication Using Unmanned Flying Platform

    Directory of Open Access Journals (Sweden)

    Chin E. Lin

    2015-01-01

    Full Text Available This paper presents a preliminary study on establishing a mobile point-to-point (P2P microwave air-bridging (MAB between Unmanned Low Altitude Flying Platform (ULAFP and backhaul telecommunication network. The proposed Sky-Net system relays telecom signal for general mobile cellphone users via ULAFP when natural disaster sweeps off Base Transceiver Stations (BTSs. Unlike the conventional fix point microwave bridging application, the ULAFP is cruising on a predefined mission flight path to cover a wider range of service. The difficulty and challenge fall on how to maintain antenna alignment accurately in order to provide the signal strength for MAB. A dual-axis rotation mechanism with embedded controller is designed and implemented on airborne and ground units for stabilizing airborne antenna and tracking the moving ULAFP. The MAB link is established in flight tests using the proposed antenna stabilizing/tracking mechanism with correlated control method. The result supports backbone technique of the Sky-Net mobile communication and verifies the feasibility of airborne e-Cell BTS.

  6. A similarity-based framework for the alignment of an ontology for remote sensing

    Science.gov (United States)

    Farah, Mohamed; Nefzi, Hafedh; Farah, Imed Riadh

    2016-11-01

    Building remote sensing (RS) ontologies can undoubtedly help automatic interpretation of RS images content. Ontology alignment is proven to be an effective ontology building process that enables reusing already existing semantic resources. The quality of the ontology alignment output highly depends on the similarity measures that have been considered as well as the way they are combined together. In the literature, research on similarity measures mainly focuses on how to build new or refine already existing similarity measures leading to a wide range of measures. However, few research addresses their dependencies and combination in order to evaluate the overall similarity of the concepts to be compared. In this paper, we first show how to select a reduced set of similarity measures to be used in the alignment process. Afterwards, we present a ranking model that allows sorting mappings between concepts coming from two different ontologies in a decreasing order of global similarity score. First experimentation shows that the proposed approach is promising.

  7. Embedded-Based Graphics Processing Unit Cluster Platform for Multiple Sequence Alignments

    Directory of Open Access Journals (Sweden)

    Jyh-Da Wei

    2017-08-01

    Full Text Available High-end graphics processing units (GPUs, such as NVIDIA Tesla/Fermi/Kepler series cards with thousands of cores per chip, are widely applied to high-performance computing fields in a decade. These desktop GPU cards should be installed in personal computers/servers with desktop CPUs, and the cost and power consumption of constructing a GPU cluster platform are very high. In recent years, NVIDIA releases an embedded board, called Jetson Tegra K1 (TK1, which contains 4 ARM Cortex-A15 CPUs and 192 Compute Unified Device Architecture cores (belong to Kepler GPUs. Jetson Tegra K1 has several advantages, such as the low cost, low power consumption, and high applicability, and it has been applied into several specific applications. In our previous work, a bioinformatics platform with a single TK1 (STK platform was constructed, and this previous work is also used to prove that the Web and mobile services can be implemented in the STK platform with a good cost-performance ratio by comparing a STK platform with the desktop CPU and GPU. In this work, an embedded-based GPU cluster platform will be constructed with multiple TK1s (MTK platform. Complex system installation and setup are necessary procedures at first. Then, 2 job assignment modes are designed for the MTK platform to provide services for users. Finally, ClustalW v2.0.11 and ClustalWtk will be ported to the MTK platform. The experimental results showed that the speedup ratios achieved 5.5 and 4.8 times for ClustalW v2.0.11 and ClustalWtk, respectively, by comparing 6 TK1s with a single TK1. The MTK platform is proven to be useful for multiple sequence alignments.

  8. Application of vertex and mass constraints in track-based alignment

    CERN Document Server

    Amoraal, J; Blusk, S; Borghi, S; Cattaneo, M; Chiapolini, N; Conti, G; Deissenroth, M; Dupertuis, F; van der Eijk, R; Fave, V; Gersabeck, M; Hicheur, A; Hulsbergen, W; Hutchcroft, D; Kozlinskiy, A; Lambert, R W; Maciuc, F; Märki, R; Martinelli, M; Merk, M; Needham, M; Nicolas, L; Palacios, J; Parkes, C; Pellegrino, A; Pozzi, S; Raven, G; Rodrigues, E; Salzmann, C; Schiller, M; Schneider, O; Simioni, E; Steinkamp, O; van Tilburg, J; Tuning, N; Uwer, U; Vecchi, S; Viret, S

    2013-01-01

    The software alignment of planar tracking detectors using samples of charged particle trajectories may lead to global detector distortions that affect vertex and momentum resolution. We present an alignment procedure that constrains such distortions by making use of samples of decay vertices reconstructed from two or more trajectories and putting constraints on their invariant mass. We illustrate the method by using a sample of invariant-mass constrained vertices from D^0 --> K^- pi^+ decays to remove a curvature bias in the LHCb spectrometer.

  9. CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping

    Directory of Open Access Journals (Sweden)

    Shi Weisong

    2011-06-01

    Full Text Available Abstract Background Research in genetics has developed rapidly recently due to the aid of next generation sequencing (NGS. However, massively-parallel NGS produces enormous amounts of data, which leads to storage, compatibility, scalability, and performance issues. The Cloud Computing and MapReduce framework, which utilizes hundreds or thousands of shared computers to map sequencing reads quickly and efficiently to reference genome sequences, appears to be a very promising solution for these issues. Consequently, it has been adopted by many organizations recently, and the initial results are very promising. However, since these are only initial steps toward this trend, the developed software does not provide adequate primary functions like bisulfite, pair-end mapping, etc., in on-site software such as RMAP or BS Seeker. In addition, existing MapReduce-based applications were not designed to process the long reads produced by the most recent second-generation and third-generation NGS instruments and, therefore, are inefficient. Last, it is difficult for a majority of biologists untrained in programming skills to use these tools because most were developed on Linux with a command line interface. Results To urge the trend of using Cloud technologies in genomics and prepare for advances in second- and third-generation DNA sequencing, we have built a Hadoop MapReduce-based application, CloudAligner, which achieves higher performance, covers most primary features, is more accurate, and has a user-friendly interface. It was also designed to be able to deal with long sequences. The performance gain of CloudAligner over Cloud-based counterparts (35 to 80% mainly comes from the omission of the reduce phase. In comparison to local-based approaches, the performance gain of CloudAligner is from the partition and parallel processing of the huge reference genome as well as the reads. The source code of CloudAligner is available at http

  10. CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping.

    Science.gov (United States)

    Nguyen, Tung; Shi, Weisong; Ruden, Douglas

    2011-06-06

    Research in genetics has developed rapidly recently due to the aid of next generation sequencing (NGS). However, massively-parallel NGS produces enormous amounts of data, which leads to storage, compatibility, scalability, and performance issues. The Cloud Computing and MapReduce framework, which utilizes hundreds or thousands of shared computers to map sequencing reads quickly and efficiently to reference genome sequences, appears to be a very promising solution for these issues. Consequently, it has been adopted by many organizations recently, and the initial results are very promising. However, since these are only initial steps toward this trend, the developed software does not provide adequate primary functions like bisulfite, pair-end mapping, etc., in on-site software such as RMAP or BS Seeker. In addition, existing MapReduce-based applications were not designed to process the long reads produced by the most recent second-generation and third-generation NGS instruments and, therefore, are inefficient. Last, it is difficult for a majority of biologists untrained in programming skills to use these tools because most were developed on Linux with a command line interface. To urge the trend of using Cloud technologies in genomics and prepare for advances in second- and third-generation DNA sequencing, we have built a Hadoop MapReduce-based application, CloudAligner, which achieves higher performance, covers most primary features, is more accurate, and has a user-friendly interface. It was also designed to be able to deal with long sequences. The performance gain of CloudAligner over Cloud-based counterparts (35 to 80%) mainly comes from the omission of the reduce phase. In comparison to local-based approaches, the performance gain of CloudAligner is from the partition and parallel processing of the huge reference genome as well as the reads. The source code of CloudAligner is available at http://cloudaligner.sourceforge.net/ and its web version is at http

  11. Reputation-based ontology alignment for autonomy and interoperability in distributed access control

    NARCIS (Netherlands)

    Trivellato, Daniel; Spiessens, Fred; Zannone, Nicola; Etalle, Sandro

    2009-01-01

    Vocabulary alignment is a main challenge in distributedaccess control as peers should understand each other’spolicies unambiguously. Ontologies enable mutual understanding among peers by providing a precise semantics to concepts and relationships in a domain. However, due to the distributed nature

  12. Reputation-based ontology alignment for autonomy and interoperability in distributed access control

    NARCIS (Netherlands)

    Trivellato, Daniel; Spiessens, Fred; Zannone, Nicola; Etalle, Sandro

    2009-01-01

    Vocabulary alignment is a main challenge in distributedaccess control as peers should understand each other’spolicies unambiguously. Ontologies enable mutual understanding among peers by providing a precise semantics to concepts and relationships in a domain. However, due to the distributed nature o

  13. The cytodisk: A cytometer based upon a new principle of cell alignment

    NARCIS (Netherlands)

    Grooth, de B.G.; Geerken, T.H.; Greve, J.

    1985-01-01

    A new method is described for one-dimensional alignment of small particles such as biological cells. A drop of the particle suspension is spread out on a flat disk or plate equipped with V-shaped grooves such as are present on a gramophone disk. After drying, the particles are located on the bottom

  14. The cytodisk: A cytometer based upon a new principle of cell alignment

    NARCIS (Netherlands)

    de Grooth, B.G.; Geerken, T.H.; Greve, Jan

    1985-01-01

    A new method is described for one-dimensional alignment of small particles such as biological cells. A drop of the particle suspension is spread out on a flat disk or plate equipped with V-shaped grooves such as are present on a gramophone disk. After drying, the particles are located on the bottom

  15. Parameter Identification Method for SINS Initial Alignment under Inertial Frame

    Directory of Open Access Journals (Sweden)

    Haijian Xue

    2016-01-01

    Full Text Available The performance of a strapdown inertial navigation system (SINS largely depends on the accuracy and rapidness of the initial alignment. The conventional alignment method with parameter identification has been already applied widely, but it needs to calculate the gyroscope drifts through two-position method; then the time of initial alignment is greatly prolonged. For this issue, a novel self-alignment algorithm by parameter identification method under inertial frame for SINS is proposed in this paper. Firstly, this coarse alignment method using the gravity in the inertial frame as a reference is discussed to overcome the limit of dynamic disturbance on a rocking base and fulfill the requirement for the fine alignment. Secondly, the fine alignment method by parameter identification under inertial frame is formulated. The theoretical analysis results show that the fine alignment model is fully self-aligned with no external reference information and the gyrodrifts can be estimated in real time. The simulation results demonstrate that the proposed method can achieve rapid and highly accurate initial alignment for SINS.

  16. 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 ...

  17. Alignment validation

    Energy Technology Data Exchange (ETDEWEB)

    ALICE; ATLAS; CMS; LHCb; Golling, Tobias

    2008-09-06

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

  18. Distance-based classification of keystroke dynamics

    Science.gov (United States)

    Tran Nguyen, Ngoc

    2016-07-01

    This paper uses the keystroke dynamics in user authentication. The relationship between the distance metrics and the data template, for the first time, was analyzed and new distance based algorithm for keystroke dynamics classification was proposed. The results of the experiments on the CMU keystroke dynamics benchmark dataset1 were evaluated with an equal error rate of 0.0614. The classifiers using the proposed distance metric outperform existing top performing keystroke dynamics classifiers which use traditional distance metrics.

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

    Science.gov (United States)

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

    2016-06-24

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

  20. Information Technology Project Portfolio and Strategy Alignment Assessment Based on Data Envelopment Analysis

    Directory of Open Access Journals (Sweden)

    Marisa Analía Sánchez

    2012-11-01

    Full Text Available Recent researches have shown that companies face considerable difficulties in assessing the strategy value contribution of Information Technology (IT investments. One of the major obstacles to achieving strategy alignment is that organizations find extremely difficult to link and quantify the IT investments benefits with strategic goals. The aim of this paper is to define an approach to assess portfolio-strategy alignment. To this end a formal specification of Kaplan and Norton Strategy Map is developed utilizing Unified Modeling Language (UML. The approach uses the Strategy Map as a framework for defining the portfolio value contribution and Data Envelopment Analysis (DEA is used as the methodology for measuring efficiency of project portfolios.DOI:10.5585/gep.v3i2.66

  1. Performance and track-based alignment of the Phase-1 upgraded CMS pixel detector

    CERN Document Server

    Botta, Valeria

    2017-01-01

    The Compact Muon Solenoid (CMS) detector is a multi-purpose detector constructed in order to study high-energy particle collisions at the Large Hadron Collider (LHC) at CERN. The all-silicon design of the tracking system of the CMS experiment provided excellent resolution for charged tracks and an efficient tagging of jets during Run 1 and Run 2 of the LHC. After the pixel detector of the CMS experiment was upgraded and installed during the shutdown in the beginning of 2017, the positions and orientations of the tracker modules needed to be determined with a precision of several micrometers. The alignment also needs to be quickly recalculated each time the state of the CMS magnet is changed between 0 T and 3.8 T. The latest results of the CMS tracker performance in the 2017 run are presented, with a special focus on alignment and resolution performance using several million reconstructed tracks from cosmic rays and collision data.

  2. CWDM based HDMI interconnect incorporating passively aligned POF linked optical subassembly modules

    Science.gov (United States)

    Lee, Hak-Soon; Lee, Sang-Shin; Son, Yung-Sung

    2011-08-01

    A four-channel transmitter OSA (TOSA) and a receiver optical sub-assembly (ROSA) module were presented. They take advantage of a coarse WDM (CWDM) scheme, employing two types of VCSELs at 780 and 850 nm, where no wavelength filters are involved in the TOSA. The ROSA and TOSA were constructed through a fully passive alignment process using components produced by virtue of a cost effective plastic injection molding technique. In order to build a high quality optical HDMI interconnect, four channel optical links between these modules ware established via two graded-index plastic optical fibers (GI-POFs). The HDMI interconnect was thoroughly evaluated in terms of the alignment tolerance, the light beam propagation, and the data transmission capability. For the ROSA, the measured tolerance, as affected by the photodiode alignment, was ~45 μm and over 200 μm for the transverse and longitudinal directions, respectively. For the TOSA, the tolerance, which is mostly dependent upon the VCSEL alignment, was ~20 μm and more than 200 μm for the transverse and longitudinal directions, respectively. The beam profiles for the TOSA and ROSA were monitored to confirm their feasibility from the optical coupling perspective. A digital signal at 2.5 Gb/s was efficiently transmitted through the HDMI interconnect with a bit error ratio of below 10-16. A 1080p HDMI signal from a Blu-ray player was delivered through the interconnect to an LCD monitor and successfully displayed a high quality video.

  3. Morphing Downwind-Aligned Rotor Concept Based on a 13-MW Wind Turbine

    Energy Technology Data Exchange (ETDEWEB)

    Ichter, Brian; Steele, Adam; Loth, Eric; Moriarty, Patrick; Selig, Michael

    2016-04-01

    To alleviate the mass-scaling issues associated with conventional upwind rotors of extreme-scale wind turbines (>/=10 MW), a morphing downwind-aligned rotor (MoDaR) concept is proposed herein. The concept employs a downwind rotor with blades whose elements are stiff (no intentional flexibility) but with hub-joints that can be unlocked to allow for moment-free downwind alignment. Aligning the combination of gravitational, centrifugal and thrust forces along the blade path reduces downwind cantilever loads, resulting in primarily tensile loading. For control simplicity, the blade curvature can be fixed with a single morphing degree of freedom using a near-hub joint for coning angle: 22 degrees at rated conditions. The conventional baseline was set as the 13.2-MW Sandia 100-m all glass blade in a three-bladed upwind configuration. To quantify potential mass savings, a downwind load-aligning, two-bladed rotor was designed. Because of the reduced number of blades, the MoDaR concept had a favorable 33% mass reduction. The blade reduction and coning led to a reduction in rated power, but morphing increased energy capture at lower speeds such that both the MoDaR and conventional rotors have the same average power: 5.4 MW. A finite element analysis showed that quasi-steady structural stresses could be reduced, over a range of operating wind speeds and azimuthal angles, despite the increases in loading per blade. However, the concept feasibility requires additional investigation of the mass, cost and complexity of the morphing hinge, the impact of unsteady aeroelastic influence because of turbulence and off-design conditions, along with system-level Levelized Cost of Energy analysis.

  4. Method for auto-alignment of digital optical phase conjugation systems based on digital propagation.

    Science.gov (United States)

    Jang, Mooseok; Ruan, Haowen; Zhou, Haojiang; Judkewitz, Benjamin; Yang, Changhuei

    2014-06-16

    Optical phase conjugation (OPC) has enabled many optical applications such as aberration correction and image transmission through fiber. In recent years, implementation of digital optical phase conjugation (DOPC) has opened up the possibility of its use in biomedical optics (e.g. deep-tissue optical focusing) due to its ability to provide greater-than-unity OPC reflectivity (the power ratio of the phase conjugated beam and input beam to the OPC system) and its flexibility to accommodate additional wavefront manipulations. However, the requirement for precise (pixel-to-pixel matching) alignment of the wavefront sensor and the spatial light modulator (SLM) limits the practical usability of DOPC systems. Here, we report a method for auto-alignment of a DOPC system by which the misalignment between the sensor and the SLM is auto-corrected through digital light propagation. With this method, we were able to accomplish OPC playback with a DOPC system with gross sensor-SLM misalignment by an axial displacement of up to~1.5 cm, rotation and tip/tilt of ~5° and in-plane displacement of ~5 mm (dependent on the physical size of the sensor and the SLM). Our auto-alignment method robustly achieved a DOPC playback peak-to-background ratio (PBR) corresponding to more than ~30 % of the theoretical maximum. As an additional advantage, the auto-alignment procedure can be easily performed at will and, as such, allows us to correct for small mechanical drifts within the DOPC systems, thus overcoming a previously major DOPC system vulnerability. We believe that this reported method for implementing robust DOPC systems will broaden the practical utility of DOPC systems.

  5. Eigen-Direction Alignment Based Physical-Layer Network Coding for MIMO Two-Way Relay Channels

    CERN Document Server

    Yang, Tao; Ping, Li; Collings, Iain B; Yuan, Jinhong

    2012-01-01

    In this paper, we propose a novel communication strategy which incorporates physical-layer network coding (PNC) into multiple-input multiple output (MIMO) two-way relay channels (TWRCs). At the heart of the proposed scheme lies a new key technique referred to as eigen-direction alignment (EDA) precoding. The EDA precoding efficiently aligns the two-user's eigen-modes into the same directions. Based on that, we carry out multi-stream PNC over the aligned eigen-modes. We derive an achievable rate of the proposed EDA-PNC scheme, based on nested lattice codes, over a MIMO TWRC. Asymptotic analysis shows that the proposed EDA-PNC scheme approaches the capacity upper bound as the number of user antennas increases towards infinity. For a finite number of user antennas, we formulate the design criterion of the optimal EDA precoder and present solutions. Numerical results show that there is only a marginal gap between the achievable rate of the proposed EDA-PNC scheme and the capacity upper bound of the MIMO TWRC, in ...

  6. A user-friendly nano-CT image alignment and 3D reconstruction platform based on LabVIEW

    Science.gov (United States)

    Wang, Sheng-Hao; Zhang, Kai; Wang, Zhi-Li; Gao, Kun; Wu, Zhao; Zhu, Pei-Ping; Wu, Zi-Yu

    2015-01-01

    X-ray computed tomography at the nanometer scale (nano-CT) offers a wide range of applications in scientific and industrial areas. Here we describe a reliable, user-friendly, and fast software package based on LabVIEW that may allow us to perform all procedures after the acquisition of raw projection images in order to obtain the inner structure of the investigated sample. A suitable image alignment process to address misalignment problems among image series due to mechanical manufacturing errors, thermal expansion, and other external factors has been considered, together with a novel fast parallel beam 3D reconstruction procedure that was developed ad hoc to perform the tomographic reconstruction. We have obtained remarkably improved reconstruction results at the Beijing Synchrotron Radiation Facility after the image calibration, the fundamental role of this image alignment procedure was confirmed, which minimizes the unwanted blurs and additional streaking artifacts that are always present in reconstructed slices. Moreover, this nano-CT image alignment and its associated 3D reconstruction procedure are fully based on LabVIEW routines, significantly reducing the data post-processing cycle, thus making the activity of the users faster and easier during experimental runs.

  7. High Performance Flexible Piezoelectric Nanogenerators based on BaTiO3 Nanofibers in Different Alignment Modes.

    Science.gov (United States)

    Yan, Jing; Jeong, Young Gyu

    2016-06-22

    Piezoelectric nanogenerators, harvesting energy from mechanical stimuli in our living environments, hold great promise to power sustainable self-sufficient micro/nanosystems and mobile/portable electronics. BaTiO3 as a lead-free material with high piezoelectric coefficient and dielectric constant has been widely examined to realize nanogenerators, capacitors, sensors, etc. In this study, polydimethylsiloxane (PDMS)-based flexible composites including BaTiO3 nanofibers with different alignment modes were manufactured and their piezoelectric performance was examined. For the study, BaTiO3 nanofibers were prepared by an electrospinning technique utilizing a sol-gel precursor and following calcination process, and they were then aligned vertically or horizontally or randomly in PDMS matrix-based nanogenerators. The morphological structures of BaTiO3 nanofibers and their nanogenerators were analyzed by using SEM images. The crystal structures of the nanogenerators before and after poling were characterized by X-ray diffraction. The dielectric and piezoelectric properties of the nanogenerators were investigated as a function of the nanofiber alignment mode. The nanogenerator with BaTiO3 nanofibers aligned vertically in the PDMS matrix sheet achieved high piezoelectric performance of an output power of 0.1841 μW with maximum voltage of 2.67 V and current of 261.40 nA under a low mechanical stress of 0.002 MPa, in addition to a high dielectric constant of 40.23 at 100 Hz. The harvested energy could thus power a commercial LED directly or be stored into capacitors after rectification.

  8. glyXalign: high-throughput migration time alignment preprocessing of electrophoretic data retrieved via multiplexed capillary gel electrophoresis with laser-induced fluorescence detection-based glycoprofiling.

    Science.gov (United States)

    Behne, Alexander; Muth, Thilo; Borowiak, Matthias; Reichl, Udo; Rapp, Erdmann

    2013-08-01

    Glycomics has become a rapidly emerging field and monitoring of protein glycosylation is needed to ensure quality and consistency during production processes of biologicals such as therapeutic antibodies or vaccines. Glycoanalysis via multiplexed CGE with LIF detection (xCGE-LIF) represents a powerful technique featuring high resolution, high sensitivity as well as high-throughput performance. However, sample data retrieved from this method exhibit challenges for downstream computational analysis due to intersample migration time shifts as well as stretching and compression of electropherograms. Here, we present glyXalign, a freely available and easy-to-use software package to automatically correct for distortions in xCGE-LIF based glycan data. We demonstrate its ability to outperform conventional algorithms such as dynamic time warping and correlation optimized warping in terms of processing time and alignment accuracy for high-resolution datasets. Built upon a set of rapid algorithms, the tool includes an intuitive graphical user interface and allows full control over all parameters. Additionally, it visualizes the alignment process and enables the user to readjust misaligned results. Software and documentation are available at http://www.glyxera.com. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. 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.

  10. Dynamic Pattern Based Image Steganography

    OpenAIRE

    Thiyagarajan, P.; G. Aghila; Venkatesan, V. Prasanna

    2012-01-01

    Steganography is the art of hiding secret information in media such as image, audio and video. The purpose of steganography is to conceal the existence of the secret information in any given medium. This work aims at strengthening the security in steganography algorithm by generating dynamic pattern in selection of indicator sequence. In addition to this dynamicity is also encompassed in number of bits embedded in data channel. This technique has been implemented and the results have been com...

  11. Reliable Alignment in Total Knee Arthroplasty by the Use of an iPod-Based Navigation System

    Directory of Open Access Journals (Sweden)

    Paola Koenen

    2016-01-01

    Full Text Available Axial alignment is one of the main objectives in total knee arthroplasty (TKA. Computer-assisted surgery (CAS is more accurate regarding limb alignment reconstruction compared to the conventional technique. The aim of this study was to analyse the precision of the innovative navigation system DASH® by Brainlab and to evaluate the reliability of intraoperatively acquired data. A retrospective analysis of 40 patients was performed, who underwent CAS TKA using the iPod-based navigation system DASH. Pre- and postoperative axial alignment were measured on standardized radiographs by two independent observers. These data were compared with the navigation data. Furthermore, interobserver reliability was measured. The duration of surgery was monitored. The mean difference between the preoperative mechanical axis by X-ray and the first intraoperatively measured limb axis by the navigation system was 2.4°. The postoperative X-rays showed a mean difference of 1.3° compared to the final navigation measurement. According to radiographic measurements, 88% of arthroplasties had a postoperative limb axis within ±3°. The mean additional time needed for navigation was 5 minutes. We could prove very good precision for the DASH system, which is comparable to established navigation devices with only negligible expenditure of time compared to conventional TKA.

  12. Reliable Alignment in Total Knee Arthroplasty by the Use of an iPod-Based Navigation System.

    Science.gov (United States)

    Koenen, Paola; Schneider, Marco M; Fröhlich, Matthias; Driessen, Arne; Bouillon, Bertil; Bäthis, Holger

    2016-01-01

    Axial alignment is one of the main objectives in total knee arthroplasty (TKA). Computer-assisted surgery (CAS) is more accurate regarding limb alignment reconstruction compared to the conventional technique. The aim of this study was to analyse the precision of the innovative navigation system DASH® by Brainlab and to evaluate the reliability of intraoperatively acquired data. A retrospective analysis of 40 patients was performed, who underwent CAS TKA using the iPod-based navigation system DASH. Pre- and postoperative axial alignment were measured on standardized radiographs by two independent observers. These data were compared with the navigation data. Furthermore, interobserver reliability was measured. The duration of surgery was monitored. The mean difference between the preoperative mechanical axis by X-ray and the first intraoperatively measured limb axis by the navigation system was 2.4°. The postoperative X-rays showed a mean difference of 1.3° compared to the final navigation measurement. According to radiographic measurements, 88% of arthroplasties had a postoperative limb axis within ±3°. The mean additional time needed for navigation was 5 minutes. We could prove very good precision for the DASH system, which is comparable to established navigation devices with only negligible expenditure of time compared to conventional TKA.

  13. 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

    2017-01-01

    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. PMID:28272474

  14. Semiautomated improvement of RNA alignments

    DEFF Research Database (Denmark)

    Andersen, Ebbe Sloth; Lind-Thomsen, Allan; Knudsen, Bjarne

    2007-01-01

    We have developed a semiautomated RNA sequence editor (SARSE) that integrates tools for analyzing RNA alignments. The editor highlights different properties of the alignment by color, and its integrated analysis tools prevent the introduction of errors when doing alignment editing. SARSE readily...... connects to external tools to provide a flexible semiautomatic editing environment. A new method, Pcluster, is introduced for dividing the sequences of an RNA alignment into subgroups with secondary structure differences. Pcluster was used to evaluate 574 seed alignments obtained from the Rfam database...... and we identified 71 alignments with significant prediction of inconsistent base pairs and 102 alignments with significant prediction of novel base pairs. Four RNA families were used to illustrate how SARSE can be used to manually or automatically correct the inconsistent base pairs detected by Pcluster...

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

    Science.gov (United States)

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

    2007-08-01

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

  16. Improving the quality of biomarker candidates in untargeted metabolomics via peak table-based alignment of comprehensive two-dimensional gas chromatography-mass spectrometry data

    Science.gov (United States)

    Bean, Heather D.; Hill, Jane E.; Dimandja, Jean-Marie D.

    2015-01-01

    The potential of high-resolution analytical technologies like GC×GC/TOF MS in untargeted metabolomics and biomarker discovery has been limited by the development of fully automated software that can efficiently align and extract information from multiple chromatographic data sets. In this work we report the first investigation on a peak-by-peak basis of the chromatographic factors that impact GC×GC data alignment. A representative set of 16 compounds of different chromatographic characteristics were followed through the alignment of 63 GC×GC chromatograms. We found that varying the mass spectral match parameter had a significant influence on the alignment for poorly- resolved peaks, especially those at the extremes of the detector linear range, and no influence on well- chromatographed peaks. Therefore, optimized chromatography is required for proper GC×GC data alignment. Based on these observations, a workflow is presented for the conservative selection of biomarker candidates from untargeted metabolomics analyses. PMID:25857541

  17. Improving polyphonic and poly-instrumental music to score alignment

    OpenAIRE

    Soulez, Ferréol; Rodet, Xavier; Schwarz, Diemo

    2003-01-01

    6pp; International audience; Music alignment links events in a score and points on the audio performance time axis. All the parts of a recording can be thus indexed according to score information. The automatic alignment presented in this paper is based on a dynamic time warping method. Local distances are computed using the signal's spectral features through an attack plus sustain note modeling. The method is applied to mixtures of harmonic sustained instruments, excluding percussion for the...

  18. Simple scalable nucleotic FPGA based short read aligner for exhaustive search of substitution errors

    Directory of Open Access Journals (Sweden)

    Fehér Péter

    2015-12-01

    Full Text Available With the advent of the new and continuously improving technologies, in a couple of years DNA sequencing can be as commonplace as a simple blood test. The growth of sequencing efficiency has a larger exponent than the Moore’s law of standard processors, hence alignment and further processing of sequenced data is the bottleneck. The usage of FPGA (Field Programmable Gate Arrays technology may provide an efficient alternative. We propose a simple algorithm for DNA sequence alignment, which can be realized efficiently by nucleotic principal agents of Non.Neumann nature. The prototype FPGA implementation runs on a small Terasic DE1-SoC demo board with a Cyclone V chip. We present test results and furthermore analyse the theoretical scalability of this system, showing that the execution time is independent of the length of reference genome sequences. A special advantage of this parallel algorithm is that it performs exhaustive search producing all match variants up to a predetermined number of point (mutation errors.

  19. Study and development of a laser based alignment system for the compact linear collider

    CERN Document Server

    AUTHOR|(CDS)2083149

    The first objective of the PhD thesis is to develop a new type of positioning sensor to align components at micrometre level over 200 m with respect to a laser beam as straight line reference. The second objective is to estimate the measurement accuracy of the total alignment system over 200 m. The context of the PhD thesis is the Compact Linear Collider project, which is a study for a future particle accelerator. The proposed positioning sensor is made of a camera and an open/close shutter. The sensor can measure the position of the laser beam with respect to its own coordinate system. To do a measurement, the shutter closes, a laser spot appears on it, the camera captures a picture of the laser spot and the coordinates of the laser spot centre are reconstructed in the sensor coordinate system with image processing. Such a measurement requires reference targets on the positioning sensor. To reach the rst objective of the PhD thesis, we used laser theory...

  20. Magnetic field aligned assembly of nonmagnetic composite dumbbells in nanoparticle-based aqueous ferrofluid.

    Science.gov (United States)

    Takahashi, Hayato; Nagao, Daisuke; Watanabe, Kanako; Ishii, Haruyuki; Konno, Mikio

    2015-05-26

    Monodisperse, nonmagnetic, asymmetrical composite dumbbells in a suspension of magnetic nanoparticles (ferrofluid) were aligned by application of an external magnetic field to the ferrofluid. The asymmetrical composite dumbbells were prepared by two-step soap-free emulsion polymerization consisting of the first polymerization to coat spherical silica cores with cross-linked poly(methyl methacrylate) (PMMA) shell and the second polymerization to protrude a polystyrene (PSt) lobe from the core-shell particles. A chain structure of nonmagnetic dumbbells oriented to the applied magnetic field was observed at nanoparticle content of 2.0 vol % and field strengths higher than 1.0 mT. A similar chain structure of the dumbbells was observed under application of alternating electric field at strengths higher than 50 V/mm. Parallel and orthogonally combined applications of the electric and magnetic fields were also conducted to examine independence of the electric and magnetic applications as operational factors in the dumbbell assembling. Dumbbell chains stiffer than those in a single application of external field were formed in the parallel combined application of electric and magnetic fields. The orthogonal combination of the different applied fields could form a magnetically aligned chain structure of the nonmagnetic dumbbells oriented to the electric field. The present work experimentally indicated that the employment of inverse magnetorheological effect for nonmagnetic, anisotropic particles can be a useful method for the simultaneous controls over the orientation and the positon of anisotropic particles in their assembling.

  1. Transparent electronics based on transfer printed aligned carbon nanotubes on rigid and flexible substrates.

    Science.gov (United States)

    Ishikawa, Fumiaki N; Chang, Hsiao-Kang; Ryu, Koungmin; Chen, Po-Chiang; Badmaev, Alexander; Gomez De Arco, Lewis; Shen, Guozhen; Zhou, Chongwu

    2009-01-27

    We report high-performance fully transparent thin-film transistors (TTFTs) on both rigid and flexible substrates with transfer printed aligned nanotubes as the active channel and indium-tin oxide as the source, drain, and gate electrodes. Such transistors have been fabricated through low-temperature processing, which allowed device fabrication even on flexible substrates. Transparent transistors with high effective mobilities (approximately 1300 cm(2) V(-1) s(-1)) were first demonstrated on glass substrates via engineering of the source and drain contacts, and high on/off ratio (3 x 10(4)) was achieved using electrical breakdown. In addition, flexible TTFTs with good transparency were also fabricated and successfully operated under bending up to 120 degrees . All of the devices showed good transparency (approximately 80% on average). The transparent transistors were further utilized to construct a fully transparent and flexible logic inverter on a plastic substrate and also used to control commercial GaN light-emitting diodes (LEDs) with light intensity modulation of 10(3). Our results suggest that aligned nanotubes have great potential to work as building blocks for future transparent electronics.

  2. Beyond Alignment

    DEFF Research Database (Denmark)

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

  3. Interpretation of Polarization Features in Ground-Based Microwave Observations as Caused by Horizontally Aligned Oblate Raindrops.

    Science.gov (United States)

    Czekala, Harald; Crewell, Susanne; Simmer, Clemens; Thiele, Ariane; Hornbostel, Achim; Schroth, Arno

    2001-11-01

    Based on a comparison of ground-based radiometer measurements with microwave radiative transfer calculations, it is shown that raindrops with an oblate shape and a preferred horizontal orientation have a significant effect on microwave polarization signals when compared with spherical particle shape. Measurements with a dual-polarized 19-GHz radiometer reveal a polarization difference of as much as 18 K in the downwelling microwave radiation at 30° elevation angle. Averaging all rain observations within 19 months leads to a signal of 6 K. Model calculations covering roughly the same range of weather conditions as that inferred from the meteorological data recorded with the radiometer measurements were carried out with spherical raindrop shape and an oblate particle shape with a fixed horizontal alignment. From the model results, positive polarization difference is expected for spherical particles. This signal was never observed in the recorded data. For oblate drops, the averaged model results lead to a polarization difference of 8 K, which is in reasonable agreement with the long-term averaged observations. Case studies that compare isolated rain events usually lead to a better match of model and observations. However, there are some major discrepancies in some cases. Possible reasons for the remaining differences are the short-term variations in the cloud microphysics for which the model does not correctly account, such as variations in the melting layer, drop oscillations, or variations in the drop size distribution or angular distribution of the drop alignment. Three-dimensional effects are also important when observing small-scale heavy precipitation. Despite remaining small uncertainties, the comparison presents strong evidence that the oblate raindrop shape, with fixed horizontal alignment, is by far the better choice for accurate radiative transfer calculations than is the spherical shape. The omission of this shape effect can cause significant errors when

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

    Directory of Open Access Journals (Sweden)

    Andrew Kuziemko

    2011-10-01

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

  5. Electronic level alignment at the deeply buried absorber/Mo interface in chalcopyrite-based thin film solar cells

    Science.gov (United States)

    Bär, M.; Nishiwaki, S.; Weinhardt, L.; Pookpanratana, S.; Shafarman, W. N.; Heske, C.

    2008-07-01

    We have investigated the electronic structure of the absorber/back contact interface for S-free [Cu(In ,Ga)Se2 ("CIGSe")] and S-containing [Cu(In ,Ga)(S,Se)2 ("CIGSSe")] chalcopyrites with direct and inverse photoemission. Comparison of the electronic levels of the cleavage planes reveals a pronounced cliff in the conduction band at the CIG(S )Se/Mo interface. For the valence band, we find a flat alignment and a small spike for the CIGSe- and CIGSSe-based structures, respectively.

  6. Shear Flow Induced Alignment of Carbon Nanotubes in Natural Rubber

    Directory of Open Access Journals (Sweden)

    Yan He

    2015-01-01

    Full Text Available A new procedure for the fabrication of natural rubber composite with aligned carbon nanotubes is provided in this study. The two-step approach is based on (i the preparation of mixture latex of natural rubber, multiwalled carbon nanotubes, and other components and (ii the orientation of carbon nanotubes by a flow field. Rubber composite sheets filled with variable volume fraction of aligned carbon nanotubes were fabricated and then confirmed by transmission electron microscopy and Raman spectroscopy studies. An obvious increase in thermal conductivity has been obtained after the alignment of carbon nanotubes. The dynamic mechanical analysis was carried out in a tear mode for the composite.

  7. CdTe microwire-based ultraviolet photodetectors aligned by a non-uniform electric field

    Science.gov (United States)

    Park, Hyunik; Yang, Gwangseok; Chun, Seungju; Kim, Donghwan; Kim, Jihyun

    2013-07-01

    We report on ultraviolet (UV) photodetectors fabricated by positioning Cadmium Telluride (CdTe) microwires (μWs) precisely by dielectrophoretic (DEP) force, where CdTe μWs were grown using an Au-catalyst-assisted closed-space-sublimation (CSS) method. The optical properties of CSS-grown CdTe μWs were characterized by micro-photoluminescence and micro-Raman spectroscopies. Optoelectronic characteristics were obtained after CdTe μWs were aligned on a pre-patterned SiO2/Si substrate by a non-uniform electric field. Photocurrents were increased with increasing the light intensities. Fast and reliable photoresponse and recovery were observed when CdTe μWs were exposed to UV illuminations. We demonstrated that high quality CdTe μWs grown by the CSS method have significant potentials as optoelectronic devices.

  8. A robust, alignment-free broadband CARS system based on stimulated processes in heavy water

    Science.gov (United States)

    Yuan, Hong; Gai, Baodong; Liu, Jinbo; Guo, Jingwei; Cai, Xianglong; Xia, Xusheng; Li, Xueyang; Zhang, Baichao; Deng, Liezheng; Jin, Yuqi

    2017-06-01

    We have established a new method for realizing a typical "2-color" collinear CARS (coherent anti-Stokes Raman scattering) system. The system mainly consists of a laser source, a D2O cell, and a spectrometer. The pump/probe beam and the Stokes beam are provided by SBS (stimulated Brillouin scattering) and BSRS (backward stimulated Raman scattering) of D2O, respectively. The CARS system is statistically stable, and it is also a broadband and alignment-free system. Measurement of N2 signal in air with this system is demonstrated. Detection of N2 in 0.006 bar air is realized with this system. Time-resolved pulse shapes of SBS and BSRS are measured to confirm their generation. Transference of energy from the SBS pulse to the BSRS pulse is realized with a Rhodamine 101 dye cuvette and discussed. This results in a better energy distribution between the pump/probe and Stokes pulses for CARS.

  9. Surface-conduction electron-emitter characteristics and fabrication based on vertically aligned carbon nanotube arrays

    Science.gov (United States)

    Shih, Yi-Ting; Li, Kuan-Wei; Honda, Shin-ichi; Lin, Pao-Hung; Huang, Ying-Sheng; Lee, Kuei-Yi

    2017-06-01

    The carbon nanotube (CNT) has replaced palladium oxide (PdO) as the electrode material for surface-conduction electron-emitter (SCE) applications. Vertically aligned CNT arrays with a delta-star arrangement were patterned and synthesized onto a quartz substrate using photolithography and thermal chemical vapor deposition. Delta-star shaped VACNT arrays with 20° tips are used as cathodes that easily emit electrons because of their high electrical field gradient. In order to improve the field emission and secondary electrons (SEs) in SCE applications, magnesium oxide (MgO) nanostructures were coated onto the VACNT arrays to promote the surface-conduction electron-emitter display (SED) efficiency (η). According to the definition of η in SCE applications, in this study, the η was stably maintained in the 75-85% range. The proposed design provides a facile new method for developing SED applications.

  10. Observers can always generate nonlocal correlations without aligning measurements by covering all their bases

    CERN Document Server

    Wallman, Joel J

    2011-01-01

    Quantum theory allows for correlations between the outcomes of distant measurements that are inconsistent with any locally causal theory, as demonstrated by the violation of a Bell inequality. Typical demonstrations of these correlations require careful alignment between the measurements, which requires distant parties to share a reference frame. Here, we prove, following a numerical observation by Shadbolt et al., that if two parties share a Bell state and each party randomly chooses three orthogonal measurements, then the parties will always violate a Bell inequality. Furthermore, we prove that this probability is highly robust against local depolarizing noise, in that small levels of noise only decrease the probability of violating a Bell inequality by a small amount. We also show that generalizing to N parties increases the robustness against noise. These results improve on previous ones that only allowed a high probability of violating a Bell inequality for large numbers of parties.

  11. An immune based dynamic intrusion detection model

    Institute of Scientific and Technical Information of China (English)

    LI Tao

    2005-01-01

    With the dynamic description method for self and antigen, and the concept of dynamic immune tolerance for lymphocytes in network-security domain presented in this paper, a new immune based dynamic intrusion detection model (Idid) is proposed. In Idid, the dynamic models and the corresponding recursive equations of the lifecycle of mature lymphocytes, and the immune memory are built. Therefore, the problem of the dynamic description of self and nonself in computer immune systems is solved, and the defect of the low efficiency of mature lymphocyte generating in traditional computer immune systems is overcome. Simulations of this model are performed, and the comparison experiment results show that the proposed dynamic intrusion detection model has a better adaptability than the traditional methods.

  12. Propagation and stability characteristics of a 500-m-long laser-based fiducial line for high-precision alignment of long-distance linear accelerators.

    Science.gov (United States)

    Suwada, Tsuyoshi; Satoh, Masanori; Telada, Souichi; Minoshima, Kaoru

    2013-09-01

    A laser-based alignment system with a He-Ne laser has been newly developed in order to precisely align accelerator units at the KEKB injector linac. The laser beam was first implemented as a 500-m-long fiducial straight line for alignment measurements. We experimentally investigated the propagation and stability characteristics of the laser beam passing through laser pipes in vacuum. The pointing stability at the last fiducial point was successfully obtained with the transverse displacements of ±40 μm level in one standard deviation by applying a feedback control. This pointing stability corresponds to an angle of ±0.08 μrad. This report contains a detailed description of the experimental investigation for the propagation and stability characteristics of the laser beam in the laser-based alignment system for long-distance linear accelerators.

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

    Directory of Open Access Journals (Sweden)

    Chin-Sheng Chen

    2016-05-01

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

  14. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    S. Szillasi

    2013-01-01

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

  15. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez

    2012-01-01

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

  16. Analysis of dynamic characteristics of self-aligning ball bearing%调心球轴承动态特性参数分析

    Institute of Scientific and Technical Information of China (English)

    袁丁; 蒋书运

    2010-01-01

    基于Jones-Harris方法建立了调心球轴承的动力学模型,应用Newton-Raphson方法对轴承动力学方程组进行了求解,开发了相应的计算程序.完成了该轴承的离心力、陀螺力矩、接触载荷、接触角、径向变形与径向刚度等动态特性参数分析.分析结果表明:转速与载荷是影响接触角大小与接触载荷分布最主要的2个因素;滚子的离心力与陀螺力矩随着转速的上升而增大,在此影响下外圈接触载荷增大而内圈接触载荷减小;受离心力的影响,外圈的接触角减小而内圈的接触角增大,且随着转速的增加,内外圈接触角的差值越来越大;轴承的径向刚度随着转速的上升而下降,而滚道沟曲率系数也对轴承径向刚度有一定程度的影响.%A dynamics model of the self-aligning ball bearing is proposed based on the Jones-Harris method (JHM), and a computer program is developed to solve the equations by using the Newton-Raphson method. A parametric analysis of the centrifugal force and the gyroscopic moment, the contact loads, the contact angles, the radial deformation and the radial stiffness is carried out. The analytical results show that the applied loads and the rotational speed are two main factors that can influence the distributions of the contact loads and values of the contact angles. The centrifugal force and the gyroscopic moment increase with the increase in the rotational speed, resulting in the decrease of the inner raceway contact load and the increase of the outer raceway contact load. The outer raceway contact angle increases under the centrifugal force; on the contrary, the inner raceway contact angle decreases. Furthermore, the differences between the inner and the outer contact angles increase with the increase in the rotational speed. The higher rotational speed results in the decrease in radial stiffness for the self-aligning ball bearing, and the raceway curvature coefficient, to some extent, also

  17. Rotational alignment in total knee arthroplasty: nonimage-based navigation system versus conventional technique

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xian-long; ZHANG Wen; SHAO Jun-jie

    2012-01-01

    Background Proper rotational alignment during total knee arthroplasty (TKA) is important for adequate postoperative patellofemoral and tibiofemoral kinematics,as well as for achieving balanced flexion space at 90°.The effects of computer navigation-assisted total knee replacement and conventional total knee arthroplasty on rotational alignment,mechanical axis,component position and clinical outcomes were compared.Methods Two methods were used in 82 patients and the rotation of the femoral and tibial components in the transverse plane,the combined rotation of the two components,the mismatch between them,and the mechanical axis of the lower limb were analyzed.All of these parameters were measured from postoperative radiographs and computed tomography images.Functional outcomes were compared at 6 weeks and 6 months postoperatively.Results Significant differences were found between the two techniques (P <0.05) in the following parameters:average rotation of the femoral component ((1.51±3.55)° vs.(-0.63±3.04)°); combined rotation of the femoral and tibial components (2.85±4.07)° vs.(0.28±3.43)°); and mismatch between the femoral and tibial components ((1.44±4.55)° vs.(-0.43±2.86)°).Differences in the rotation of the tibial component were not statistically significant.The prevalence of outliers (malalignment >±3° intemal/external rotation) of the femoral component (31.7% vs.12.5%) and the tibial component (36.6% vs.15%) were significantly reduced when the navigation system was used (P<0.05).In addition,while patients in the navigation group had significantly better mechanical axis and functional outcomes at 6 weeks after surgery (P <0.05),there was no significant difference between the two groups (P >0.05) with respect to functional outcomes at 6 months.Conclusion The navigation system exhibited higher accuracy than the conventional technique in the transverse and coronal plane,and provided better early functional outcomes.

  18. General Alignment Concept of the CMS experiment

    CERN Document Server

    Lampen, T

    2006-01-01

    Efficient and accurate track reconstruction requires proper alignment of the tracking devices used. Here we describe the general alignment strategy envisaged for the CMS experiment. The hardware alignment devices of CMS are presented as well as the different track based alignment approaches.

  19. Component Based Dynamic Reconfigurable Test System

    Institute of Scientific and Technical Information of China (English)

    LAI Hong; HE Lingsong; ZHANG Dengpan

    2006-01-01

    In this paper, a novel component based framework of test system is presented for the new requirements of dynamic changes of test functions and reconfiguration of test resources. The complexity of dynamic reconfiguration arises from the scale, redirection, extensibility and interconnection of components in test system. The paper is started by discussing the component assembly based framework which provide the open platform to the deploy of components and then the script interpreter model is introduced to dynamically create the components and build the test system by analyzing XML based information of test system. A pipeline model is presented to provide the data channels and behavior reflection among the components. Finally, a dynamic reconfigurable test system is implemented on the basis of COM and applied in the remote test and control system of CNC machine.

  20. Mathis software for controlling BCAM-based monitoring and alignment systems

    CERN Document Server

    Klumb, Francis; Kautzmann, Guillaume; CERN. Geneva. ATS Department

    2016-01-01

    The MATHIS Software (Monitoring and Alignment Tracking for HIE-Isolde Software) aims at providing 3D positions of physical components of the HIE-Isolde superconducting modules, accurately and permanently measured by well-designed networks of BCAM devices (Brandeis Camera Angle Monitoring). Although it is originally intended for the HIE-Isolde project, its architecture and its use cases have been extended and optimized for more general setups. Most of the configuration data are stored either within XML-formatted files or within databases. The adaptation of MATHIS for different BCAM monitoring systems therefore does not require any further code rewriting. Moreover, the software is fully cross-platform and can either be run on the specific Linux machines driving the accelerator electronic devices, or be used on independent Windows workstations as a stand-alone software. In the first case, the software mainly relies on FESA (Front End Software Architecture) which is an object-oriented real-time framework that ens...

  1. Versatile Particle-Based Route to Engineer Vertically Aligned Silicon Nanowire Arrays and Nanoscale Pores.

    Science.gov (United States)

    Elnathan, Roey; Isa, Lucio; Brodoceanu, Daniel; Nelson, Adrienne; Harding, Frances J; Delalat, Bahman; Kraus, Tobias; Voelcker, Nicolas H

    2015-10-28

    Control over particle self-assembly is a prerequisite for the colloidal templating of lithographical etching masks to define nanostructures. This work integrates and combines for the first time bottom-up and top-down approaches, namely, particle self-assembly at liquid-liquid interfaces and metal-assisted chemical etching, to generate vertically aligned silicon nanowire (VA-SiNW) arrays and, alternatively, arrays of nanoscale pores in a silicon wafer. Of particular importance, and in contrast to current techniques, including conventional colloidal lithography, this approach provides excellent control over the nanowire or pore etching site locations and decouples nanowire or pore diameter and spacing. The spacing between pores or nanowires is tuned by adjusting the specific area of the particles at the liquid-liquid interface before deposition. Hence, the process enables fast and low-cost fabrication of ordered nanostructures in silicon and can be easily scaled up. We demonstrate that the fabricated VA-SiNW arrays can be used as in vitro transfection platforms for transfecting human primary cells.

  2. Prediction of antimicrobial peptides based on sequence alignment and feature selection methods.

    Directory of Open Access Journals (Sweden)

    Ping Wang

    Full Text Available Antimicrobial peptides (AMPs represent a class of natural peptides that form a part of the innate immune system, and this kind of 'nature's antibiotics' is quite promising for solving the problem of increasing antibiotic resistance. In view of this, it is highly desired to develop an effective computational method for accurately predicting novel AMPs because it can provide us with more candidates and useful insights for drug design. In this study, a new method for predicting AMPs was implemented by integrating the sequence alignment method and the feature selection method. It was observed that, the overall jackknife success rate by the new predictor on a newly constructed benchmark dataset was over 80.23%, and the Mathews correlation coefficient is 0.73, indicating a good prediction. Moreover, it is indicated by an in-depth feature analysis that the results are quite consistent with the previously known knowledge that some amino acids are preferential in AMPs and that these amino acids do play an important role for the antimicrobial activity. For the convenience of most experimental scientists who want to use the prediction method without the interest to follow the mathematical details, a user-friendly web-server is provided at http://amp.biosino.org/.

  3. High performance piezoelectric devices based on aligned arrays of nanofibers of poly(vinylidenefluoride-co-trifluoroethylene).

    Science.gov (United States)

    Persano, Luana; Dagdeviren, Canan; Su, Yewang; Zhang, Yihui; Girardo, Salvatore; Pisignano, Dario; Huang, Yonggang; Rogers, John A

    2013-01-01

    Multifunctional capability, flexible design, rugged lightweight construction and self-powered operation are desired attributes for electronics that directly interface with the human body or with advanced robotic systems. For these applications, piezoelectric materials, in forms that offer the ability to bend and stretch, are attractive for pressure/force sensors and mechanical energy harvesters. Here, we introduce a large area, flexible piezoelectric material that consists of sheets of electrospun fibres of the polymer poly[(vinylidenefluoride-co-trifluoroethylene]. The flow and mechanical conditions associated with the spinning process yield free-standing, three-dimensional architectures of aligned arrangements of such fibres, in which the polymer chains adopt strongly preferential orientations. The resulting material offers exceptional piezoelectric characteristics, to enable ultra-high sensitivity for measuring pressure, even at exceptionally small values (0.1 Pa). Quantitative analysis provides detailed insights into the pressure sensing mechanisms, and establishes engineering design rules. Potential applications range from self-powered micro-mechanical elements, to self-balancing robots and sensitive impact detectors.

  4. High performance piezoelectric devices based on aligned arrays of nanofibers of poly(vinylidenefluoride-co-trifluoroethylene)

    Science.gov (United States)

    Persano, Luana; Dagdeviren, Canan; Su, Yewang; Zhang, Yihui; Girardo, Salvatore; Pisignano, Dario; Huang, Yonggang; Rogers, John A.

    2013-03-01

    Multifunctional capability, flexible design, rugged lightweight construction and self-powered operation are desired attributes for electronics that directly interface with the human body or with advanced robotic systems. For these applications, piezoelectric materials, in forms that offer the ability to bend and stretch, are attractive for pressure/force sensors and mechanical energy harvesters. Here, we introduce a large area, flexible piezoelectric material that consists of sheets of electrospun fibres of the polymer poly[(vinylidenefluoride-co-trifluoroethylene]. The flow and mechanical conditions associated with the spinning process yield free-standing, three-dimensional architectures of aligned arrangements of such fibres, in which the polymer chains adopt strongly preferential orientations. The resulting material offers exceptional piezoelectric characteristics, to enable ultra-high sensitivity for measuring pressure, even at exceptionally small values (0.1 Pa). Quantitative analysis provides detailed insights into the pressure sensing mechanisms, and establishes engineering design rules. Potential applications range from self-powered micro-mechanical elements, to self-balancing robots and sensitive impact detectors.

  5. HAlign: Fast multiple similar DNA/RNA sequence alignment based on the centre star strategy.

    Science.gov (United States)

    Zou, Quan; Hu, Qinghua; Guo, Maozu; Wang, Guohua

    2015-08-01

    Multiple sequence alignment (MSA) is important work, but bottlenecks arise in the massive MSA of homologous DNA or genome sequences. Most of the available state-of-the-art software tools cannot address large-scale datasets, or they run rather slowly. The similarity of homologous DNA sequences is often ignored. Lack of parallelization is still a challenge for MSA research. We developed two software tools to address the DNA MSA problem. The first employed trie trees to accelerate the centre star MSA strategy. The expected time complexity was decreased to linear time from square time. To address large-scale data, parallelism was applied using the hadoop platform. Experiments demonstrated the performance of our proposed methods, including their running time, sum-of-pairs scores and scalability. Moreover, we supplied two massive DNA/RNA MSA datasets for further testing and research. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  6. Matt: local flexibility aids protein multiple structure alignment.

    Directory of Open Access Journals (Sweden)

    Matthew Menke

    2008-01-01

    Full Text Available Even when there is agreement on what measure a protein multiple structure alignment should be optimizing, finding the optimal alignment is computationally prohibitive. One approach used by many previous methods is aligned fragment pair chaining, where short structural fragments from all the proteins are aligned against each other optimally, and the final alignment chains these together in geometrically consistent ways. Ye and Godzik have recently suggested that adding geometric flexibility may help better model protein structures in a variety of contexts. We introduce the program Matt (Multiple Alignment with Translations and Twists, an aligned fragment pair chaining algorithm that, in intermediate steps, allows local flexibility between fragments: small translations and rotations are temporarily allowed to bring sets of aligned fragments closer, even if they are physically impossible under rigid body transformations. After a dynamic programming assembly guided by these "bent" alignments, geometric consistency is restored in the final step before the alignment is output. Matt is tested against other recent multiple protein structure alignment programs on the popular Homstrad and SABmark benchmark datasets. Matt's global performance is competitive with the other programs on Homstrad, but outperforms the other programs on SABmark, a benchmark of multiple structure alignments of proteins with more distant homology. On both datasets, Matt demonstrates an ability to better align the ends of alpha-helices and beta-strands, an important characteristic of any structure alignment program intended to help construct a structural template library for threading approaches to the inverse protein-folding problem. The related question of whether Matt alignments can be used to distinguish distantly homologous structure pairs from pairs of proteins that are not homologous is also considered. For this purpose, a p-value score based on the length of the common core

  7. A Rapid Transfer Alignment Method for SINS Based on the Added Backward-Forward SINS Resolution and Data Fusion

    Directory of Open Access Journals (Sweden)

    Xixiang Liu

    2013-01-01

    Full Text Available Two viewpoints are given: (1 initial alignment of strapdown inertial navigation system (SINS can be fulfilled with a set of inertial sensor data; (2 estimation time for sensor errors can be shortened by repeated data fusion on the added backward-forward SINS resolution results and the external reference data. Based on the above viewpoints, aiming to estimate gyro bias in a shortened time, a rapid transfer alignment method, without any changes for Kalman filter, is introduced. In this method, inertial sensor data and reference data in one reference data update cycle are stored, and one backward and one forward SINS resolutions are executed. Meanwhile, data fusion is executed when the corresponding resolution ends. With the added backward-forward SINS resolution, in the above mentioned update cycle, the estimating operations for gyro bias are added twice, and the estimation time for it is shortened. In the ship swinging condition, with the “velocity plus yaw” matching, the effectiveness of this method is proved by the simulation.

  8. Postural bipedance in paraplegics under Neuromuscular Electrical Stimulation: Is it possible to improve it based on Sagittal Spinal Alignment?

    Science.gov (United States)

    Medeiros, Rodrigo C.; Jaccard, Alexandre P. B.; Cliquet, Alberto

    2011-01-01

    Study design Experimental trial based on the analytical study of the radiographic standards of the sagittal spinal alignment in paraplegics in upright position under surface Neuromuscular Electrical Stimulation (NMES). Objectives To evaluate changes in radiographic standards of the sagittal spinal alignment of paraplegics under three different models of NMES used to optimize the global bipedal posture. Setting The University Hospital Ambulatory (UNICAMP), Campinas, SP, Brazil Methods Ten paraplegic patients were selected. Each patient underwent three different models of NMES. The influence that each NMES models exerted over the sagittal balance of the spine was evaluated by lateral panoramic x-rays. Wilcoxon’s Test was used to compare the modifications observed in each NMES model in the group studied. Results Using the femoral quadriceps muscles’ NMES as the starting point, the inclusion of the gluteus maximus’ NMES generated an increase of the lumbar lordosis and an decrease of the spinal tilt angle. These alterations resulted in partial improvement of the anterior sagittal imbalance. NMES of the paralyzed paravertebral lumbar muscles resulted in a more expressive increase on the lumbar lordosis with no important change on the spinal tilt. On the latter model, however, an improvement of 20% was observed in the global sagittal imbalance due to a posterior translation of the spine as pointed out by the decrease in the C7-HA horizontal distance. Conclusions The proposed NMES models were able to partially amend the anterior sagittal imbalance of the paraplegic patients in bipedal posture. PMID:22333891

  9. Implementing a search for aligned-spin neutron star -- black hole systems with advanced ground based gravitational wave detectors

    CERN Document Server

    Canton, Tito Dal; Lundgren, Andrew P; Nielsen, Alex B; Brown, Duncan A; Harry, Ian W; Krishnan, Badri; Miller, Andrew J; Wiesner, Karsten; Willis, Joshua L

    2014-01-01

    We study the effect of spins on searches for gravitational waves from compact binary coalescence events in realistic early advanced LIGO data. We construct a realistic detection pipeline which includes matched filtering, signal-based vetoes, coincidence tests between different detectors, clustering of events, and an estimate of the rate of background events. We restrict attention to neutron star--black hole (NS-BH) binary systems, and we compare a search using non-spinning templates to a search using templates which include spins aligned with the orbital angular momentum. We introduce a new implementation of the gravitational-wave matched-filter computation in a new software toolkit for gravitational-wave data analysis called PyCBC, and use this to run our search. We find that the inclusion of aligned-spin effects significantly improves the astrophysical reach of the search. If the dimensionless spin of the black hole in astrophysical NS-BH systems were uniformly distributed between (-1,1), the sensitive volu...

  10. Onorbit IMU alignment error budget

    Science.gov (United States)

    Corson, R. W.

    1980-01-01

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

  11. MUON DETECTORS: ALIGNMENT

    CERN Document Server

    M. Dallavalle

    2013-01-01

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

  12. Detection and alignment of 3D domain swapping proteins using angle-distance image-based secondary structural matching techniques.

    Directory of Open Access Journals (Sweden)

    Chia-Han Chu

    Full Text Available This work presents a novel detection method for three-dimensional domain swapping (DS, a mechanism for forming protein quaternary structures that can be visualized as if monomers had "opened" their "closed" structures and exchanged the opened portion to form intertwined oligomers. Since the first report of DS in the mid 1990s, an increasing number of identified cases has led to the postulation that DS might occur in a protein with an unconstrained terminus under appropriate conditions. DS may play important roles in the molecular evolution and functional regulation of proteins and the formation of depositions in Alzheimer's and prion diseases. Moreover, it is promising for designing auto-assembling biomaterials. Despite the increasing interest in DS, related bioinformatics methods are rarely available. Owing to a dramatic conformational difference between the monomeric/closed and oligomeric/open forms, conventional structural comparison methods are inadequate for detecting DS. Hence, there is also a lack of comprehensive datasets for studying DS. Based on angle-distance (A-D image transformations of secondary structural elements (SSEs, specific patterns within A-D images can be recognized and classified for structural similarities. In this work, a matching algorithm to extract corresponding SSE pairs from A-D images and a novel DS score have been designed and demonstrated to be applicable to the detection of DS relationships. The Matthews correlation coefficient (MCC and sensitivity of the proposed DS-detecting method were higher than 0.81 even when the sequence identities of the proteins examined were lower than 10%. On average, the alignment percentage and root-mean-square distance (RMSD computed by the proposed method were 90% and 1.8Å for a set of 1,211 DS-related pairs of proteins. The performances of structural alignments remain high and stable for DS-related homologs with less than 10% sequence identities. In addition, the quality of its

  13. Detection and alignment of 3D domain swapping proteins using angle-distance image-based secondary structural matching techniques.

    Science.gov (United States)

    Chu, Chia-Han; Lo, Wei-Cheng; Wang, Hsin-Wei; Hsu, Yen-Chu; Hwang, Jenn-Kang; Lyu, Ping-Chiang; Pai, Tun-Wen; Tang, Chuan Yi

    2010-10-14

    This work presents a novel detection method for three-dimensional domain swapping (DS), a mechanism for forming protein quaternary structures that can be visualized as if monomers had "opened" their "closed" structures and exchanged the opened portion to form intertwined oligomers. Since the first report of DS in the mid 1990s, an increasing number of identified cases has led to the postulation that DS might occur in a protein with an unconstrained terminus under appropriate conditions. DS may play important roles in the molecular evolution and functional regulation of proteins and the formation of depositions in Alzheimer's and prion diseases. Moreover, it is promising for designing auto-assembling biomaterials. Despite the increasing interest in DS, related bioinformatics methods are rarely available. Owing to a dramatic conformational difference between the monomeric/closed and oligomeric/open forms, conventional structural comparison methods are inadequate for detecting DS. Hence, there is also a lack of comprehensive datasets for studying DS. Based on angle-distance (A-D) image transformations of secondary structural elements (SSEs), specific patterns within A-D images can be recognized and classified for structural similarities. In this work, a matching algorithm to extract corresponding SSE pairs from A-D images and a novel DS score have been designed and demonstrated to be applicable to the detection of DS relationships. The Matthews correlation coefficient (MCC) and sensitivity of the proposed DS-detecting method were higher than 0.81 even when the sequence identities of the proteins examined were lower than 10%. On average, the alignment percentage and root-mean-square distance (RMSD) computed by the proposed method were 90% and 1.8Å for a set of 1,211 DS-related pairs of proteins. The performances of structural alignments remain high and stable for DS-related homologs with less than 10% sequence identities. In addition, the quality of its hinge loop

  14. Mechanism for collective cell alignment in Myxococcus xanthus bacteria

    CERN Document Server

    Balagam, Rajesh

    2015-01-01

    M. xanthus cells self-organize into clusters, aligned cell groups, at various stages of its lifecycle. Formation of these clusters is crucial for complex dynamic multi-cellular behavior of these bacteria. However the mechanism underlying the cell alignment and clustering is not fully understood. Motivated by studies of clustering in self-propelled rods, we hypothesized that M. xanthus cells can align and form clusters through pure mechanical interactions among cells and between cells and substrate. We test this hypothesis using an agent-based simulation framework where each agent is based on biophysical model of individual M. xanthus cell. We show that model agents, under realistic cell flexibility values, can align and form cell clusters but only when periodic reversals of cell directions are suppressed. However, by extending our model to introduce observed ability of cells to lay and follow slime trails, we show that effective trail following leads to clusters in reversing cells. Furthermore, we conclude th...

  15. Protein sequence alignment with family-specific amino acid similarity matrices

    Science.gov (United States)

    2011-01-01

    Background Alignment of amino acid sequences by means of dynamic programming is a cornerstone sequence comparison method. The quality of alignments produced by dynamic programming critically depends on the choice of the alignment scoring function. Therefore, for a specific alignment problem one needs a way of selecting the best performing scoring function. This work is focused on the issue of finding optimized protein family- and fold-specific scoring functions for global similarity matrix-based sequence alignment. Findings I utilize a comprehensive set of reference alignments obtained from structural superposition of homologous and analogous proteins to design a quantitative statistical framework for evaluating the performance of alignment scoring functions in global pairwise sequence alignment. This framework is applied to study how existing general-purpose amino acid similarity matrices perform on individual protein families and structural folds, and to compare them to family-specific and fold-specific matrices derived in this work. I describe an adaptive alignment procedure that automatically selects an appropriate similarity matrix and optimized gap penalties based on the properties of the sequences being aligned. Conclusions The results of this work indicate that using family-specific similarity matrices significantly improves the quality of the alignment of homologous sequences over the traditional sequence alignment based on a single general-purpose similarity matrix. However, using fold-specific similarity matrices can only marginally improve sequence alignment of proteins that share the same structural fold but do not share a common evolutionary origin. The family-specific matrices derived in this work and the optimized gap penalties are available at http://taurus.crc.albany.edu/fsm. PMID:21846354

  16. Workflow-Based Dynamic Enterprise Modeling

    Institute of Scientific and Technical Information of China (English)

    黄双喜; 范玉顺; 罗海滨; 林慧萍

    2002-01-01

    Traditional systems for enterprise modeling and business process control are often static and cannot adapt to the changing environment. This paper presents a workflow-based method to dynamically execute the enterprise model. This method gives an explicit representation of the business process logic and the relationships between the elements involved in the process. An execution-oriented integrated enterprise modeling system is proposed in combination with other enterprise views. The enterprise model can be established and executed dynamically in the actual environment due to the dynamic properties of the workflow model.

  17. Radio lighting based on dynamic chaos generators

    CERN Document Server

    Dmitriev, Alexander; Gerasimov, Mark; Itskov, Vadim

    2016-01-01

    A problem of lighting objects and surfaces with artificial sources of noncoherent microwave radiation with the aim to observe them using radiometric equipment is considered. Transmitters based on dynamic chaos generators are used as sources of noncoherent wideband microwave radiation. An experimental sample of such a device, i.e., a radio lighting lamp based on a chaos microgenerator and its performance are presented.

  18. A Base-Emitter Self-Aligned Multi-Finger Si1-xGex/Si Power Heterojunction Bipolar Transistor

    Institute of Scientific and Technical Information of China (English)

    XUE Chun-Lai; YAO Fei; SHI Wen-Hua; CHENG Bu-Wen; WANG Hong-Jie; YU Jin-Zhong; WANG Qi-Ming

    2007-01-01

    With a crystal orientation dependent on the etch rate of Si in KOH-based solution, a base-emitter self-aligned large-area multi-finger configuration power SiGe heterojunction bipolar transistor (HBT) device (with an emitter area of about 880μm2) is fabricated with 2μm double-mesa technology. The maximum dc current gain is 226.1. The collector-emitter junction breakdown voltage BVCEO is 10V and the collector-base junction breakdown voltage BVcBo is 16 V with collector doping concentration of 1 × 1017 cm-3 and thickness of 400nm. The device exhibited a maximum oscillation frequency fmax of 35.5 GHz and a cut-off frequency fT of 24.9 GHz at a dc bias point of Ic = 70 mA and the voltage between collector and emitter is VCE = 3 V. Load pull measurements in class-A operation of the SiGe HBT are performed at 1.9 GHz with input power ranging from 0dBm to 21 dBm.A maximum output power of 29.9dBm (about 977mW) is obtained at an input power of 18.5dBm with a gain of 11.47dB. Compared to a non-self-aligned SiGe HBT with the same heterostructure and process, fmax and fT are improved by about 83.9% and 38.3%, respectively.

  19. Dynamics of O2 Chemisorption on a Flat Platinum Surface Probed by an Alignment-Controlled O2 Beam.

    Science.gov (United States)

    Ueta, Hirokazu; Kurahashi, Mitsunori

    2017-04-03

    O2 adsorption on Pt surfaces is of great technological importance owing to its relevance to reactions for the purification of car exhaust gas and the oxygen reduction on fuel-cell electrodes. Although the O2 /Pt(111) system has been investigated intensively, questions still remain concerning the origin of the low O2 sticking probability and its unusual energy dependence. We herein clarify the alignment dependence of the initial sticking probability (S0 ) using the single spin-rotational state-selected [(J,M)=(2,2)] O2 beam. The results indicate that, at low translational energy (E0 ) conditions, direct activated chemisorption occurs only when the O2 axis is nearly parallel to the surface. At high energy conditions (E0 >0.5 eV), however, S0 for the parallel O2 decreases with increasing E0 while that of the perpendicular O2 increases, accounting for the nearly energy-independent O2 sticking probability determined previously by a non-state-resolved experiment. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Mitochondrial phylogeny of the Chrysisignita (Hymenoptera: Chrysididae) species group based on simultaneous Bayesian alignment and phylogeny reconstruction.

    Science.gov (United States)

    Soon, Villu; Saarma, Urmas

    2011-07-01

    The ignita species group within the genus Chrysis includes over 100 cuckoo wasp species, which all lead a parasitic lifestyle and exhibit very similar morphology. The lack of robust, diagnostic morphological characters has hindered phylogenetic reconstructions and contributed to frequent misidentification and inconsistent interpretations of species in this group. Therefore, molecular phylogenetic analysis is the most suitable approach for resolving the phylogeny and taxonomy of this group. We present a well-resolved phylogeny of the Chrysis ignita species group based on mitochondrial sequence data from 41 ingroup and six outgroup taxa. Although our emphasis was on European taxa, we included samples from most of the distribution range of the C. ignita species group to test for monophyly. We used a continuous mitochondrial DNA sequence consisting of 16S rRNA, tRNA(Val), 12S rRNA and ND4. The location of the ND4 gene at the 3' end of this continuous sequence, following 12S rRNA, represents a novel mitochondrial gene arrangement for insects. Due to difficulties in aligning rRNA genes, two different Bayesian approaches were employed to reconstruct phylogeny: (1) using a reduced data matrix including only those positions that could be aligned with confidence; or (2) using the full sequence dataset while estimating alignment and phylogeny simultaneously. In addition maximum-parsimony and maximum-likelihood analyses were performed to test the robustness of the Bayesian approaches. Although all approaches yielded trees with similar topology, considerably more nodes were resolved with analyses using the full data matrix. Phylogenetic analysis supported the monophyly of the C. ignita species group and divided its species into well-supported clades. The resultant phylogeny was only partly in accordance with published subgroupings based on morphology. Our results suggest that several taxa currently treated as subspecies or names treated as synonyms may in fact constitute

  1. 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...

  2. Ergodic Secret Alignment

    CERN Document Server

    Bassily, Raef

    2010-01-01

    In this paper, we introduce two new achievable schemes for the fading multiple access wiretap channel (MAC-WT). In the model that we consider, we assume that perfect knowledge of the state of all channels is available at all the nodes in a causal fashion. Our schemes use this knowledge together with the time varying nature of the channel model to align the interference from different users at the eavesdropper perfectly in a one-dimensional space while creating a higher dimensionality space for the interfering signals at the legitimate receiver hence allowing for better chance of recovery. While we achieve this alignment through signal scaling at the transmitters in our first scheme (scaling based alignment (SBA)), we let nature provide this alignment through the ergodicity of the channel coefficients in the second scheme (ergodic secret alignment (ESA)). For each scheme, we obtain the resulting achievable secrecy rate region. We show that the secrecy rates achieved by both schemes scale with SNR as 1/2log(SNR...

  3. Dynamic measurement of patello-femoral joint alignment using weight-bearing magnetic resonance imaging (WB-MRI).

    Science.gov (United States)

    Mariani, Silvia; La Marra, Alice; Arrigoni, Francesco; Necozione, Stefano; Splendiani, Alessandra; Di Cesare, Ernesto; Barile, Antonio; Masciocchi, Carlo

    2015-12-01

    Aim of our work was to compare standard and weight-bearing WB-MRI to define their contribution in unmasking patello-femoral (PF) maltracking and to define what measurement of patellar alignment is the most reliable. We prospectively collected 95 non consecutive patients, clinically divided into 2 groups: group A (the control group), including 20 patients (negative for patellar maltracking), and group B including 75 patients (positive for patellar maltracking). The patients underwent a dedicated 0.25 T MRI, in supine and WB position, with knee flexion of 12-15°. The following measurements were performed: Insall-Salvati index (IS), lateral patellar displacement (LPD), lateral patello-femoral angle (LPA) and lateral patellar tilt (LPT). Quantitative and qualitative statistical analyses were performed to compare the results obtained before and after WB-MRI. Measurements were subsequently performed on both groups. Group A patients showed no statistically significant variations at all measurements both on standard and WB-MRI. On the basis of measurements made on standard MRI, group B patients were divided into group B1 (23 patients) (negative or positive at 1 measurement) and group B2 (52 patients) (positive at 2 or more measurements). After WB-MRI, group B1 patients were divided into group B1a (6 patients), in case they remained positive at 0/1 measurement, and group B1b (17 patients), in case they became positive at 2 or more measurements. All group B2 patients confirmed to be positive at 2 or more measurements at WB-MRI. Quantitative statistical analysis showed that LPT and LPA were the most reproducible and clinically useful measurements. Qualitative statistical analysis performed on standard and WB-MRI demonstrated that LPT was the best predictive measurement. This study demonstrates both the high diagnostic value of WB-MRI in unmasking PF-maltracking and the best predictive value of LPT measurement. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  4. Aligning Theory and Design: The Development of an Online Learning Intervention to Teach Evidence-based Practice for Maximal Reach.

    Science.gov (United States)

    Delagran, Louise; Vihstadt, Corrie; Evans, Roni

    2015-09-01

    Online educational interventions to teach evidence-based practice (EBP) are a promising mechanism for overcoming some of the barriers to incorporating research into practice. However, attention must be paid to aligning strategies with adult learning theories to achieve optimal outcomes. We describe the development of a series of short self-study modules, each covering a small set of learning objectives. Our approach, informed by design-based research (DBR), involved 6 phases: analysis, design, design evaluation, redesign, development/implementation, and evaluation. Participants were faculty and students in 3 health programs at a complementary and integrative educational institution. We chose a reusable learning object approach that allowed us to apply 4 main learning theories: events of instruction, cognitive load, dual processing, and ARCS (attention, relevance, confidence, satisfaction). A formative design evaluation suggested that the identified theories and instructional approaches were likely to facilitate learning and motivation. Summative evaluation was based on a student survey (N=116) that addressed how these theories supported learning. Results suggest that, overall, the selected theories helped students learn. The DBR approach allowed us to evaluate the specific intervention and theories for general applicability. This process also helped us define and document the intervention at a level of detail that covers almost all the proposed Guideline for Reporting Evidence-based practice Educational intervention and Teaching (GREET) items. This thorough description will facilitate the interpretation of future research and implementation of the intervention. Our approach can also serve as a model for others considering online EBP intervention development.

  5. Organizational Alignment Through Information Technology: A Web-Based Approach to Change

    Science.gov (United States)

    Heinrichs, W.; Smith, J.

    1999-01-01

    This paper reports on the effectiveness of web-based internet tools and databases to facilitate integration of technical organizations with interfaces that minimize modification of each technical organization.

  6. RiboGalaxy: A browser based platform for the alignment, analysis and visualization of ribosome profiling data.

    Science.gov (United States)

    Michel, Audrey M; Mullan, James P A; Velayudhan, Vimalkumar; O'Connor, Patrick B F; Donohue, Claire A; Baranov, Pavel V

    2016-01-01

    Ribosome profiling (ribo-seq) is a technique that uses high-throughput sequencing to reveal the exact locations and densities of translating ribosomes at the entire transcriptome level. The technique has become very popular since its inception in 2009. Yet experimentalists who generate ribo-seq data often have to rely on bioinformaticians to process and analyze their data. We present RiboGalaxy ( http://ribogalaxy.ucc.ie ), a freely available Galaxy-based web server for processing and analyzing ribosome profiling data with the visualization functionality provided by GWIPS-viz ( http://gwips.ucc.ie ). RiboGalaxy offers researchers a suite of tools specifically tailored for processing ribo-seq and corresponding mRNA-seq data. Researchers can take advantage of the published workflows which reduce the multi-step alignment process to a minimum of inputs from the user. Users can then explore their own aligned data as custom tracks in GWIPS-viz and compare their ribosome profiles to existing ribo-seq tracks from published studies. In addition, users can assess the quality of their ribo-seq data, determine the strength of the triplet periodicity signal, generate meta-gene ribosome profiles as well as analyze the relative impact of mRNA sequence features on local read density. RiboGalaxy is accompanied by extensive documentation and tips for helping users. In addition we provide a forum ( http://gwips.ucc.ie/Forum ) where we encourage users to post their questions and feedback to improve the overall RiboGalaxy service.

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

    Energy Technology Data Exchange (ETDEWEB)

    Burkhard, Boeckem [Institute for Geodesy and Photogrammetry, ETH Zurich (Switzerland)

    1999-07-01

    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 {delta}{beta}, is to first approximation proportional to the refraction angle: {beta}{sub IR} {nu}({beta}{sub blue} - {beta}{sub IR}) = {nu} {delta}{beta}, 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

  8. Fusion angle affects intervertebral adjacent spinal segment joint forces-Model-based analysis of patient specific alignment.

    Science.gov (United States)

    Senteler, Marco; Weisse, Bernhard; Rothenfluh, Dominique A; Farshad, Mazda T; Snedeker, Jess G

    2017-01-01

    This study addresses the hypothesis that adjacent segment intervertebral joint loads are sensitive to the degree of lordosis that is surgically imposed during vertebral fusion. Adjacent segment degeneration is often observed after lumbar fusion, but a causative mechanism is not yet clearly evident. Altered kinematics of the adjacent segments and potentially nonphysiological mechanical joint loads have been implicated in this process. However, little is known of how altered alignment and kinematics influence loading of the adjacent intervertebral joints under consideration of active muscle forces. This study investigated these effects by simulating L4/5 fusions using kinematics-driven musculoskeletal models of one generic and eight sagittal alignment-specific models. Models featured different spinopelvic configurations but were normalized by body height, masses, and muscle properties. Fusion of the L4/5 segment was implemented in an in situ (22°), hyperlordotic (32°), and hypolordotic (8°) fashion and kinematic input parameters were changed accordingly based on findings of an in vitro investigation. Bending motion from upright standing to 45° forward flexion and back was simulated for all models in intact and fused conditions. Joint loads at adjacent levels and moment arms of spinal muscles experienced changes after all types of fusion. Hypolordotic configuration led to an increase of adjacent segment (L3/4) shear forces of 29% on average, whereas hyperlordotic fusion reduced shear by 39%. Overall, L4/5 in situ fusion resulted in intervertebral joint forces closest to intact loading conditions. An artificial decrease in lumbar lordosis (minus 14° on average) caused by an L4/5 fusion lead to adverse loading conditions, particularly at the cranial adjacent levels, and altered muscle moment arms, in particular for muscles in the vicinity of the fusion. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:131-139, 2017.

  9. Dynamic Analysis of Multilayers Based MEMS Resonators

    Directory of Open Access Journals (Sweden)

    Hassen M. Ouakad

    2017-01-01

    Full Text Available The dynamic behavior of a microelectromechanical system (MEMS parallel and electrically coupled double-layers (microbeams based resonator is investigated. Two numerical methods were used to solve the dynamical problem: the reduced-order modeling (ROM and the perturbation method. The ROM was derived using the so-called Galerkin expansion with considering the linear undamped mode shapes of straight beam as the basis functions. The perturbation method was generated using the method of multiple scales by direct attack of the equations of motion. Dynamic analyses, assuming the above two numerical methods were performed, and a comparison of the results showed good agreement. Finally, a parametric study was performed using the perturbation on different parameters and the results revealed different interesting features, which hopefully can be useful for some MEMS based applications.

  10. Vertically aligned carbon nanotube field emitter arrays with Ohmic base contact to silicon by Fe-catalyzed chemical vapor deposition

    NARCIS (Netherlands)

    Morassutto, M.; Tiggelaar, Roald M.; Smithers, M.A.; Smithers, M.A.; Gardeniers, Johannes G.E.

    2016-01-01

    Abstract In this study, dense arrays of aligned carbon nanotubes are obtained by thermal catalytic chemical vapor deposition, using Fe catalyst dispersed on a thin Ta layer. Alignment of the carbon nanotubes depends on the original Fe layer thickness from which the catalyst dispersion is obtained by

  11. Nearly complete rRNA genes from 371 Animalia: updated structure-based alignment and detailed phylogenetic analysis.

    Science.gov (United States)

    Mallatt, Jon; Craig, Catherine Waggoner; Yoder, Matthew J

    2012-09-01

    This study presents a manually constructed alignment of nearly complete rRNA genes from most animal clades (371 taxa from ~33 of the ~36 metazoan phyla), expanded from the 197 sequences in a previous study. This thorough, taxon-rich alignment, available at http://www.wsu.edu/~jmallatt/research/rRNAalignment.html and in the Dryad Repository (doi: http://dx.doi.org/10.5061/dryad.1v62kr3q), is based rigidly on the secondary structure of the SSU and LSU rRNA molecules, and is annotated in detail, including labeling of the erroneous sequences (contaminants). The alignment can be used for future studies of the molecular evolution of rRNA. Here, we use it to explore if the larger number of sequences produces an improved phylogenetic tree of animal relationships. Disappointingly, the resolution did not improve, neither when the standard maximum-likelihood method was used, nor with more sophisticated methods that partitioned the rRNA into paired and unpaired sites (stem, loop, bulge, junction), or accounted for the evolution of the paired sites. For example, no doublet model of paired-site substitutions (16-state, 16A and 16B, 7A-F, or 6A-C models) corrected the placement of any rogue taxa or increased resolution. The following findings are from the simplest, standard, ML analysis. The 371-taxon tree only imperfectly supported the bilaterian clades of Lophotrochozoa and Ecdysozoa, and this problem remained after 17 taxa with unstably positioned sequences were omitted from the analysis. The problem seems to stem from base-compositional heterogeneity across taxa and from an overrepresentation of highly divergent sequences among the newly added taxa (e.g., sequences from Cephalopoda, Rotifera, Acoela, and Myxozoa). The rogue taxa continue to concentrate in two locations in the rRNA tree: near the base of Arthropoda and of Bilateria. The approximately uncertain (AU) test refuted the monophyly of Mollusca and of Chordata, probably due to long-branch attraction of the highly

  12. Haptics-based dynamic implicit solid modeling.

    Science.gov (United States)

    Hua, Jing; Qin, Hong

    2004-01-01

    This paper systematically presents a novel, interactive solid modeling framework, Haptics-based Dynamic Implicit Solid Modeling, which is founded upon volumetric implicit functions and powerful physics-based modeling. In particular, we augment our modeling framework with a haptic mechanism in order to take advantage of additional realism associated with a 3D haptic interface. Our dynamic implicit solids are semi-algebraic sets of volumetric implicit functions and are governed by the principles of dynamics, hence responding to sculpting forces in a natural and predictable manner. In order to directly manipulate existing volumetric data sets as well as point clouds, we develop a hierarchical fitting algorithm to reconstruct and represent discrete data sets using our continuous implicit functions, which permit users to further design and edit those existing 3D models in real-time using a large variety of haptic and geometric toolkits, and visualize their interactive deformation at arbitrary resolution. The additional geometric and physical constraints afford more sophisticated control of the dynamic implicit solids. The versatility of our dynamic implicit modeling enables the user to easily modify both the geometry and the topology of modeled objects, while the inherent physical properties can offer an intuitive haptic interface for direct manipulation with force feedback.

  13. Component alignment and functional outcome following computer assisted and jig based total knee arthroplasty

    Directory of Open Access Journals (Sweden)

    Dnyanesh G Lad

    2013-01-01

    Conclusions: A significantly improved placement of the component was found in the coronal and sagittal planes of the tibial component by CAS. The placement of the components in the other planes was comparable with the values recorded in the jig-based surgery group. Functional outcome was not significantly different.

  14. Aligning Cost Assessment with Community-Based Participatory Research: The Kin Keeper (superscript SM) Intervention

    Science.gov (United States)

    Meghea, Cristian Ioan; Williams, Karen Patricia

    2015-01-01

    The few existing economic evaluations of community-based health promotion interventions were reported retrospectively at the end of the trial. We report an evaluation of the costs of the Kin Keeper(superscript SM) Cancer Prevention Intervention, a female family-focused educational intervention for underserved women applied to increase breast and…

  15. Aligning Web-Based Tools to the Research Process Cycle: A Resource for Collaborative Research Projects

    Science.gov (United States)

    Price, Geoffrey P.; Wright, Vivian H.

    2012-01-01

    Using John Creswell's Research Process Cycle as a framework, this article describes various web-based collaborative technologies useful for enhancing the organization and efficiency of educational research. Visualization tools (Cacoo) assist researchers in identifying a research problem. Resource storage tools (Delicious, Mendeley, EasyBib)…

  16. The South African legislative environment, in critical need of scientific evidence based alignment for airborne control

    CSIR Research Space (South Africa)

    Fleming, EJ

    2014-07-01

    Full Text Available Review of evidence based research indicates that there are best practice principles that can be applied to the design of the built environment with regard to the reduction of the risk of cross infection from airborne diseases in health facilities...

  17. Aligning Web-Based Tools to the Research Process Cycle: A Resource for Collaborative Research Projects

    Science.gov (United States)

    Price, Geoffrey P.; Wright, Vivian H.

    2012-01-01

    Using John Creswell's Research Process Cycle as a framework, this article describes various web-based collaborative technologies useful for enhancing the organization and efficiency of educational research. Visualization tools (Cacoo) assist researchers in identifying a research problem. Resource storage tools (Delicious, Mendeley, EasyBib)…

  18. Automatic array alignment in data-parallel programs

    Science.gov (United States)

    Chatterjee, Siddhartha; Gilbert, John R.; Schreiber, Robert; Teng, Shang-Hua

    1993-01-01

    FORTRAN 90 and other data-parallel languages express parallelism in the form of operations on data aggregates such as arrays. Misalignment of the operands of an array operation can reduce program performance on a distributed-memory parallel machine by requiring nonlocal data accesses. Determining array alignments that reduce communication is therefore a key issue in compiling such languages. We present a framework for the automatic determination of array alignments in array-based, data-parallel languages. Our language model handles array sectioning, reductions, spreads, transpositions, and masked operations. We decompose alignment functions into three constituents: axis, stride, and offset. For each of these subproblems, we show how to solve the alignment problem for a basic block of code, possibly containing common subexpressions. Alignments are generated for all array objects in the code, both named program variables and intermediate results. We assign computation to processors by virtue of explicit alignment of all temporaries; the resulting work assignment is in general better than that provided by the 'owner-computes' rule. Finally, we present some ideas for dealing with control flow, replication, and dynamic alignments that depend on loop induction variables.

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

  20. 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...

  1. Towards 3D ultrasound image based soft tissue tracking: a transrectal ultrasound prostate image alignment system

    CERN Document Server

    Baumann, Michael; Daanen, Vincent; Troccaz, Jocelyne

    2007-01-01

    The emergence of real-time 3D ultrasound (US) makes it possible to consider image-based tracking of subcutaneous soft tissue targets for computer guided diagnosis and therapy. We propose a 3D transrectal US based tracking system for precise prostate biopsy sample localisation. The aim is to improve sample distribution, to enable targeting of unsampled regions for repeated biopsies, and to make post-interventional quality controls possible. Since the patient is not immobilized, since the prostate is mobile and due to the fact that probe movements are only constrained by the rectum during biopsy acquisition, the tracking system must be able to estimate rigid transformations that are beyond the capture range of common image similarity measures. We propose a fast and robust multi-resolution attribute-vector registration approach that combines global and local optimization methods to solve this problem. Global optimization is performed on a probe movement model that reduces the dimensionality of the search space a...

  2. 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.

  3. Shape-based assessment of vertebral fracture risk in postmenopausal women using discriminative shape alignment

    DEFF Research Database (Denmark)

    Crimi, Alessandro; Loog, Marco; de Bruijne, Marleen

    2012-01-01

    but the result of a decaying process. To evaluate fracture risk, a shape-based classifier, identifying possible small prefracture deformities, may be constructed. MATERIALS AND METHODS: During a longitudinal case-control study, a large population of postmenopausal women, fracture free at baseline, were followed....... The 22 women who sustained at least one lumbar fracture on follow-up represented the case group. The control group comprised 91 women who maintained skeletal integrity and matched the case group according to the standard osteoporosis risk factors. On radiographs, a radiologist and two technicians...

  4. Aligned carbon nanotubes catalytically grown on iron-based nanoparticles obtained by laser-induced CVD

    OpenAIRE

    Le Normand, Francois; Cojocaru, Costel Sorin; Ersen, Ovidiu; Legagneux, Pierre; Gangloff, Laurent; Fleaca, C.; Alexandrescu, Rodica; Dumitrache, Florin; Morjan, Ion

    2007-01-01

    International audience; Iron-based nanoparticles are prepared by a laser-induced chemical vapor deposition (CVD) process. They are characterized as body-centered Fe and Fe2O3 (maghemite/magnetite) particles with sizes ::;5 and 10 nm, respectively. The Fe particles are embedded in a protective carbon matrix. Both kind of particles are dispersed by spin-coating on SiO2/Si(1 0 0) flat substrates. They are used as catalyst to grow carbon nanotubes by a plasma- and filaments-assisted catalytic CVD...

  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. Vertically aligned ZnO nanorod grown by hydrothermal based chemical method on glass substrate

    Science.gov (United States)

    Srivastava, R.; Majumdar, S.; Bhunia, S.

    2012-06-01

    A low-temperature and effective precursor-based method has been demonstrated to synthesize nanostructured ZnO. It is found that the morphology of ZnO precursors has a strong dependence on the reaction conditions that include the molar ratio of reagents, solvent, and reaction temperature. In this work, ZnO nanostructures were synthesized via hydrothermal based chemical method. Zinc acetate dehydrate [Zn(Ac)2 2H2O] and 1-propanol(C3H8O) were adopted for a seed layer growth on glass substrate via spin coating technique. Zinc nitrate hexahydrate [Zn(NO3)2 6H2O], hexamethylenetetramine(C6H12N4) and diethylamine(C4H11N) were adopted as synthesis precursors. The ZnO nanostructures obtained were characterized by scanning electronic microscopy (SEM) and the PL method. The SEM image of the sample showed that the thin film of ZnO on glass substrate has, predominantly, a nanometric rod-like morphology with hexagonal wurtzite structure.

  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. ALIGNING INFORMATION SECURITY WITH THE IMAGE OF THE ORGANIZATION AND PRIORITIZATION BASED ON FUZZY LOGIC FOR THE INDUSTRIAL AUTOMATION SECTOR

    Directory of Open Access Journals (Sweden)

    Adolfo Alberto Vanti

    2011-12-01

    Full Text Available This paper develops the strategic alignment of organizational behavior through the organizations´ image, prioritization and information security practices. To this end, information security is studied based on the business requirements of confidentiality, integrity and availability by applying a tool which integrates the strategic, tactical and operational vision through the following framework: Balanced Scorecard - BSC (strategic x Control Objectives for Information and Related Technology - COBIT (tactical x International Organization for Standardization - ISO/International Electro Technical Commission - IEC27002 (operational. Another image instrument of the organization is applied in parallel with this analysis to identify and analyze performance involving profiles related to mechanistic, psychic prisons, political systems, instruments of domination, organisms, cybernetics, flux and transformation (MORGAN, 1996. Finally, a model of strategic prioritization, based on compensatory fuzzy logic (ESPIN and VANTI, 2005, is applied. The method was applied to an industrial company located in southern Brazil. The results with the application show two organizational images: "organism" and "flux and transformation ". The strategic priorities indicated a significant search for new business services and international markets. Regarding protection of information, security found the gap between "minimum" and "Reasonable" and in domain 8 (HR of standard ISO/IEC27002, considered 71% protection as "inappropriate" and "minimal" in the IT Governance context.

  9. Acoustic Emission Analysis of Damage during Compressive Deformation of Amorphous Zr-Based Foams with Aligned, Elongated Pores

    Science.gov (United States)

    Cox, Marie E.; Dunand, David C.

    2013-07-01

    Acoustic emission methods are used to investigate the evolution of internal microfractural damage during uniaxial compression of amorphous Zr-based foams with aligned, elongated pores. The foams are fabricated by means of densifying a blend of crystalline W powders and amorphous Zr-based powders with two oxygen contents (0.078 and 0.144 wt pct) by warm equal channel angular extrusion, followed by dissolution of the elongated W phase from the fully densified amorphous matrix. For the high-oxygen foams, prior powder boundaries in the amorphous struts promote damage that accumulates during compression, resulting in energy-absorbing properties comparable with the low-oxygen foams without stress-concentrating powder boundaries. The influence of pore orientation on the evolution of microfracture damage and the ability of the foams to accumulate damage without catastrophic failure is also investigated: pores oriented from 24 to 68 deg to the loading direction promote wall bending, resulting in foams with more diffuse damage and better energy-absorbing properties.

  10. CoMFA 3D-QSAR Analysis of Epothilones Based on Docking Conformation and Alignment

    Institute of Scientific and Technical Information of China (English)

    YUAN,Wei; LUAN,Lin-Bo; LI,Yan-Ni

    2007-01-01

    Epothilones belong to a class of novel microtubule stabilizing and anti-mitotic agents.which have a paclitaxel-like mechanism of action.A three-dimensional quantitative structure-activity relationship(3D-QSAR)model was built for epothilones by the method of comparative molecular field analysis (CoMFA)combined with the flexible docking technology.The docking CoMFA model gave a good cross-validated value of q2=0.784 with an optimized component of 6 and the conventional correlation coefficient of r2=0.985.The statistical results show that the model has good ability to predict the activity of the studied compounds.At last.the docking CoMFA model was analyzed through contour maps complemented with MOLCAD-generated active site potential surface in the α,β-tubulin receptor,which can provide important information for the structure-based drug design.

  11. Aligned carbon nanotubes catalytically grown on iron-based nanoparticles obtained by laser-induced CVD

    Energy Technology Data Exchange (ETDEWEB)

    Le Normand, F. [Groupe Surfaces and Interfaces, IPCMS, UMR 7504 CNRS, Bat 70, 23 rue du Loess, 67034 Strasbourg Cedex (France)], E-mail: Francois.Le-Normand@ipcms.u-strasbg.fr; Cojocaru, C.S.; Ersen, O. [Groupe Surfaces and Interfaces, IPCMS, UMR 7504 CNRS, Bat 70, 23 rue du Loess, 67034 Strasbourg Cedex (France); Legagneux, P.; Gangloff, L. [THALES R and T, Departementale 128, 91747 Palaiseau Cedex (France); Fleaca, C. [Groupe Surfaces and Interfaces, IPCMS, UMR 7504 CNRS, Bat 70, 23 rue du Loess, 67034 Strasbourg Cedex (France); National Institute for Lasers, Plasma and Radiation Physics, Laser Department, P.O. Box MG-36, R-76900 Bucharest (Romania); Alexandrescu, R.; Dumitrache, F.; Morjan, I. [National Institute for Lasers, Plasma and Radiation Physics, Laser Department, P.O. Box MG-36, R-76900 Bucharest (Romania)

    2007-12-15

    Iron-based nanoparticles are prepared by a laser-induced chemical vapor deposition (CVD) process. They are characterized as body-centered Fe and Fe{sub 2}O{sub 3} (maghemite/magnetite) particles with sizes {<=}5 and 10 nm, respectively. The Fe particles are embedded in a protective carbon matrix. Both kind of particles are dispersed by spin-coating on SiO{sub 2}/Si(1 0 0) flat substrates. They are used as catalyst to grow carbon nanotubes by a plasma- and filaments-assisted catalytic CVD process (PE-HF-CCVD). Vertically oriented and thin carbon nanotubes (CNTs) were grown with few differences between the two samples, except the diameter in relation to the initial size of the iron particles, and the density. The electron field emission of these samples exhibit quite interesting behavior with a low turn-on voltage at around 1 V/{mu}m.

  12. Aligned carbon nanotubes catalytically grown on iron-based nanoparticles obtained by laser-induced CVD

    Science.gov (United States)

    Le Normand, F.; Cojocaru, C. S.; Ersen, O.; Legagneux, P.; Gangloff, L.; Fleaca, C.; Alexandrescu, R.; Dumitrache, F.; Morjan, I.

    2007-12-01

    Iron-based nanoparticles are prepared by a laser-induced chemical vapor deposition (CVD) process. They are characterized as body-centered Fe and Fe 2O 3 (maghemite/magnetite) particles with sizes ≤5 and 10 nm, respectively. The Fe particles are embedded in a protective carbon matrix. Both kind of particles are dispersed by spin-coating on SiO 2/Si(1 0 0) flat substrates. They are used as catalyst to grow carbon nanotubes by a plasma- and filaments-assisted catalytic CVD process (PE-HF-CCVD). Vertically oriented and thin carbon nanotubes (CNTs) were grown with few differences between the two samples, except the diameter in relation to the initial size of the iron particles, and the density. The electron field emission of these samples exhibit quite interesting behavior with a low turn-on voltage at around 1 V/μm.

  13. Control of a Thrust Alignment Table for Modeling the Coning Dynamics of a Spinning Spacecraft with a Follower Force

    Science.gov (United States)

    Halsmer, Dominic; Bennett, J. Damon; DeHaven, Max; Ligard, Vidar

    1999-01-01

    This document presents a system controlling the motion of a spherical air bearing used in the modeling of spacecraft dynamics and controls in a laboratory environment. The system is part of the Spinning Rocket Simulator (SRS), used to simulate the coning of spacecraft during a thrusting stage. The reaction force at the spherical air bearing supporting the spacecraft model must coincide with the thrust axis of the model for proper simulation. Therefore, the bearing is translated in a circular path to introduce a centrifugal force. This horizontal force along with the gravitational reaction force at the bearing combines to simulate the direction of the spacecraft's thrust force. The control system receives attitude information from the spacecraft model via a laser beam embedded in the model that impinges on a photosensitive array. The non-linear system is controlled using high-speed lookup tables and digital techniques. A vector-controlled motor and a stepper motor are given the necessary signals to accurately control the turntable and platform supporting the air bearing. Preliminary performance data is presented. Mechanical elements of the table and platform are described in detail. A wireless (RF) data path for all devices on the spacecraft model to an off-table command computer is also described.

  14. Orbit Alignment in Triple Stars

    Science.gov (United States)

    Tokovinin, Andrei

    2017-08-01

    The statistics of the angle Φ between orbital angular momenta in hierarchical triple systems with known inner visual or astrometric orbits are studied. A correlation between apparent revolution directions proves the partial orbit alignment known from earlier works. The alignment is strong in triples with outer projected separation less than ∼50 au, where the average Φ is about 20^\\circ . In contrast, outer orbits wider than 1000 au are not aligned with the inner orbits. It is established that the orbit alignment decreases with the increasing mass of the primary component. The average eccentricity of inner orbits in well-aligned triples is smaller than in randomly aligned ones. These findings highlight the role of dissipative interactions with gas in defining the orbital architecture of low-mass triple systems. On the other hand, chaotic dynamics apparently played a role in shaping more massive hierarchies. The analysis of projected configurations and triples with known inner and outer orbits indicates that the distribution of Φ is likely bimodal, where 80% of triples have {{Φ }}< 70^\\circ and the remaining ones are randomly aligned.

  15. Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS): A web-based tool for addressing the challenges of cross-species extrapolation of chemical toxicity

    Science.gov (United States)

    Conservation of a molecular target across species can be used as a line-of-evidence to predict the likelihood of chemical susceptibility. The web-based Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool was developed to simplify, streamline, and quantitat...

  16. Thermal Conductivity of Polymer-Based Composites with Magnetic Aligned Hexagonal Boron Nitride Platelets.

    Science.gov (United States)

    Yuan, Chao; Duan, Bin; Li, Lan; Xie, Bin; Huang, Mengyu; Luo, Xiaobing

    2015-06-17

    Hexagonal boron nitride (hBN) platelets are widely used as the reinforcing fillers for enhancing the thermal conductivity of polymer-based composites. Since hBN platelets have high aspect ratio and show a highly anisotropic thermal property, the thermal conductivity of the hBNs-filled composites should be strongly associated with the platelets' orientation. However, the orientation effect has been explored less frequently due to the technical difficulties in precontrol of the platelets' orientation in the polymer matrix. In this paper, we report the use of magnetic fields to assemble the platelets into various microstructures and to study the thermal conductivities of the designed composites. The experimental results showed that thermal conductivities are dramatically different among these composites. For instance, the thermal conductivities of the composites with platelets oriented parallel and perpendicular to the heat flux direction are respectively 44.5% higher and 37.9% lower than that of unaligned composites at the volume fraction of 9.14%. The results were also analyzed by a theoretical model. The model suggests that the orientation of the hBN platelets is the main reason for the variance in the thermal conductivity.

  17. Dynamic reliability of digital-based transmitters

    Energy Technology Data Exchange (ETDEWEB)

    Brissaud, Florent, E-mail: florent.brissaud.2007@utt.f [Institut National de l' Environnement Industriel et des Risques (INERIS), Parc Technologique Alata, BP 2, 60550 Verneuil-en-Halatte (France) and Universite de Technologie de Troyes - UTT, Institut Charles Delaunay - ICD and UMR CNRS 6279 STMR, 12 rue Marie Curie, BP 2060, 10010 Troyes Cedex (France); Smidts, Carol [Ohio State University (OSU), Nuclear Engineering Program, Department of Mechanical Engineering, Scott Laboratory, 201 W 19th Ave, Columbus OH 43210 (United States); Barros, Anne; Berenguer, Christophe [Universite de Technologie de Troyes (UTT), Institut Charles Delaunay (ICD) and UMR CNRS 6279 STMR, 12 rue Marie Curie, BP 2060, 10010 Troyes Cedex (France)

    2011-07-15

    Dynamic reliability explicitly handles the interactions between the stochastic behaviour of system components and the deterministic behaviour of process variables. While dynamic reliability provides a more efficient and realistic way to perform probabilistic risk assessment than 'static' approaches, its industrial level applications are still limited. Factors contributing to this situation are the inherent complexity of the theory and the lack of a generic platform. More recently the increased use of digital-based systems has also introduced additional modelling challenges related to specific interactions between system components. Typical examples are the 'intelligent transmitters' which are able to exchange information, and to perform internal data processing and advanced functionalities. To make a contribution to solving these challenges, the mathematical framework of dynamic reliability is extended to handle the data and information which are processed and exchanged between systems components. Stochastic deviations that may affect system properties are also introduced to enhance the modelling of failures. A formalized Petri net approach is then presented to perform the corresponding reliability analyses using numerical methods. Following this formalism, a versatile model for the dynamic reliability modelling of digital-based transmitters is proposed. Finally the framework's flexibility and effectiveness is demonstrated on a substantial case study involving a simplified model of a nuclear fast reactor.

  18. Evaluating a community-based program to improve healthcare quality: research design for the Aligning Forces for Quality initiative.

    Science.gov (United States)

    Scanlon, Dennis P; Alexander, Jeffrey A; Beich, Jeff; Christianson, Jon B; Hasnain-Wynia, Romana; McHugh, Megan C; Mittler, Jessica N; Shi, Yunfeng; Bodenschatz, Laura J

    2012-09-01

    The Aligning Forces for Quality (AF4Q) initiative is the Robert Wood Johnson Foundation's (RWJF's) signature effort to increase the overall quality of healthcare in targeted communities throughout the country. In addition to sponsoring this 16-site, complex program, the RWJF funds an independent scientific evaluation to support objective research on the initiative's effectiveness and contributions to basic knowledge in 5 core programmatic areas. The research design, data, and challenges faced in the evaluation of this 10-year initiative are discussed. A descriptive overview of the evaluation research design for a multi-site, community based, healthcare quality improvement initiative is provided. The multiphase research design employed by the evaluation team is discussed. Evaluation provides formative feedback to the RWJF, participants, and other interested audiences in real time; develops approaches to assess innovative and under-studied interventions; furthers the analysis and understanding of effective community-based collaborative work in healthcare; and helps to differentiate the various facilitators, barriers, and contextual dimensions that affect the implementation and outcomes of community-based health interventions. The AF4Q initiative is arguably the largest community-level healthcare improvement demonstration in the United States to date; it is being implemented at a time of rapid change in national healthcare policy. The implementation of large-scale, multi-site initiatives is becoming an increasingly common approach for addressing problems in healthcare. The evaluation research design for the AF4Q initiative, and the lessons learned from its approach, may be valuable to others tasked with evaluating similar community-based initiatives.

  19. Keystroke Dynamics-Based Credential Hardening Systems

    Science.gov (United States)

    Bartlow, Nick; Cukic, Bojan

    abstract Keystroke dynamics are becoming a well-known method for strengthening username- and password-based credential sets. The familiarity and ease of use of these traditional authentication schemes combined with the increased trustworthiness associated with biometrics makes them prime candidates for application in many web-based scenarios. Our keystroke dynamics system uses Breiman’s random forests algorithm to classify keystroke input sequences as genuine or imposter. The system is capable of operating at various points on a traditional ROC curve depending on application-specific security needs. As a username/password authentication scheme, our approach decreases the system penetration rate associated with compromised passwords up to 99.15%. Beyond presenting results demonstrating the credential hardening effect of our scheme, we look into the notion that a user’s familiarity to components of a credential set can non-trivially impact error rates.

  20. Coarse Alignment of Marine Strapdown INS Based on the Trajectory Fitting of Gravity Movement in the Inertial Space

    Directory of Open Access Journals (Sweden)

    Lin Zhao

    2016-10-01

    Full Text Available A ship experiences the random motion of sea waves during its travels. Hence, the coarse alignment of the marine strapdown Inertial Navigation System (INS suffers from rocking disturbances such as pitch and roll. In this paper, a novel approach of marine coarse alignment was proposed for avoiding the resulting loss of accuracy from rocking disturbances. Unlike several current techniques, our alignment scheme is intuitional and concise. Moreover, the coarse alignment can be implemented without any external information. The gravity vector and its derivative expressed within the inertial frame can describe the attitude matrix between an inertial frame and the local geographic frame. We address the challenge of calculating the gravity derivative by the least-squares fitting of the trajectory of the gravity movement in the inertial frame. Meanwhile, the integration of angular rates measured by gyroscopes allows one to compute the attitude matrix between the inertial frame and the body frame. The coarse alignment can be thus accomplished by the combination of the above two attitude matrices. The experimental results show that the coarse alignment is effective with high accuracy and stability for demanding marine applications.

  1. Lasso整脸形状回归的人脸配准算法%Lasso Based Shape Regression for Face Alignment

    Institute of Scientific and Technical Information of China (English)

    杨律; 丁守鸿; 谢志峰; 马利庄

    2015-01-01

    人脸配准是人脸识别、美化和面部表情分析等人脸相关应用的重要组成部分,这些应用通过人脸配准以精准定位人脸五官及面部轮廓特征点。在整脸形状回归的人脸配准框架基础上,使用 Lasso 回归来解决人脸配准问题,提出基于 Lasso 的整脸回归人脸配准算法。首先对人脸配准过程中的回归系数施加 L1模惩罚,以在不牺牲效果的基础上减少模型大小;然后提出人脸变换比例调整方法,在回归过程中使用人脸变换比例对特征点位置进行调整,用于解决小规模样本条件下不同尺度样本相互干扰的问题。在相关数据集上的实验结果表明,该算法配准精确度高,可以达到实时的速度,且适用于不同姿态下的人脸配准问题。%Face alignment focuses on the problem for localizing facial landmarks and it is an important topic of face recognition, beautification and facial expression analysis etc. Based on Explicit Shape Regression (ESR) framework, we proposed a face alignment algorithm using Lasso regression by adding aL1 norm con-straint on the model parameters to reduce the size of shape model while maintaining the resultant perform-ance. Meanwhile, a face ratio transformation method is proposed by using the face ratio to adjust the estima-tion result of face landmarks. The method can be used to solve the problem of mutual influence among various training samples in different scales. Experimental results show that the overall system performs well in related dataset and it can run in real-time and be insensitive to human faces in multiple poses.

  2. Strategy-aligned fuzzy approach for market segment evaluation and selection: a modular decision support system by dynamic network process (DNP)

    Science.gov (United States)

    Mohammadi Nasrabadi, Ali; Hosseinpour, Mohammad Hossein; Ebrahimnejad, Sadoullah

    2013-05-01

    In competitive markets, market segmentation is a critical point of business, and it can be used as a generic strategy. In each segment, strategies lead companies to their targets; thus, segment selection and the application of the appropriate strategies over time are very important to achieve successful business. This paper aims to model a strategy-aligned fuzzy approach to market segment evaluation and selection. A modular decision support system (DSS) is developed to select an optimum segment with its appropriate strategies. The suggested DSS has two main modules. The first one is SPACE matrix which indicates the risk of each segment. Also, it determines the long-term strategies. The second module finds the most preferred segment-strategies over time. Dynamic network process is applied to prioritize segment-strategies according to five competitive force factors. There is vagueness in pairwise comparisons, and this vagueness has been modeled using fuzzy concepts. To clarify, an example is illustrated by a case study in Iran's coffee market. The results show that success possibility of segments could be different, and choosing the best ones could help companies to be sure in developing their business. Moreover, changing the priority of strategies over time indicates the importance of long-term planning. This fact has been supported by a case study on strategic priority difference in short- and long-term consideration.

  3. SLAM - Based Approach to Dynamic Ship Positioning

    Directory of Open Access Journals (Sweden)

    Krzysztof Wrobel

    2014-03-01

    Full Text Available Dynamically positioned vessels, used by offshore industry, use not only satellite navigation but also different positioning systems, often referred to as reference' systems. Most of them use multiple technical devices located outside the vessel which creates some problems with their accessibility and performance. In this paper, a basic concept of reference system independent from any external device is presented, basing on hydroacoustics and Simultaneous Localization and Mapping (SLAM method. Theoretical analysis of its operability is also performed.

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

    Science.gov (United States)

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

    2009-01-01

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

  5. Fabrication and Optimization of Vertically Aligned ZnO Nanorod Array-Based UV Photodetectors via Selective Hydrothermal Synthesis

    Science.gov (United States)

    Ko, Yeong Hwan; Nagaraju, Goli; Yu, Jae Su

    2015-08-01

    Vertically aligned ZnO nanorod array (NRA)-based ultraviolet (UV) photodetectors (PDs) were successfully fabricated and optimized via a facile hydrothermal process. Using a shadow mask technique, the thin ZnO seed layer was deposited between the patterned Au/Ti electrodes to bridge the electrodes. Thus, both the Au electrodes could be connected by the ZnO seed layer. As the sample was immersed into growth solution and heated at 90 °C, the ZnO NRAs were crystallized and vertically grown on the ZnO seed layer, thus creating a metal-semiconductor-metal PD structure. To investigate the size effect of ZnO NRAs on photocurrent, the PDs were readily prepared with different concentrations of growth solution. For the ZnO NRAs grown at 25 mM of concentration, the PD with 10 μm of channel width (i.e., gap distance between two electrodes) exhibited a high photocurrent of 1.91 × 10-4 A at an applied bias of 10 V under 365 nm of UV light illumination. The PD was optimized by adjusting the channel width. For 15 μm of channel width, a relatively high photocurrent on-off ratio of 37.4 and good current transient characteristics were observed at the same applied bias. These results are expected to be useful for cost-effective and practical UV PD applications.

  6. Liquid crystal alignment in electro-responsive nanostructured thermosetting materials based on block copolymer dispersed liquid crystal

    Energy Technology Data Exchange (ETDEWEB)

    Tercjak, A; Garcia, I; Mondragon, I [Materials-Technologies Group, Departamento IngenierIa Quimica y M Ambiente, Escuela Politecnica, Universidad PaIs Vasco/Euskal Herriko Unibertsitatea, Plaza Europa 1, E-20018 Donostia-San Sebastian (Spain)], E-mail: scptesza@sc.ehu.es, E-mail: inaki.mondragon@ehu.es

    2008-07-09

    Novel well-defined nanostructured thermosetting systems were prepared by modification of a diglicydylether of bisphenol-A epoxy resin (DGEBA) with 10 or 15 wt% amphiphilic poly(styrene-b-ethylene oxide) block copolymer (PSEO) and 30 or 40 wt% low molecular weight liquid crystal 4'-(hexyl)-4-biphenyl-carbonitrile (HBC) using m-xylylenediamine (MXDA) as a curing agent. The competition between well-defined nanostructured materials and the ability for alignment of the liquid crystal phase in the materials obtained has been studied by atomic and electrostatic force microscopy, AFM and EFM, respectively. Based on our knowledge, this is the first time that addition of an adequate amount (10 wt%) of a block copolymer to 40 wt% HBC-(DGEBA/MXDA) leads to a well-organized nanostructured thermosetting system (between a hexagonal and worm-like ordered structure), which is also electro-responsive with high rate contrast. This behavior was confirmed using electrostatic force microscopy (EFM), by means of the response of the HBC liquid crystal phase to the voltage applied to the EFM tip. In contrast, though materials containing 15 wt% PSEO and 30 wt% HBC also form a well-defined nanostructured thermosetting system, they do not show such a high contrast between the uncharged and charged surface.

  7. Liquid crystal alignment in electro-responsive nanostructured thermosetting materials based on block copolymer dispersed liquid crystal

    Science.gov (United States)

    Tercjak, A.; Garcia, I.; Mondragon, I.

    2008-07-01

    Novel well-defined nanostructured thermosetting systems were prepared by modification of a diglicydylether of bisphenol-A epoxy resin (DGEBA) with 10 or 15 wt% amphiphilic poly(styrene-b-ethylene oxide) block copolymer (PSEO) and 30 or 40 wt% low molecular weight liquid crystal 4'-(hexyl)-4-biphenyl-carbonitrile (HBC) using m-xylylenediamine (MXDA) as a curing agent. The competition between well-defined nanostructured materials and the ability for alignment of the liquid crystal phase in the materials obtained has been studied by atomic and electrostatic force microscopy, AFM and EFM, respectively. Based on our knowledge, this is the first time that addition of an adequate amount (10 wt%) of a block copolymer to 40 wt% HBC-(DGEBA/MXDA) leads to a well-organized nanostructured thermosetting system (between a hexagonal and worm-like ordered structure), which is also electro-responsive with high rate contrast. This behavior was confirmed using electrostatic force microscopy (EFM), by means of the response of the HBC liquid crystal phase to the voltage applied to the EFM tip. In contrast, though materials containing 15 wt% PSEO and 30 wt% HBC also form a well-defined nanostructured thermosetting system, they do not show such a high contrast between the uncharged and charged surface.

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

    Directory of Open Access Journals (Sweden)

    Xin Yi Ng

    2015-01-01

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

  9. Fabrication and Optimization of Vertically Aligned ZnO Nanorod Array-Based UV Photodetectors via Selective Hydrothermal Synthesis.

    Science.gov (United States)

    Ko, Yeong Hwan; Nagaraju, Goli; Yu, Jae Su

    2015-12-01

    Vertically aligned ZnO nanorod array (NRA)-based ultraviolet (UV) photodetectors (PDs) were successfully fabricated and optimized via a facile hydrothermal process. Using a shadow mask technique, the thin ZnO seed layer was deposited between the patterned Au/Ti electrodes to bridge the electrodes. Thus, both the Au electrodes could be connected by the ZnO seed layer. As the sample was immersed into growth solution and heated at 90 °C, the ZnO NRAs were crystallized and vertically grown on the ZnO seed layer, thus creating a metal-semiconductor-metal PD structure. To investigate the size effect of ZnO NRAs on photocurrent, the PDs were readily prepared with different concentrations of growth solution. For the ZnO NRAs grown at 25 mM of concentration, the PD with 10 μm of channel width (i.e., gap distance between two electrodes) exhibited a high photocurrent of 1.91 × 10(-4) A at an applied bias of 10 V under 365 nm of UV light illumination. The PD was optimized by adjusting the channel width. For 15 μm of channel width, a relatively high photocurrent on-off ratio of 37.4 and good current transient characteristics were observed at the same applied bias. These results are expected to be useful for cost-effective and practical UV PD applications.

  10. CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy.

    Science.gov (United States)

    Zuo, Guanghong; Hao, Bailin

    2015-10-01

    A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. We now provide one solution in the latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster of 64 cores and is equipped with an interactive, collapsible, and expandable tree display. It is capable of comparing the tree branching order with prokaryotic classification at all taxonomic ranks from domains down to species and strains. CVTree3 allows for inquiry by taxon names and trial on lineage modifications. In addition, it reports a summary of monophyletic and non-monophyletic taxa at all ranks as well as produces print-quality subtree figures. After giving an overview of retrospective verification of the CVTree approach, the power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes. A few discrepancies between CVTree and 16S rRNA analyses are also summarized with regard to possible taxonomic revisions. CVTree3 is freely accessible to all users at http://tlife.fudan.edu.cn/cvtree3/ without login requirements.

  11. CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy

    Directory of Open Access Journals (Sweden)

    Guanghong Zuo

    2015-10-01

    Full Text Available A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. We now provide one solution in the latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster of 64 cores and is equipped with an interactive, collapsible, and expandable tree display. It is capable of comparing the tree branching order with prokaryotic classification at all taxonomic ranks from domains down to species and strains. CVTree3 allows for inquiry by taxon names and trial on lineage modifications. In addition, it reports a summary of monophyletic and non-monophyletic taxa at all ranks as well as produces print-quality subtree figures. After giving an overview of retrospective verification of the CVTree approach, the power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes. A few discrepancies between CVTree and 16S rRNA analyses are also summarized with regard to possible taxonomic revisions. CVTree3 is freely accessible to all users at http://tlife.fudan.edu.cn/cvtree3/ without login requirements.

  12. Alignment of lower-limb prostheses.

    Science.gov (United States)

    Zahedi, M S; Spence, W D; Solomonidis, S E; Paul, J P

    1986-04-01

    Alignment of a prosthesis is defined as the position of the socket relative to the other prosthetic components of the limb. During dynamic alignment the prosthetist, using subjective judgment and feedback from the patient, aims to achieve the most suitable limb geometry for best function and comfort. Until recently it was generally believed that a patient could only be satisfied with a unique "optimum alignment." The purpose of this systematic study of lower-limb alignment parameters was to gain an understanding of the factors that make a limb configuration or optimum alignment, acceptable to the patient, and to obtain a measure of the variation of this alignment that would be acceptable to the amputee. In this paper, the acceptable range of alignments for 10 below- and 10 above-knee amputees are established. Three prosthetists were involved in the majority of the 183 below-knee and 100 above-knee fittings, although several other prosthetists were also involved. The effects of each different prosthetist on the established range of alignment for each patient are reported to be significant. It is now established that an amputee can tolerate several alignments ranging in some parameters by as much as 148 mm in shifts and 17 degrees in tilts. This paper describes the method of defining and measuring the alignment of lower-limb prostheses. It presents quantitatively established values for bench alignment position and the range of adjustment required for incorporation into the design of new alignment units.

  13. CATO: The Clone Alignment Tool.

    Directory of Open Access Journals (Sweden)

    Peter V Henstock

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

  14. CATO: The Clone Alignment Tool.

    Science.gov (United States)

    Henstock, Peter V; LaPan, Peter

    2016-01-01

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

  15. Gait Recognition based on Dynamic Texture descriptors

    Directory of Open Access Journals (Sweden)

    B. Abdolahi

    2013-09-01

    Full Text Available The human movement analysis is an attractive topic in biometric research. Recent studies indicate that people have considerable ability to recognize others by their natural walking. Therefore, gait recognition has obtained great interest in biometric systems. The common biometrics is usually time-consuming, limited and collaborative. These drawbacks pose major challenges to the recognition process. Gait analysis is inconspicuous, needs no contact, is difficult to hide and can be evaluated at distance. This paper presents a bag of word method for gait recognition based on dynamic textures. Dynamic textures combine appearance and motion information. Since human walking has statistical variations in both spatial and temporal space, it can be described with dynamic texture features. To obtain these features, we extract spatiotemporal interest points and describe them by a dynamic texture descriptor. Afterwards, the hierarchical K-means as a clustering algorithm is applied to obtain the visual dictionary of video-words. As a result, human walking is represented as a histogram of video-words occurrences. The performance of our method is evaluated on two dataset: the KTH and IXMAS multiview datasets.

  16. 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...... alignment by 'reverse translation' of the aligned protein sequences. In the resulting DNA alignment, gaps occur in groups of three corresponding to entire codons, and analogous codon positions are therefore always lined up. These features are useful when constructing multiple DNA alignments for phylogenetic...

  17. Primordial alignment of elliptical galaxies in intermediate redshift clusters

    CERN Document Server

    Rong, Yu; Liao, Jin-Yuan

    2015-01-01

    We measure primordial alignments for the red galaxies in the sample of eight massive galaxy clusters in the southern sky from the CLASH-VLT Large Programme, at a median redshift of 0.375. We find primordial alignment with about $3\\sigma$ significance in the four dynamically young clusters, but null detection of primordial alignment in the four highly relaxed clusters. The observed primordial alignment is not dominated by any single one of the four dynamically young clusters, and is primarily due to a population of bright galaxies ($M_r<-20.5\\ \\rm{m}$) residing in the region 300 to 810 kpc from the cluster centers. For the first time, we point out that the combination of radial alignment and halo alignment can cause fake primordial alignment. Finally, we find that the detected alignment for the dynamically young clusters is real rather than fake primordial alignment.

  18. A highly sensitive hydrogen peroxide amperometric sensor based on MnO{sub 2}-modified vertically aligned multiwalled carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Xu Bin; Ye Minling; Yu Yuxiang [Nano Science Research Center, School of Chemistry and Chemical Engineering, South China University of Technology, 381 Wushan Road, Guangzhou 510640, Guangdong (China); Zhang Weide, E-mail: zhangwd@scut.edu.cn [Nano Science Research Center, School of Chemistry and Chemical Engineering, South China University of Technology, 381 Wushan Road, Guangzhou 510640, Guangdong (China)

    2010-07-26

    In this report, a highly sensitive amperometric sensor based on MnO{sub 2}-modified vertically aligned multiwalled carbon nanotubes (MnO{sub 2}/VACNTs) for determination of hydrogen peroxide (H{sub 2}O{sub 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{sub 2}/VACNTs nanocomposite electrode. The mechanism for the electrochemical reaction of H{sub 2}O{sub 2} at the MnO{sub 2}/VACNTs nanocomposite electrode was also discussed. In borate buffer (pH 7.8, 0.20 M), the MnO{sub 2}/VACNTs nanocomposite electrode exhibits a linear dependence (R = 0.998) on the concentration of H{sub 2}O{sub 2} from 1.2 x 10{sup -6} M to 1.8 x 10{sup -3} M, a high sensitivity of 1.08 x 10{sup 6} {mu}A M{sup -1} cm{sup -2} and a detection limit of 8.0 x 10{sup -7} M (signal/noise = 3). Meanwhile, the MnO{sub 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{sub 2}/VACNTs nanocomposite electrode was applied for the determination of trace of H{sub 2}O{sub 2} in milk with high accuracy, demonstrating its potential for practical application.

  19. High-throughput and high-yield fabrication of uniaxially-aligned chitosan-based nanofibers by centrifugal electrospinning.

    Science.gov (United States)

    Erickson, Ariane E; Edmondson, Dennis; Chang, Fei-Chien; Wood, Dave; Gong, Alex; Levengood, Sheeny Lan; Zhang, Miqin

    2015-12-10

    The inability to produce large quantities of nanofibers has been a primary obstacle in advancement and commercialization of electrospinning technologies, especially when aligned nanofibers are desired. Here, we present a high-throughput centrifugal electrospinning (HTP-CES) system capable of producing a large number of highly-aligned nanofiber samples with high-yield and tunable diameters. The versatility of the design was revealed when bead-less nanofibers were produced from copolymer chitosan/polycaprolactone (C-PCL) solutions despite variations in polymer blend composition or spinneret needle gauge. Compared to conventional electrospinning techniques, fibers spun with the HTP-CES not only exhibited superior alignment, but also better diameter uniformity. Nanofiber alignment was quantified using Fast Fourier Transform (FFT) analysis. In addition, a concave correlation between the needle diameter and resultant fiber diameter was identified. This system can be easily scaled up for industrial production of highly-aligned nanofibers with tunable diameters that can potentially meet the requirements for various engineering and biomedical applications.

  20. Cluster-based control of nonlinear dynamics

    CERN Document Server

    Kaiser, Eurika; Spohn, Andreas; Cattafesta, Louis N; Morzynski, Marek

    2016-01-01

    The ability to manipulate and control fluid flows is of great importance in many scientific and engineering applications. Here, a cluster-based control framework is proposed to determine optimal control laws with respect to a cost function for unsteady flows. The proposed methodology frames high-dimensional, nonlinear dynamics into low-dimensional, probabilistic, linear dynamics which considerably simplifies the optimal control problem while preserving nonlinear actuation mechanisms. The data-driven approach builds upon a state space discretization using a clustering algorithm which groups kinematically similar flow states into a low number of clusters. The temporal evolution of the probability distribution on this set of clusters is then described by a Markov model. The Markov model can be used as predictor for the ergodic probability distribution for a particular control law. This probability distribution approximates the long-term behavior of the original system on which basis the optimal control law is de...

  1. 用动态扣分策略消除序列局部联配中的马赛克问题%Fixing Mosaic Effect on Sequence Local Alignment with Dynamic Penalty Strategy

    Institute of Scientific and Technical Information of China (English)

    佘堃; 黄均才; 周明天

    2003-01-01

    The local alignment problem for two sequences requires determining similar regions, one from each sequence, and aligning those regions. The Smith-Waterman algorithm for local sequence alignment is one of the most well-known algorithm in computational molecular biology. This ingenious dynamic programming approach is designed to reveal the highly conserved fragments by discarding poorly conserved initial and terminal segments. However, the local alignment sometimes produces a mosaic of well conserved fragments artificially connected by poorly conserved or even unrelated fragments. This may lead to problems in comparison of long genomic sequences and comparative gene prediction. In this paper we propose a new strategy of dynamic penalty strategy to {ix this problem. In the process of computing similarity matrix, if similarity value is larger than the pre-specified threshold X then starting our strategy, when related character mismatches, then penalizing more than others until similarity value is 0 or the process ends. Test results show that this algorithm has better performance by comparison to the standard Smith-Waterman while dose not increase signally the computational complexity both in time and space.

  2. Isolated digit recognition without time alignment

    Science.gov (United States)

    Gay, Jeffrey Mark

    1994-12-01

    This thesis examines methods for isolated digit recognition without using time alignment. Resource requirements for isolated word recognizers that use time alignment can become prohibitively large as the vocabulary to be classified grows. Thus, methods capable of achieving recognition rates comparable to those obtained with current methods using these techniques are needed. The goals of this research are to find feature sets for speech recognition that perform well without using time alignment, and to identify classifiers that provide good performance with these features. Using the digits from the TI46 database, baseline speaker-independent recognition rates of 95.2% for the complete speaker set and 98.1% for the male speaker set are established using dynamic time warping (DTW). This work begins with features derived from spectrograms of each digit. Based on a critical band frequency scale covering the telephone bandwidth (300-3000 Hz), these critical band energy features are classified alone and in combination with several other feature sets, with several different classifiers. With this method, there is one 'short' feature vector per word. For speaker-independent recognition using the complete speaker set and a multi-layer perceptron (MLP) classifier, a recognition rate of 92.4% is achieved. For the same classifier with the male speaker set, a recognition rate of 97.1% is achieved. For the male speaker set, there is no statistical difference between results using DTW, and those using the MLP and no time alignment. This shows that there are feature sets that may provide high recognition rates for isolated word recognition without the need for time alignment.

  3. Study of Pre-Alignment tolerances in the RTML

    CERN Document Server

    Lienart, Thibaut

    2012-01-01

    In this document a study of the impact of jitter and static misalignment on the elements of the Ring To Main Linac transport (RTML) on the emittance growth through Monte Carlo simulations using the tracking code PLACET is presented. Tolerances are proposed for the dynamic alignment requirements of the RTML in order to meet the budget emittance growth. A study of the impact of static misalignment and correction thereof with basic Beam-Based Alignment techniques is also presented and resulting tolerances are proposed for the prealignment phase of the machine.

  4. Physician-Hospital Alignment in Orthopedic Surgery.

    Science.gov (United States)

    Bushnell, Brandon D

    2015-09-01

    The concept of "alignment" between physicians and hospitals is a popular buzzword in the age of health care reform. Despite their often tumultuous histories, physicians and hospitals find themselves under increasing pressures to work together toward common goals. However, effective alignment is more than just simple cooperation between parties. The process of achieving alignment does not have simple, universal steps. Alignment will differ based on individual situational factors and the type of specialty involved. Ultimately, however, there are principles that underlie the concept of alignment and should be a part of any physician-hospital alignment efforts. In orthopedic surgery, alignment involves the clinical, administrative, financial, and even personal aspects of a surgeon's practice. It must be based on the principles of financial interest, clinical authority, administrative participation, transparency, focus on the patient, and mutual necessity. Alignment can take on various forms as well, with popular models consisting of shared governance and comanagement, gainsharing, bundled payments, accountable care organizations, and other methods. As regulatory and financial pressures continue to motivate physicians and hospitals to develop alignment relationships, new and innovative methods of alignment will also appear. Existing models will mature and evolve, with individual variability based on local factors. However, certain trends seem to be appearing as time progresses and alignment relationships deepen, including regional and national collaboration, population management, and changes in the legal system. This article explores the history, principles, and specific methods of physician-hospital alignment and its critical importance for the future of health care delivery.

  5. The Cluster Substructure - Alignment Connection

    OpenAIRE

    Plionis, Manolis

    2001-01-01

    Using the APM cluster data we investigate whether the dynamical status of clusters is related to the large-scale structure of the Universe. We find that cluster substructure is strongly correlated with the tendency of clusters to be aligned with their nearest neighbour and in general with the nearby clusters that belong to the same supercluster. Furthermore, dynamically young clusters are more clustered than the overall cluster population. These are strong indications that cluster develop in ...

  6. Inflation by alignment

    Energy Technology Data Exchange (ETDEWEB)

    Burgess, C.P. [PH -TH Division, CERN,CH-1211, Genève 23 (Switzerland); Department of Physics & Astronomy, McMaster University,1280 Main Street West, Hamilton ON (Canada); Perimeter Institute for Theoretical Physics,31 Caroline Street North, Waterloo ON (Canada); Roest, Diederik [Van Swinderen Institute for Particle Physics and Gravity, University of Groningen,Nijenborgh 4, 9747 AG Groningen (Netherlands)

    2015-06-08

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

  7. Aligning component upgrades

    Directory of Open Access Journals (Sweden)

    Roberto Di Cosmo

    2011-08-01

    Full Text Available Modern software systems, like GNU/Linux distributions or Eclipse-based development environment, are often deployed by selecting components out of large component repositories. Maintaining such software systems by performing component upgrades is a complex task, and the users need to have an expressive preferences language at their disposal to specify the kind of upgrades they are interested in. Recent research has shown that it is possible to develop solvers that handle preferences expressed as a combination of a few basic criteria used in the MISC competition, ranging from the number of new components to the freshness of the final configuration. In this work we introduce a set of new criteria that allow the users to specify their preferences for solutions with components aligned to the same upstream sources, provide an efficient encoding and report on the experimental results that prove that optimising these alignment criteria is a tractable problem in practice.

  8. Inflation by Alignment

    CERN Document Server

    Burgess, Cliff

    2015-01-01

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

  9. Aligning component upgrades

    CERN Document Server

    Di Cosmo, Roberto; Michel, Claude; 10.4204/EPTCS.65.1

    2011-01-01

    Modern software systems, like GNU/Linux distributions or Eclipse-based development environment, are often deployed by selecting components out of large component repositories. Maintaining such software systems by performing component upgrades is a complex task, and the users need to have an expressive preferences language at their disposal to specify the kind of upgrades they are interested in. Recent research has shown that it is possible to develop solvers that handle preferences expressed as a combination of a few basic criteria used in the MISC competition, ranging from the number of new components to the freshness of the final configuration. In this work we introduce a set of new criteria that allow the users to specify their preferences for solutions with components aligned to the same upstream sources, provide an efficient encoding and report on the experimental results that prove that optimising these alignment criteria is a tractable problem in practice.

  10. Design and application of a laser beam alignment system based on the imaging properties of a multi-pass amplifier

    Institute of Scientific and Technical Information of China (English)

    Daizhong Liu; Fengnian Lü; Jinzhou Cao; Renfang Xu; Jianqiang Zhu; Dianyuan Fan; Jianbo Xiao; Xiaojun Zhou

    2006-01-01

    Image relaying is presented as a technique for aligning beams onto mm-sized target of high power laser. On the basis of summarizing the preceeding work on the near-field image relaying of multiple spatial filters,the far-filed image relaying is suggested firstly. The near-field and far-field image relaying properties of multiple spatial filters in laser beams automatic alignment system are analyzed. A geometrical optics approach and an ABCD ray matrix theory are used throughout. The reasonable and optimum scheme for automatically aligning multi-pass beam paths is presented and demonstrated on the multi-pass amplifier system of the SG-Ⅲ prototype.

  11. 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.

  12. Magnetic alignment and the Poisson alignment reference system

    Science.gov (United States)

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

    1990-08-01

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

  13. Mechanism of cell alignment in groups of Myxococcus xanthus bacteria

    Science.gov (United States)

    Balgam, Rajesh; Igoshin, Oleg

    2015-03-01

    Myxococcus xanthus is a model for studying self-organization in bacteria. These flexible cylindrical bacteria move along. In groups, M. xanthus cells align themselves into dynamic cell clusters but the mechanism underlying their formation is unknown. It has been shown that steric interactions can cause alignment in self-propelled hard rods but it is not clear how flexibility and reversals affect the alignment and cluster formation. We have investigated cell alignment process using our biophysical model of M. xanthus cell in an agent-based simulation framework under realistic cell flexibility values. We observed that flexible model cells can form aligned cell clusters when reversals are suppressed but these clusters disappeared when reversals frequency becomes similar to the observed value. However, M. xanthus cells follow slime (polysaccharide gel like material) trails left by other cells and we show that implementing this into our model rescues cell clustering for reversing cells. Our results show that slime following along with periodic cell reversals act as positive feedback to reinforce existing slime trails and recruit more cells. Furthermore, we have observed that mechanical cell alignment combined with slime following is sufficient to explain the distinct clustering patterns of reversing and non-reversing cells as observed in recent experiments. This work is supported by NSF MCB 0845919 and 1411780.

  14. HomBlocks: A multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching.

    Science.gov (United States)

    Bi, Guiqi; Mao, Yunxiang; Xing, Qikun; Cao, Min

    2017-08-03

    Organelle phylogenomic analysis requires precisely constructed multi-gene alignment matrices concatenated by pre-aligned single gene datasets. For non-bioinformaticians, it can take days to weeks to manually create high-quality multi-gene alignments comprising tens or hundreds of homologous genes. Here, we describe a new and highly efficient pipeline, HomBlocks, which uses a homologous block searching method to construct multiple sequence alignment. This approach can automatically recognize locally collinear blocks among organelle genomes and excavate phylogenetically informative regions to construct multiple sequence alignment in a few hours. In addition, HomBlocks supports organelle genomes without annotation and makes adjustment to different taxon datasets, thereby enabling the inclusion of as many common genes as possible. Topology comparison of trees built by conventional multi-gene and HomBlocks alignments implemented in different taxon categories shows that the same efficiency can be achieved by HomBlocks as when using the traditional method. The availability of Homblocks makes organelle phylogenetic analyses more accessible to non-bioinformaticians, thereby promising to lead to a better understanding of phylogenic relationships at an organelle genome level. HomBlocks is implemented in Perl and is supported by Unix-like operative systems, including Linux and macOS. The Perl source code is freely available for download from https://github.com/fenghen360/HomBlocks.git, and documentation and tutorials are available at https://github.com/fenghen360/HomBlocks. yxmao@ouc.edu.cn or fenghen360@126.com. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. How well does consumer-based brand equity align with sales-based brand equity and marketing mix response?

    NARCIS (Netherlands)

    Datta, Hannes; Ailawadi, Kusum L.; van Heerde, H.J.

    Brand equity is the differential preference and response to marketing effort that a product obtains because of its brand identification. Brand equity can be measured based on either consumer perceptions or on sales. Consumer-based brand equity (CBBE) measures what consumers think and feel about the

  16. How well does consumer-based brand equity align with sales-based brand equity and marketing mix response?

    NARCIS (Netherlands)

    Datta, Hannes; Ailawadi, Kusum L.; van Heerde, H.J.

    2016-01-01

    Brand equity is the differential preference and response to marketing effort that a product obtains because of its brand identification. Brand equity can be measured based on either consumer perceptions or on sales. Consumer-based brand equity (CBBE) measures what consumers think and feel about the

  17. How well does consumer-based brand equity align with sales-based brand equity and marketing mix response?

    NARCIS (Netherlands)

    Datta, Hannes; Ailawadi, Kusum L.; van Heerde, H.J.

    2017-01-01

    Brand equity is the differential preference and response to marketing effort that a product obtains because of its brand identification. Brand equity can be measured based on either consumer perceptions or on sales. Consumer-based brand equity (CBBE) measures what consumers think and feel about the

  18. The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies.

    Directory of Open Access Journals (Sweden)

    Patrick D Schloss

    Full Text Available Pyrosequencing of PCR-amplified fragments that target variable regions within the 16S rRNA gene has quickly become a powerful method for analyzing the membership and structure of microbial communities. This approach has revealed and introduced questions that were not fully appreciated by those carrying out traditional Sanger sequencing-based methods. These include the effects of alignment quality, the best method of calculating pairwise genetic distances for 16S rRNA genes, whether it is appropriate to filter variable regions, and how the choice of variable region relates to the genetic diversity observed in full-length sequences. I used a diverse collection of 13,501 high-quality full-length sequences to assess each of these questions. First, alignment quality had a significant impact on distance values and downstream analyses. Specifically, the greengenes alignment, which does a poor job of aligning variable regions, predicted higher genetic diversity, richness, and phylogenetic diversity than the SILVA and RDP-based alignments. Second, the effect of different gap treatments in determining pairwise genetic distances was strongly affected by the variation in sequence length for a region; however, the effect of different calculation methods was subtle when determining the sample's richness or phylogenetic diversity for a region. Third, applying a sequence mask to remove variable positions had a profound impact on genetic distances by muting the observed richness and phylogenetic diversity. Finally, the genetic distances calculated for each of the variable regions did a poor job of correlating with the full-length gene. Thus, while it is tempting to apply traditional cutoff levels derived for full-length sequences to these shorter sequences, it is not advisable. Analysis of beta-diversity metrics showed that each of these factors can have a significant impact on the comparison of community membership and structure. Taken together, these results

  19. Dynamics-based centrality for directed networks

    Science.gov (United States)

    Masuda, Naoki; Kori, Hiroshi

    2010-11-01

    Determining the relative importance of nodes in directed networks is important in, for example, ranking websites, publications, and sports teams, and for understanding signal flows in systems biology. A prevailing centrality measure in this respect is the PageRank. In this work, we focus on another class of centrality derived from the Laplacian of the network. We extend the Laplacian-based centrality, which has mainly been applied to strongly connected networks, to the case of general directed networks such that we can quantitatively compare arbitrary nodes. Toward this end, we adopt the idea used in the PageRank to introduce global connectivity between all the pairs of nodes with a certain strength. Numerical simulations are carried out on some networks. We also offer interpretations of the Laplacian-based centrality for general directed networks in terms of various dynamical and structural properties of networks. Importantly, the Laplacian-based centrality defined as the stationary density of the continuous-time random walk with random jumps is shown to be equivalent to the absorption probability of the random walk with sinks at each node but without random jumps. Similarly, the proposed centrality represents the importance of nodes in dynamics on the original network supplied with sinks but not with random jumps.

  20. Agent-based modeling and network dynamics

    CERN Document Server

    Namatame, Akira

    2016-01-01

    The book integrates agent-based modeling and network science. It is divided into three parts, namely, foundations, primary dynamics on and of social networks, and applications. The book begins with the network origin of agent-based models, known as cellular automata, and introduce a number of classic models, such as Schelling’s segregation model and Axelrod’s spatial game. The essence of the foundation part is the network-based agent-based models in which agents follow network-based decision rules. Under the influence of the substantial progress in network science in late 1990s, these models have been extended from using lattices into using small-world networks, scale-free networks, etc. The book also shows that the modern network science mainly driven by game-theorists and sociophysicists has inspired agent-based social scientists to develop alternative formation algorithms, known as agent-based social networks. The book reviews a number of pioneering and representative models in this family. Upon the gi...

  1. Dynamic Digital Channelizer Based on Spectrum Sensing.

    Science.gov (United States)

    Hu, Junpeng; Zuo, Zhen; Huang, Zhiping; Dong, Zhi

    2015-01-01

    The ability to efficiently channelize a received signal with dynamic sub-channel bandwidths is a key requirement of software defined radio (SDR) systems. The digital channelizer, which is used to split the received signal into a number of sub-channels, plays an important role in SDR systems. In this paper, a design of dynamic digital channelizer is presented. The proposed method is novel in that it employs a cosine modulated filter bank (CMFB) to divide the received signal into multiple frequency sub-bands and a spectrum sensing technique, which is mostly used in cognitive radio, is introduced to detect the presence of signal of each sub-band. The method of spectrum sensing is carried out based on the eigenvalues of covariance matrix of received signal. The ratio of maximum-minimum eigenvalue of each sub-band is vulnerable to noise fluctuation. This paper suggests an optimized method to calculate the ratio of maximum-minimum eigenvalue. The simulation results imply that the design of digital channelizer can effectively separate the received signal with dynamically changeable sub-channel signals.

  2. Dynamic Loadability of Cable Based Transmission Grids

    DEFF Research Database (Denmark)

    Olsen, Rasmus Schmidt

    This thesis is the product of three years research within the field of dynamic loadability of cable based transmission grids. The report contains a summary of the three year PhD project which has been conducted in a collaboration between the Danish Transmission System Operator (TSO), Energinet...... supervised 2 master projects, as well as 5 special courses at DTU. Furthermore I created and taught a cable course, with approximately 25 students, throughout 13 weeks during the spring of 2011. The PhD project has until now contributed with 3 journal papers and 4 conference papers. Selected papers can...

  3. 基于D2shepp统计法的非序列局部比对%Local Alignment-Free Sequences Based on D2shepp Statistics

    Institute of Scientific and Technical Information of China (English)

    刘雪梅; 文德华; 於黄忠; 高亚妮

    2012-01-01

    两条生物序列间的相似性比对是计算生物学探讨的主要问题之一,一种快速的依赖于k-元组的D2shepp统计法目前已被应用到非序列比对中.文中在零模型的基础上产生两条相互独立的随机序列,基于D2shepp统计法进行了两条序列的局部比对,找到局部比对的最优值并求和.在此基础上模拟了Power值的分布情况,并分析了不同k参数下的Power值分布.在相同参数下将文中提出的局部比对与已有的D2shepp统计的全局比对进行比较,发现局部比对D2shepp统计的Power值随着序列长度的增大而快速地接近于1,比全局比对更加快速、准确.%The similarities between two biological sequences is a major issue in computational biology, and a fast D2shepp statistics method based on the joint i-tuple content in two sequences has been used in the alignment-free sequence comparison. In this paper, two separate random sequences are generated based on the zero model, and their local alignment is conducted based on D2shepp statistics, thus obtaining the optimal values and the sum of these values. Then, the Power distribution is simulated and the distributions with different k values are analyzed. Finally, with the same parameters, the proposed local alignment is compared with the global alignment based on D2shepp statistics. It is found that the Power value of the proposed local alignment rapidly approaches 1 with the increase of the sequence length and that the proposed local alignment is quicker and more accurate than the global one.

  4. Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System.

    Science.gov (United States)

    Liu, Yu; Hong, Yang; Lin, Chun-Yuan; Hung, Che-Lun

    2015-01-01

    The Smith-Waterman (SW) algorithm has been widely utilized for searching biological sequence databases in bioinformatics. Recently, several works have adopted the graphic card with Graphic Processing Units (GPUs) and their associated CUDA model to enhance the performance of SW computations. However, these works mainly focused on the protein database search by using the intertask parallelization technique, and only using the GPU capability to do the SW computations one by one. Hence, in this paper, we will propose an efficient SW alignment method, called CUDA-SWfr, for the protein database search by using the intratask parallelization technique based on a CPU-GPU collaborative system. Before doing the SW computations on GPU, a procedure is applied on CPU by using the frequency distance filtration scheme (FDFS) to eliminate the unnecessary alignments. The experimental results indicate that CUDA-SWfr runs 9.6 times and 96 times faster than the CPU-based SW method without and with FDFS, respectively.

  5. 基于CKF的SINS大方位失准角初始对准%Initial alignment of large azimuth misalignment angle in SINS based on CKF

    Institute of Scientific and Technical Information of China (English)

    孙枫; 唐李军

    2012-01-01

    The error equation of large azimuth misalignment angle in SINS is nonlinear. To improve the accuracy of the initial alignment in nonlinear model, a new nonlinear filtering method named cubature Kalman filter (CKF) is applied in the initial alignment of SINS. Therefore, an initial alignment nonlinear model under large azimuth misalignment angle is established, and the CKF filter theory based on the spherical-radial cubature criteria is analyzed; then the nonlinear model is simulated with CKF. Simulation results show that the CKF can nicely deal with the nonlinear problems in initial alignment and improve the precision of initial alignment; and the azimuth misalignment angle error can converge to -33.13', which is close to the theoretical estimation precision -32.40' and is better than the-84.14' of EKF.%大方位失准角捷联惯导系统(strapdown inertial narigation system,SINS)误差方程是非线性的,为改善非线性模型下初始对准的精度,提出将一种新的非线性滤波方法(cubature Kalman filter,CKF)应用于捷联惯导系统初始对准中.为此建立了大方位失准角下初始对准非线性模型,分析了基于spherical-radial cubature准则的CKF滤波原理,对非线性模型进行了CKF滤波仿真.仿真结果表明CKF能够很好地处理初始对准中的非线性问题,提高初始对准精度,方位失准角误差能够收敛到- 33.13′,接近理论估计精度-32.40′,优于EKF的-84.14′.

  6. Dynamic graph cut based segmentation of mammogram.

    Science.gov (United States)

    Angayarkanni, S Pitchumani; Kamal, Nadira Banu; Thangaiya, Ranjit Jeba

    2015-01-01

    This work presents the dynamic graph cut based Otsu's method to segment the masses in mammogram images. Major concern that threatens human life is cancer. Breast cancer is the most common type of disease among women in India and abroad. Breast cancer increases the mortality rate in India especially in women since it is considered to be the second largest form of disease which leads to death. Mammography is the best method for diagnosing early stage of cancer. The computer aided diagnosis lacks accuracy and it is time consuming. The main approach which makes the detection of cancerous masses accurate is segmentation process. This paper is a presentation of the dynamic graph cut based approach for effective segmentation of region of interest (ROI). The sensitivity, the specificity, the positive prediction value and the negative prediction value of the proposed algorithm are determined and compared with the existing algorithms. Both qualitative and quantitative methods are used to detect the accuracy of the proposed system. The sensitivity, the specificity, the positive prediction value and the negative prediction value of the proposed algorithm accounts to 98.88, 98.89, 93 and 97.5% which rates very high when compared to the existing algorithms.

  7. Dynamic Responses of Mobile Offshore Base Connectors

    Institute of Scientific and Technical Information of China (English)

    余澜; 李润培; 舒志

    2003-01-01

    A Mobile Offshore Base (MOB) is a multi-purpose logistics base, which can be stationed in coastal or international waters. In the conceptual design of the MOB, attention should be paid to the dynamic responses of the inter-module connectors because tremendous loads occur in the connectors. In this paper, a study on dynamic responses of the MOB connectors is carried out by use of the Rigid Module Flexible Connector (RMFC) model which assumes that the module stiffness is significantly larger than that of the connector. In the analysis, the connector is modeled as a linear spring, which restricts relative translations but allows for relative rotations of modules. The 3-D source distribution method is adopted to determine the hydrodynamic forces of the modules, and the hydrodynamic interaction between modules is taken into account. The module motions and connector loads for 12 connector stiffness cases in regular and irregular waves are calculated with the multi-rigid-body motion equations. And the calculated results are compared with those from relative references. It is shown that the results obtained by different methods are in good agreement.

  8. Convergent algorithms for protein structural alignment

    Directory of Open Access Journals (Sweden)

    Martínez José

    2007-08-01

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

  9. Aligning Sequences by Minimum Description Length

    Directory of Open Access Journals (Sweden)

    John S. Conery

    2008-01-01

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

  10. Interference Alignment-based Precoding and User Selection with Limited Feedback in Two-cell Downlink Multi-user MIMO Systems

    Directory of Open Access Journals (Sweden)

    Yin Zhu

    2016-05-01

    Full Text Available Interference alignment (IA is a new approach to address interference in modern multiple-input multiple-out (MIMO cellular networks in which interference is an important factor that limits the system throughput. System throughput in most IA implementation schemes is significantly improved only with perfect channel state information and in a high signal-to-noise ratio (SNR region. Designing a simple IA scheme for the system with limited feedback and investigating system performance at a low-to-medium SNR region is important and practical. This paper proposed a precoding and user selection scheme based on partial interference alignment in two-cell downlink multi-user MIMO systems under limited feedback. This scheme aligned inter-cell interference to a predefined direction by designing user’s receive antenna combining vectors. A modified singular value decomposition (SVD-based beamforming method and a corresponding user-selection algorithm were proposed for the system with low rate limited feedback to improve sum rate performance. Simulation results show that the proposed scheme achieves a higher sum rate than traditional schemes without IA. The modified SVD-based beamforming scheme is also superior to the traditional zero-forcing beamforming scheme in low-rate limited feedback systems. The proposed partial IA scheme does not need to collaborate between transmitters and joint design between the transmitter and the users. The scheme can be implemented with low feedback overhead in current MIMO cellular networks.

  11. Preparation and characterization of graphene-based vanadium oxide composite semiconducting films with horizontally aligned nanowire arrays

    Energy Technology Data Exchange (ETDEWEB)

    Jung, Hye-Mi; Um, Sukkee, E-mail: sukkeeum@hanyang.ac.kr

    2016-05-01

    Highly oriented crystalline hybrid thin films primarily consisting of Magnéli-phase VO{sub 2} and conductive graphene nanoplatelets are fabricated by a sol–gel process via dipping pyrolysis. A combination of chemical, microstructural, and electrical analyses reveals that graphene oxide (GO)-templated vanadium oxide (VO{sub x}) nanocomposite films exhibit a vertically stacked multi-lamellar nanostructure consisting of horizontally aligned vanadium oxide nanowire (VNW) arrays along the (hk0) set of planes on a GO template, with an average crystallite size of 41.4 Å and a crystallographic tensile strain of 0.83%. In addition, GO-derived VO{sub x} composite semiconducting films, which have an sp{sup 3}/sp{sup 2} bonding ratio of 0.862, display thermally induced electrical switching properties in the temperature range of − 20 °C to 140 °C, with a transition temperature of approximately 65 °C. We ascribe these results to the use of GO sheets, which serve as a morphological growth template as well as an electrochemically tunable platform for enhancing the charge-carrier mobility. Moreover, the experimental studies demonstrate that graphene-based Magnéli-phase VO{sub x} composite semiconducting films can be used in advanced thermo-sensitive smart sensing/switching applications because of their outstanding thermo-electrodynamic properties and high surface charge density induced by the planar-type VNWs. - Highlights: • VO{sub x}-graphene oxide composite (G/VO{sub x}) films were fabricated by sol–gel process. • The G/VO{sub x} films mainly consisted of Magnéli-phase VO{sub 2} and reduced graphene sheets. • The G/VO{sub x} films exhibited multi-lamellar textures with planar VO{sub x} nanowire arrays. • The G/VO{sub x} films showed the thermo-sensitive electrical switching properties. • Effects of GOs on the electrical characteristics of the G/VO{sub x} films were discussed.

  12. Calibration of shaft alignment instruments

    Science.gov (United States)

    Hemming, Bjorn

    1998-09-01

    Correct shaft alignment is vital for most rotating machines. Several shaft alignment instruments, ranging form dial indicator based to laser based, are commercially available. At VTT Manufacturing Technology a device for calibration of shaft alignment instruments was developed during 1997. A feature of the developed device is the similarity to the typical use of shaft alignment instruments i.e. the rotation of two shafts during the calibration. The benefit of the rotation is that all errors of the shaft alignment instrument, for example the deformations of the suspension bars, are included. However, the rotation increases significantly the uncertainty of calibration because of errors in the suspension of the shafts in the developed device for calibration of shaft alignment instruments. Without rotation the uncertainty of calibration is 0.001 mm for the parallel offset scale and 0,003 mm/m for the angular scale. With rotation the uncertainty of calibration is 0.002 mm for the scale and 0.004 mm/m for the angular scale.

  13. Perceptual grouping in Gabor lattices: proximity and alignment.

    Science.gov (United States)

    Claessens, Peter M; Wagemans, Johan

    2005-11-01

    We propose the Gabor lattice as a new stimulus designed to deal with multiple organizations in perceptual grouping, allowing both comparison between psychophysical data and neural findings and a systematic investigation of grouping based on several low-level characteristics and their interactions. A Gabor lattice is a geometric lattice with Gabor patches, evoking a multistable global orientation percept. Visual grouping in Gabor lattices with elements aligned in a global orientation was compared with grouping of nonaligned Gabor patches and of Gaussian blobs. The effect sizes of proximity and alignment were estimated in logistic regression analyses. The results confirmed the importance of proximity and local element alignment as factors in dynamic grouping. We also found a small but consistent enhancement of grouping along the global vector orthogonal to the local patch orientations. In light of these results, we further motivate the relevance of these stimuli and the associated experimental paradigm.

  14. Galaxy alignment on large and small scales

    Science.gov (United States)

    Kang, X.; Lin, W. P.; Dong, X.; Wang, Y. O.; Dutton, A.; Macciò, A.

    2016-10-01

    Galaxies are not randomly distributed across the universe but showing different kinds of alignment on different scales. On small scales satellite galaxies have a tendency to distribute along the major axis of the central galaxy, with dependence on galaxy properties that both red satellites and centrals have stronger alignment than their blue counterparts. On large scales, it is found that the major axes of Luminous Red Galaxies (LRGs) have correlation up to 30Mpc/h. Using hydro-dynamical simulation with star formation, we investigate the origin of galaxy alignment on different scales. It is found that most red satellite galaxies stay in the inner region of dark matter halo inside which the shape of central galaxy is well aligned with the dark matter distribution. Red centrals have stronger alignment than blue ones as they live in massive haloes and the central galaxy-halo alignment increases with halo mass. On large scales, the alignment of LRGs is also from the galaxy-halo shape correlation, but with some extent of mis-alignment. The massive haloes have stronger alignment than haloes in filament which connect massive haloes. This is contrary to the naive expectation that cosmic filament is the cause of halo alignment.

  15. IVUS coronary volume alignment for distinct phases

    Science.gov (United States)

    Matsumoto, Monica Mitiko Soares; Lemos, Pedro Alves; Furuie, Sergio Shiguemi

    2009-02-01

    Image-based intravascular ultrasound (IVUS) cardiac phase detection allows coronary volume reconstruction in different phases. Consecutive volumes are not necessarily spatially aligned due to longitudinal movement of the catheter. Besides ordinary pullback velocity, there is a relative longitudinal movement of the heart vessel walls and the transducer, due to myocardial contraction. In this manuscript, we aim to spatially align cardiac phase coronary IVUS volumes. In addition, we want to investigate this non-linear longitudinal catheter movement. With this purpose, we have analyzed 120 simulated IVUS images and 10 real IVUS pullbacks. We implemented the following methodology. Firstly, we built IVUS volume for each distinct phase. Secondly, each IVUS volume was transformed into a parametric signal of average frame intensity. We have used these signals to make correlation in space with a reference one. Then we estimated the spatial distance between the distinct IVUS volumes and the reference. We have tested in simulated images and real examinations. We have also observed similar pattern in real IVUS examinations. This spatial alignment method is feasible and useful as a step towards dynamic studies of IVUS examination.

  16. Mechanism for Collective Cell Alignment in Myxococcus xanthus Bacteria.

    Directory of Open Access Journals (Sweden)

    Rajesh Balagam

    2015-08-01

    Full Text Available Myxococcus xanthus cells self-organize into aligned groups, clusters, at various stages of their lifecycle. Formation of these clusters is crucial for the complex dynamic multi-cellular behavior of these bacteria. However, the mechanism underlying the cell alignment and clustering is not fully understood. Motivated by studies of clustering in self-propelled rods, we hypothesized that M. xanthus cells can align and form clusters through pure mechanical interactions among cells and between cells and substrate. We test this hypothesis using an agent-based simulation framework in which each agent is based on the biophysical model of an individual M. xanthus cell. We show that model agents, under realistic cell flexibility values, can align and form cell clusters but only when periodic reversals of cell directions are suppressed. However, by extending our model to introduce the observed ability of cells to deposit and follow slime trails, we show that effective trail-following leads to clusters in reversing cells. Furthermore, we conclude that mechanical cell alignment combined with slime-trail-following is sufficient to explain the distinct clustering behaviors observed for wild-type and non-reversing M. xanthus mutants in recent experiments. Our results are robust to variation in model parameters, match the experimentally observed trends and can be applied to understand surface motility patterns of other bacterial species.

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

    Science.gov (United States)

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

    2009-09-23

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

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

    Institute of Scientific and Technical Information of China (English)

    Kwangbaek Kim; Minhwan Kim; Youngwoon Woo

    2008-01-01

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

  19. ATLAS Inner Detector Alignment

    CERN Document Server

    Bocci, A

    2008-01-01

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

  20. [Dynamic bimaxillary osteotomy: the new occlusal base].

    Science.gov (United States)

    Audion, M; Darmon, Y

    1989-01-01

    The authors present an ortho-surgical method which unites occlusion and aesthetic without compromise and without stopping orthodontic work during the immediate post-operative period. The occlusal preparation permits us a global and simultaneous mobilisation of the two maxillars which are ostesynthezed in posterior skeletal disclosing. This disposition allows a lingual replacement and gives more facility to an eventual immediate post-operative occlusal replacement. The stiff osteosynthesis with immovable plates realize a therapeutic dissociation between the skeletal stage and the basal alveolo-dental stage. The "proprioceptive amnesia" and the "muscular sideration" permit a proprioceptive reorganisation and a new neuro-muscular fonctionnement elaborated from a new occlusal base. The free movements of the T.M.J. facilitate these acquisitions and allow a perspective supervision of the occlusion in a dynamic perspective.

  1. Behavior-based dual dynamic agent architecture

    Institute of Scientific and Technical Information of China (English)

    仵博; 吴敏; 曹卫华

    2003-01-01

    The objective of the architecture is to make agent promptly and adaptively accomplish tasks in the real-time and dynamic environment. The architecture is composed of elementary level behavior layer and high level be-havior layer. In the elementary level behavior layer, the reactive architecture is introduced to make agent promptlyreact to events; in the high level behavior layer, the deliberation architecture is used to enhance the intelligence ofthe agent. A confidence degree concept is proposed to combine the two layers of the architecture. An agent decisionmaking process is also presented, which is based on the architecture. The results of experiment in RoboSoccer simu-lation team show that the proposed architecture and the decision process are successful.

  2. Optic Fiber-Based Dynamic Pressure Sensor

    Institute of Scientific and Technical Information of China (English)

    Jiu-Lin Gan; Hai-Wen Cai; Jian-Xin Geng; Zheng-Qing Pan; Rong-Hui Qu; Zu-Jie Fang

    2008-01-01

    Weigh-in-Motion(WIM) technique is the process of measuring the dynamic tire forces of a moving vehicle and estimating the corresponding tire loads of the static vehicle. Compared with the static weigh station, WIM station is an efficient and cost effective choice that will minimize unneccessary stops and delay for truckers. The way to turn birefringence of single-mode fiber into a prime quality for a powerful and reliable sensor is shown. Preliminary results for the development of a weigh-in-motion (WIM) technique based on sagnac-loop sensor are presented. After a brief description of the sensor and its principle of operation, the theoretical model is developed. Then, a full characterization made in static conditions is presented.

  3. Indexer Based Dynamic Web Services Discovery

    CERN Document Server

    Bashir, Saba; Javed, M Younus; Khan, Aihab; Khiyal, Malik Sikandar Hayat

    2010-01-01

    Recent advancement in web services plays an important role in business to business and business to consumer interaction. Discovery mechanism is not only used to find a suitable service but also provides collaboration between service providers and consumers by using standard protocols. A static web service discovery mechanism is not only time consuming but requires continuous human interaction. This paper proposed an efficient dynamic web services discovery mechanism that can locate relevant and updated web services from service registries and repositories with timestamp based on indexing value and categorization for faster and efficient discovery of service. The proposed prototype focuses on quality of service issues and introduces concept of local cache, categorization of services, indexing mechanism, CSP (Constraint Satisfaction Problem) solver, aging and usage of translator. Performance of proposed framework is evaluated by implementing the algorithm and correctness of our method is shown. The results of p...

  4. User Authentication Based On Keystroke Dynamics

    Directory of Open Access Journals (Sweden)

    J.R Nisha

    2014-03-01

    Full Text Available The most common way to enforce access control is user authentication based on username and password. This form of access control has many flaws which make it vulnerable to hacking. Biometric authentication such as the keystroke dynamics is used in which the keyboard is used in order to identify users. Then the classifier is tailored to each user to find out whether the given user is genuine or not. The contribution of this approach is twofold: first it reduces the possibility of over fitting second it allows scalability to a high volume of users. Here, measured mean, median values, and standard deviation of keystroke features such as latency, dwell time, digraph and their combination are used. The algorithms used for feature subset selection are Particle Swarm Optimization (PSO, Genetic Algorithm (GA, Ant Colony Optimization (ACO and the proposed Renovated Artificial Bee Colony Optimization (RABCO algorithm. Back Propagation Neural Network (BPNN is used for classification.

  5. An optimized and low-cost FPGA-based DNA sequence alignment--a step towards personal genomics.

    Science.gov (United States)

    Shah, Hurmat Ali; Hasan, Laiq; Ahmad, Nasir

    2013-01-01

    DNA sequence alignment is a cardinal process in computational biology but also is much expensive computationally when performing through traditional computational platforms like CPU. Of many off the shelf platforms explored for speeding up the computation process, FPGA stands as the best candidate due to its performance per dollar spent and performance per watt. These two advantages make FPGA as the most appropriate choice for realizing the aim of personal genomics. The previous implementation of DNA sequence alignment did not take into consideration the price of the device on which optimization was performed. This paper presents optimization over previous FPGA implementation that increases the overall speed-up achieved as well as the price incurred by the platform that was optimized. The optimizations are (1) The array of processing elements is made to run on change in input value and not on clock, so eliminating the need for tight clock synchronization, (2) the implementation is unrestrained by the size of the sequences to be aligned, (3) the waiting time required for the sequences to load to FPGA is reduced to the minimum possible and (4) an efficient method is devised to store the output matrix that make possible to save the diagonal elements to be used in next pass, in parallel with the computation of output matrix. Implemented on Spartan3 FPGA, this implementation achieved 20 times performance improvement in terms of CUPS over GPP implementation.

  6. Source Code Generator Based on Dynamic Frames

    Directory of Open Access Journals (Sweden)

    Danijel Radošević

    2011-06-01

    Full Text Available Normal 0 21 false false false HR X-NONE X-NONE MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Obična tablica"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} This paper presents the model of source code generator based on dynamic frames. The model is named as the SCT model because if its three basic components: Specification (S, which describes the application characteristics, Configuration (C, which describes the rules for building applications, and Templates (T, which refer to application building blocks. The process of code generation dynamically creates XML frames containing all building elements (S, C ant T until final code is produced. This approach is compared to existing XVCL frames based model for source code generating. The SCT model is described by both XML syntax and the appropriate graphical elements. The SCT model is aimed to build complete applications, not just skeletons. The main advantages of the presented model are its textual and graphic description, a fully configurable generator, and the reduced overhead of the generated source code. The presented SCT model is shown on development of web application example in order to demonstrate its features and justify our design choices.

  7. A novel posture alignment system for aircraft wing assembly

    Institute of Scientific and Technical Information of China (English)

    Bin ZHANG; Bao-guo YAO; Ying-lin KE

    2009-01-01

    A novel 6-degree of freedom (DOF) posture alignment system, based on 3-DOF positioners, is presented for the assembly of aircraft wings. Each positioner is connected with the wing through a rotational and adsorptive half-ball shaped end-effector, and the positioners together with the wing are considered as a 3-PPPS (P denotes a prismatic joint and S denotes a spherical joint) redundantly actuated parallel mechanism. The kinematic model of this system is established and a trajectory planning method is introduced. A complete analysis of inverse dynamics is carried out with the Newton-Euler algorithm, which is used to find the desired actuating torque in the design and path planning phase. Simulation analysis of the displacement and actuating torque of each joint of the positioners based on inverse kinematics and dynamics is conducted, and the results show that the system is feasible for the posture alignment of aircraft wings.

  8. 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...

  9. A network-based dynamical ranking system

    CERN Document Server

    Motegi, Shun

    2012-01-01

    Ranking players or teams in sports is of practical interests. From the viewpoint of networks, a ranking system is equivalent a centrality measure for sports networks, whereby a directed link represents the result of a single game. Previously proposed network-based ranking systems are derived from static networks, i.e., aggregation of the results of games over time. However, the score (i.e., strength) of a player, for example, depends on time. Defeating a renowned player in the peak performance is intuitively more rewarding than defeating the same player in other periods. To account for this factor, we propose a dynamic variant of such a network-based ranking system and apply it to professional men's tennis data. Our ranking system, also interpreted as a centrality measure for directed temporal networks, has two parameters. One parameter represents the exponential decay rate of the past score, and the other parameter controls the effect of indirect wins on the score. We derive a set of linear online update equ...

  10. Conformational fluctuations affect protein alignment in dilute liquid crystal media

    DEFF Research Database (Denmark)

    Louhivuori, M.; Otten, R.; Lindorff-Larsen, Kresten

    2006-01-01

    The discovery of dilute liquid crystalline media to align biological macromolecules has opened many new possibilities to study protein and nucleic acid structures by NMR spectroscopy. We inspect the basic alignment phenomenon for an ensemble of protein conformations to deduce relative contributions...... molecular surfaces. Furthermore, we consider the implications of a dynamic bias to structure determination using data from the weak alignment method....

  11. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed Affan

    2012-01-26

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

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

    Science.gov (United States)

    Jordan, Gregory; Goldman, Nick

    2012-04-01

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

  13. CHROMATOGATE: A TOOL FOR DETECTING BASE MIS-CALLS IN MULTIPLE SEQUENCE ALIGNMENTS BY SEMI-AUTOMATIC CHROMATOGRAM INSPECTION

    Directory of Open Access Journals (Sweden)

    Nikolaos Alachiotis

    2013-03-01

    Full Text Available Automated DNA sequencers generate chromatograms that contain raw sequencing data. They also generate data that translates the chromatograms into molecular sequences of A, C, G, T, or N (undetermined characters. Since chromatogram translation programs frequently introduce errors, a manual inspection of the generated sequence data is required. As sequence numbers and lengths increase, visual inspection and manual correction of chromatograms and corresponding sequences on a per-peak and per-nucleotide basis becomes an error-prone, time-consuming, and tedious process. Here, we introduce ChromatoGate (CG, an open-source software that accelerates and partially automates the inspection of chromatograms and the detection of sequencing errors for bidirectional sequencing runs. To provide users full control over the error correction process, a fully automated error correction algorithm has not been implemented. Initially, the program scans a given multiple sequence alignment (MSA for potential sequencing errors, assuming that each polymorphic site in the alignment may be attributed to a sequencing error with a certain probability. The guided MSA assembly procedure in ChromatoGate detects chromatogram peaks of all characters in an alignment that lead to polymorphic sites, given a user-defined threshold. The threshold value represents the sensitivity of the sequencing error detection mechanism. After this pre-filtering, the user only needs to inspect a small number of peaks in every chromatogram to correct sequencing errors. Finally, we show that correcting sequencing errors is important, because population genetic and phylogenetic inferences can be misled by MSAs with uncorrected mis-calls. Our experiments indicate that estimates of population mutation rates can be affected two- to three-fold by uncorrected errors.

  14. Quantum Phase Analysis of Field-Free Molecular Alignment

    CERN Document Server

    Yun, Sang Jae; Lee, Jongmin; Nam, Chang Hee

    2015-01-01

    We present quantum mechanical explanations for unresolved phenomena observed in field-free molecular alignment by a femtosecond laser pulse. Quantum phase analysis of molecular rotational states reveals the physical origin of the following phenomena: strong alignment peaks appear periodically, and the temporal shape of each alignment peak changes in an orderly fashion depending on molecular species; the strongest alignment is not achieved at the first peak; the transition between aligned and anti-aligned states is very fast compared to the time scale of rotational dynamics. These features are understood in a unified way analogous to that describing a carrier-envelope-phase-stabilized mode-locked laser.

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

    Science.gov (United States)

    Sudha Sadasivam, G; Baktavatchalam, G

    2010-01-01

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

  16. Laser shaft alignment measurement model

    Science.gov (United States)

    Mo, Chang-tao; Chen, Changzheng; Hou, Xiang-lin; Zhang, Guoyu

    2007-12-01

    Laser beam's track which is on photosensitive surface of the a receiver will be closed curve, when driving shaft and the driven shaft rotate with same angular velocity and rotation direction. The coordinate of arbitrary point which is on the curve is decided by the relative position of two shafts. Basing on the viewpoint, a mathematic model of laser alignment is set up. By using a data acquisition system and a data processing model of laser alignment meter with single laser beam and a detector, and basing on the installation parameter of computer, the state parameter between two shafts can be obtained by more complicated calculation and correction. The correcting data of the four under chassis of the adjusted apparatus moving on the level and the vertical plane can be calculated. This will instruct us to move the apparatus to align the shafts.

  17. 基于罗经法和CDKF的捷联惯导摇摆基座自对准%SINS swaying-base self-alignment based on compass method and CDKF

    Institute of Scientific and Technical Information of China (English)

    马涛; 孙尧; 高延滨; 郭婧

    2012-01-01

    Aiming at the problem of the decline in self-alignmem precision of the ship and the shipboard weapon systems in the presence of waves, a self-alignment approach which coarse alignment based on compass method and fine alignment based on center difference Kalman filter is proposed. The classic compass method can make the attitude convergence to a limit accuracy which the fine alignment algorithm can be tolerated with any initial error. The fine alignment algorithm based on CDKF can estimate the attitude error accurately with a relative large misalignment angle. The simulation experiment illustrate that the proposed approach is suitable for any SINS alignment without maneuvering with high precision and fast speed,simple realization.%针对舰船和舰载武器系统存在风浪的情况下自对准精度下降的问题,提出了一种改进罗经法粗对准和利用中心差分卡尔曼滤波(CDKF)法进行精对准的捷联惯导系统摇摆基座下的自对准方法.利用经典罗经算法在惯性系下对捷联系统进行粗对准,可以在方位角存任意误差时收敛到一个精对准算法可以容忍的范围内,而CDKF精对准算法在存在相对较大的失准角下仍能实现高精度的姿态角误差估计.仿真实验证明:提出的方法对准精度高,速度快,实现简单,适用与各种无机动条件下的捷联惯性系统的自始准.

  18. Paramagnetic alignment of small grains: a novel method for measuring interstellar magnetic fields

    CERN Document Server

    Hoang, Thiem; Martin, P G

    2013-01-01

    We present a novel method to measure the strength of interstellar magnetic fields based on ultraviolet (UV) polarization of starlight, which is in part produced by weakly aligned, small interstellar grains. We begin with calculating degrees of alignment of small (size a~ 0.01 micron) and very small (a ~ 0.001 micron) grains in the interstellar magnetic field by the Davis-Greenstein paramagnetic relaxation and resonance paramagnetic relaxation. We compute the degrees of paramagnetic alignment with the ambient magnetic field B using Langevin equations. In this paper, we take into account various processes essential for the dynamics of small grains, including infrared (IR) emission, electric dipole emission, plasma drag and collisions with ionized species. We find that the alignment of small grains is necessary to reproduce the observed polarization in the UV, although the polarization arising from these small grains is negligible at the optical and IR wavelengths. Based on fitting theoretical models to observed...

  19. Distributed Interference Alignment with Low Overhead

    CERN Document Server

    Ma, Yanjun; Chen, Rui

    2011-01-01

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

  20. Spatial and kinematic alignments between central and satellite halos

    OpenAIRE

    Faltenbacher, A.; Jing, Y. P.; Li, Cheng; Mao, Shude; Mo, H. J.; Pasquali, Anna; Bosch, Frank C. van den

    2007-01-01

    Based on a cosmological N-body simulation we analyze spatial and kinematic alignments of satellite halos within six times the virial radius of group size host halos (Rvir). We measure three different types of spatial alignment: halo alignment between the orientation of the group central substructure (GCS) and the distribution of its satellites, radial alignment between the orientation of a satellite and the direction towards its GCS, and direct alignment between the orientation of the GCS and...

  1. 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.

  2. Labyrinthine water flow across multilayer graphene-based membranes: molecular dynamics versus continuum predictions

    CERN Document Server

    Yoshida, Hiroaki

    2016-01-01

    In this paper we investigate the hydrodynamic permeance of water through graphene-based membranes, inspired by recent experimental findings on graphene-oxide membranes. We consider the flow across multiple graphene layers having nanoslits in a staggered alignment, with an inter-layer distance ranging from sub- nanometer to a few nanometers. We compare results for the permeability obtained by means of molecular dynamics simulations to continuum predictions obtained by using the lattice Boltzmann calculations and hydrodynamic modelization. This highlights that, in spite of extreme confinement, the permeability across the graphene-based membrane is quantitatively predicted on the basis of a continuum expression, taking properly into account entrance and slippage effects of the confined water flow. Our predictions refute the breakdown of hydrodynamics at small scales in these membrane systems. They constitute a benchmark to which we compare published experimental data.

  3. Protein sequence alignment analysis by local covariation: coevolution statistics detect benchmark alignment errors.

    Directory of Open Access Journals (Sweden)

    Russell J Dickson

    Full Text Available The use of sequence alignments to understand protein families is ubiquitous in molecular biology. High quality alignments are difficult to build and protein alignment remains one of the largest open problems in computational biology. Misalignments can lead to inferential errors about protein structure, folding, function, phylogeny, and residue importance. Identifying alignment errors is difficult because alignments are built and validated on the same primary criteria: sequence conservation. Local covariation identifies systematic misalignments and is independent of conservation. We demonstrate an alignment curation tool, LoCo, that integrates local covariation scores with the Jalview alignment editor. Using LoCo, we illustrate how local covariation is capable of identifying alignment errors due to the reduction of positional independence in the region of misalignment. We highlight three alignments from the benchmark database, BAliBASE 3, that contain regions of high local covariation, and investigate the causes to illustrate these types of scenarios. Two alignments contain sequential and structural shifts that cause elevated local covariation. Realignment of these misaligned segments reduces local covariation; these alternative alignments are supported with structural evidence. We also show that local covariation identifies active site residues in a validated alignment of paralogous structures. Loco is available at https://sourceforge.net/projects/locoprotein/files/.

  4. Theory of Dynamic Diagnosis Based on Integrated Maintenance Information

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Based on the concept of an integrated maintenance information system and related information environment, this paper discusses the process of troubleshooting in modern maintenance in detail, and gives a model of dynamic diagnosis of faults, in which a reasoning program is designed through taking advantage of information fusion and time analysis. In the end, the authors present the logic process of dynamic diagnosis through a typical example, and proposes a dynamic diagnostic system based on information fusion.

  5. Post-trial anatomical frame alignment procedure for comparison of 3D joint angle measurement from magnetic/inertial measurement units and camera-based systems.

    Science.gov (United States)

    Li, Qingguo; Zhang, Jun-Tian

    2014-11-01

    Magnetic and inertial measurement units (MIMUs) have been widely used as an alternative to traditional camera-based motion capture systems for 3D joint kinematics measurement. Since these sensors do not directly measure position, a pre-trial anatomical calibration, either with the assistance of a special protocol/apparatus or with another motion capture system is required to establish the transformation matrices between the local sensor frame and the anatomical frame (AF) of each body segment on which the sensors are attached. Because the axes of AFs are often used as the rotational axes in the joint angle calculation, any difference in the AF determination will cause discrepancies in the calculated joint angles. Therefore, a direct comparison of joint angles between MIMU systems and camera-based systems is less meaningful because the calculated joint angles contain a systemic error due to the differences in the AF determination. To solve this problem a new post-trial AF alignment procedure is proposed. By correcting the AF misalignments, the joint angle differences caused by the difference in AF determination are eliminated and the remaining discrepancies are mainly from the measurement accuracy of the systems themselves. Lower limb joint angles from 30 walking trials were used to validate the effectiveness of the proposed AF alignment procedure. This technique could serve as a new means for calibrating magnetic/inertial sensor-based motion capture systems and correcting for AF misalignment in scenarios where joint angles are compared directly.

  6. Evaluation of the quantitative accuracy of 3D reconstruction of edentulous jaw models with jaw relation based on reference point system alignment.

    Directory of Open Access Journals (Sweden)

    Weiwei Li

    Full Text Available OBJECTIVES: To apply contact measurement and reference point system (RPS alignment techniques to establish a method for 3D reconstruction of the edentulous jaw models with centric relation and to quantitatively evaluate its accuracy. METHODS: Upper and lower edentulous jaw models were clinically prepared, 10 pairs of resin cylinders with same size were adhered to axial surfaces of upper and lower models. The occlusal bases and the upper and lower jaw models were installed in the centric relation position. Faro Edge 1.8m was used to directly obtain center points of the base surface of the cylinders (contact method. Activity 880 dental scanner was used to obtain 3D data of the cylinders and the center points were fitted (fitting method. 3 pairs of center points were used to align the virtual model to centric relation. An observation coordinate system was interactively established. The straight-line distances in the X (horizontal left/right, Y (horizontal anterior/posterior, and Z (vertical between the remaining 7 pairs of center points derived from contact method and fitting method were measured respectively and analyzed using a paired t-test. RESULTS: The differences of the straight-line distances of the remaining 7 pairs of center points between the two methods were X: 0.074 ± 0.107 mm, Y: 0.168 ± 0.176 mm, and Z: -0.003± 0.155 mm. The results of paired t-test were X and Z: p >0.05, Y: p <0.05. CONCLUSION: By using contact measurement and the reference point system alignment technique, highly accurate reconstruction of the vertical distance and centric relation of a digital edentulous jaw model can be achieved, which meets the design and manufacturing requirements of the complete dentures. The error of horizontal anterior/posterior jaw relation was relatively large.

  7. 一种数字光栅无掩模光刻对准方法%A Digital-Grating-Based Alignment Technique in Maskless Lithography

    Institute of Scientific and Technical Information of China (English)

    唐路路; 胡松; 徐峰; 唐燕; 陈铭勇; 朱江平

    2012-01-01

    针对数字微反射镜装置(DMD)无掩模光刻系统,提出并研究了一种数字光栅无掩模光刻对准方法,将硅片的微位移放大显示在数字光栅与硅片物理光栅叠加产生的叠栅条纹中.建立了基于DMD的数字光栅无掩模光刻对准模型,设计了对准标记以及具体的实现方案,并对模型进行了数值仿真和初步的实验验证.结果表明,采用频率可变、图像干净、具有良好周期性结构的数字光栅代替传统的真实掩模光栅,真正实现了零掩模成本;并且采用变频率数字光栅可以扩大测量范围,减小位移测量误差.最终可以实现深亚微米的对准精度,满足目前无掩模光刻对准精度的要求.%A digital-grating-based alignment technique is brought forward and researched for digital micromirror device (DMD) maskless lithography system. Infinitesimal displacement of a silicon chip is amplified and displayed in moire fringes generated by digital grating and physical grating. A digital-grating-based alignment model is created in DMD-based maskless lithography system. The alignment marks as well as detailed realization program is designed. Numerical simulation and preliminary experimental test is carried out. Compared to the traditional real mask, the grating digital gating characterized with variable frequency, clear image, good periodic structure and zero mask cost will extend the measurement range and reduce the displacement measurement error. This technique can realize deep sub-micron alignment accuracy, and satisfy the requirements of maskless lithography.

  8. 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.

  9. Spatial and Temporal Dynamics and Value of Nature-Based Recreation, Estimated via Social Media.

    Science.gov (United States)

    Sonter, Laura J; Watson, Keri B; Wood, Spencer A; Ricketts, Taylor H

    2016-01-01

    Conserved lands provide multiple ecosystem services, including opportunities for nature-based recreation. Managing this service requires understanding the landscape attributes underpinning its provision, and how changes in land management affect its contribution to human wellbeing over time. However, evidence from both spatially explicit and temporally dynamic analyses is scarce, often due to data limitations. In this study, we investigated nature-based recreation within conserved lands in Vermont, USA. We used geotagged photographs uploaded to the photo-sharing website Flickr to quantify visits by in-state and out-of-state visitors, and we multiplied visits by mean trip expenditures to show that conserved lands contributed US $1.8 billion (US $0.18-20.2 at 95% confidence) to Vermont's tourism industry between 2007 and 2014. We found eight landscape attributes explained the pattern of visits to conserved lands; visits were higher in larger conserved lands, with less forest cover, greater trail density and more opportunities for snow sports. Some of these attributes differed from those found in other locations, but all aligned with our understanding of recreation in Vermont. We also found that using temporally static models to inform conservation decisions may have perverse outcomes for nature-based recreation. For example, static models suggest conserved land with less forest cover receive more visits, but temporally dynamic models suggest clearing forests decreases, rather than increases, visits to these sites. Our results illustrate the importance of understanding both the spatial and temporal dynamics of ecosystem services for conservation decision-making.

  10. Dynamic summarization of bibliographic-based data

    Directory of Open Access Journals (Sweden)

    Hurdle John F

    2011-02-01

    Full Text Available Abstract Background Traditional information retrieval techniques typically return excessive output when directed at large bibliographic databases. Natural Language Processing applications strive to extract salient content from the excessive data. Semantic MEDLINE, a National Library of Medicine (NLM natural language processing application, highlights relevant information in PubMed data. However, Semantic MEDLINE implements manually coded schemas, accommodating few information needs. Currently, there are only five such schemas, while many more would be needed to realistically accommodate all potential users. The aim of this project was to develop and evaluate a statistical algorithm that automatically identifies relevant bibliographic data; the new algorithm could be incorporated into a dynamic schema to accommodate various information needs in Semantic MEDLINE, and eliminate the need for multiple schemas. Methods We developed a flexible algorithm named Combo that combines three statistical metrics, the Kullback-Leibler Divergence (KLD, Riloff's RlogF metric (RlogF, and a new metric called PredScal, to automatically identify salient data in bibliographic text. We downloaded citations from a PubMed search query addressing the genetic etiology of bladder cancer. The citations were processed with SemRep, an NLM rule-based application that produces semantic predications. SemRep output was processed by Combo, in addition to the standard Semantic MEDLINE genetics schema and independently by the two individual KLD and RlogF metrics. We evaluated each summarization method using an existing reference standard within the task-based context of genetic database curation. Results Combo asserted 74 genetic entities implicated in bladder cancer development, whereas the traditional schema asserted 10 genetic entities; the KLD and RlogF metrics individually asserted 77 and 69 genetic entities, respectively. Combo achieved 61% recall and 81% precision, with an F

  11. Alignment-free phylogenetics and population genetics.

    Science.gov (United States)

    Haubold, Bernhard

    2014-05-01

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

  12. Dynamic symmetrical pattern projection based laser triangulation sensor for precise surface position measurement of various material types.

    Science.gov (United States)

    Žbontar, Klemen; Mihelj, Matjaž; Podobnik, Boštjan; Povše, Franc; Munih, Marko

    2013-04-20

    This paper describes a custom, material-type-independent laser-triangulation-based measurement system that utilizes a high-quality ultraviolet laser beam. Laser structuring applications demand material surface alignment regarding the laser focus position, where fabrication conditions are optimal. Robust alignment of various material types was solved by introducing dynamic symmetrical pattern projection, and a "double curve fitting" centroid detection algorithm with subsurface scattering compensation. Experimental results have shown that the measurement system proves robust to laser intensity variation, with measurement bias lower than 50 μm and standard deviation lower than ±6.3 μm for all materials. The developed probe has been integrated into a PCB prototyping system for material referencing purposes.

  13. Real-time fiber-optic anemometer based on a laser-heated few-layer graphene in an aligned graded-index fiber.

    Science.gov (United States)

    Gao, Ran; Lu, Danfeng; Cheng, Jin; Qi, Zhi-Mei

    2017-07-15

    A real-time all-fiber anemometer based on laser-heated few-layer graphene in aligned graded-index fibers has been proposed and experimentally demonstrated. The proposed fiber-optic anemometer was composed of a pair of all-fiber collimators by using aligned graded-index fibers that was coated with the few-layer graphene. The few-layer graphene was heated through a heating light from a 532-nm laser, which changed the optical transmittance of signal light with the wavelength of 1550 nm. The wind speed can be measured through the transmission power of the signal light based on the wind cooling effects on the heated few-layer graphene, acting as a "hot-wire" anemometer. The experimental results show that the maximum sensitivity of the anemometer reaches -22.03  μW/(m/s), and a fast response time of as 0.064 s can be achieved. The proposed fiber sensor can be used for the real-time measurement of wind speed in the fields of environmental monitoring, oil exploration, oceanography research, etc.

  14. 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...

  15. GATA: a graphic alignment tool for comparative sequence analysis

    Directory of Open Access Journals (Sweden)

    Nix David A

    2005-01-01

    Full Text Available Abstract Background Several problems exist with current methods used to align DNA sequences for comparative sequence analysis. Most dynamic programming algorithms assume that conserved sequence elements are collinear. This assumption appears valid when comparing orthologous protein coding sequences. Functional constraints on proteins provide strong selective pressure against sequence inversions, and minimize sequence duplications and feature shuffling. For non-coding sequences this collinearity assumption is often invalid. For example, enhancers contain clusters of transcription factor binding sites that change in number, orientation, and spacing during evolution yet the enhancer retains its activity. Dot plot analysis is often used to estimate non-coding sequence relatedness. Yet dot plots do not actually align sequences and thus cannot account well for base insertions or deletions. Moreover, they lack an adequate statistical framework for comparing sequence relatedness and are limited to pairwise comparisons. Lastly, dot plots and dynamic programming text outputs fail to provide an intuitive means for visualizing DNA alignments. Results To address some of these issues, we created a stand alone, platform independent, graphic alignment tool for comparative sequence analysis (GATA http://gata.sourceforge.net/. GATA uses the NCBI-BLASTN program and extensive post-processing to identify all small sub-alignments above a low cut-off score. These are graphed as two shaded boxes, one for each sequence, connected by a line using the coordinate system of their parent sequence. Shading and colour are used to indicate score and orientation. A variety of options exist for querying, modifying and retrieving conserved sequence elements. Extensive gene annotation can be added to both sequences using a standardized General Feature Format (GFF file. Conclusions GATA uses the NCBI-BLASTN program in conjunction with post-processing to exhaustively align two DNA

  16. Gene Time E{chi}pression Warper: a tool for alignment, template matching and visualization of gene expression time series.

    Science.gov (United States)

    Criel, Jo; Tsiporkova, Elena

    2006-01-15

    An application tool for alignment, template matching and visualization of gene expression time series is presented. The core algorithm is based on dynamic time warping techniques used in the speech recognition field. These techniques allow for non-linear (elastic) alignment of temporal sequences of feature vectors and consequently enable detection of similar shapes with different phases. The Java program, examples and a tutorial are available at http://www.psb.ugent.be/cbd/papers/gentxwarper/

  17. 一种基于VB的实用轴对中数学模型研究%Study on a Practical Shaft Alignment Mathematical Model Based on VB

    Institute of Scientific and Technical Information of China (English)

    慕丽; 王欣威

    2011-01-01

    A shaft alignment measuring principle which was different from the traditional measuring principle was proposed based on the existing theroy. The mathematic model was established and the shaft alignment principle was analyzed. The relative position of two axes could be obtained by calculating the spot's coordinate on the photosensitive surface which was irradiated by LD. The adjust ment formula of slave axis' forefoot and rear foot could be derived. The alignment purpose could be accomplished by adjusting the axis' position. Interface and data processing were designed with VB. It is verified that the measurement method is simple, accurate and ef fective by detecting the real engineering quantity.%在参考现有激光对中仪原理的基础上,提出一种不同于传统对中测量的测量原理.建立激光对中仪的数学模型并分析其对中原理.通过计算LD所发射的光信号落在PSD光敏面上的光斑坐标,求得两轴的相对位置,从而推导出从动轴的前脚和后脚的调整公式,调整轴的位置达到对中目的.利用VB进行界面设计和数据处理.同时进行了实际工程量检测,验证了该测量方法的简便性、准确性和有效性.

  18. Inferring Directed Road Networks from GPS Traces by Track Alignment

    Directory of Open Access Journals (Sweden)

    Xingzhe Xie

    2015-11-01

    Full Text Available This paper proposes a method to infer road networks from GPS traces. These networks include intersections between roads, the connectivity between the intersections and the possible traffic directions between directly-connected intersections. These intersections are localized by detecting and clustering turning points, which are locations where the moving direction changes on GPS traces. We infer the structure of road networks by segmenting all of the GPS traces to identify these intersections. We can then form both a connectivity matrix of the intersections and a small representative GPS track for each road segment. The road segment between each pair of directly-connected intersections is represented using a series of geographical locations, which are averaged from all of the tracks on this road segment by aligning them using the dynamic time warping (DTW algorithm. Our contribution is two-fold. First, we detect potential intersections by clustering the turning points on the GPS traces. Second, we infer the geometry of the road segments between intersections by aligning GPS tracks point by point using a “stretch and then compress” strategy based on the DTW algorithm. This approach not only allows road estimation by averaging the aligned tracks, but also a deeper statistical analysis based on the individual track’s time alignment, for example the variance of speed along a road segment.

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

    Science.gov (United States)

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

    2010-01-01

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

  20. Instructional Alignment under No Child Left Behind

    Science.gov (United States)

    Polikoff, Morgan S.

    2012-01-01

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

  1. Dynamic Gesture Recognition Based on Depth Information

    Directory of Open Access Journals (Sweden)

    GU, D.

    2015-08-01

    Full Text Available Human machine interaction by body language is becoming popular recently. With the help of 3D camera, video stream with depth information provides more detailed data to describe a movement. This paper proposed an algorithm to recognize dynamic gestures. Data preparation is needed first to eliminate some distractions. Then the start and the end of a possible meaningful gesture should be made clear. Finally, Dynamic Time Warping (DTW is employed to calculate the similarity between a sample stream and the template. The test results show that the algorithm works well

  2. Simulation Trials of Wheel Alignment Parameters Based on Elastic Bushing and Flexible Parts%基于弹性衬套和柔性零部件的车轮定位参数仿真试验

    Institute of Scientific and Technical Information of China (English)

    秦东晨; 蓝贤清; 于立

    2011-01-01

    为了分析悬架中弹性衬套替换刚性铰接及主要承栽零部件的柔化处理对车轮定位参数的影响,以多体动力学理论为基础,在Adams中建立了某车双横臂独立悬架多刚体模型Ⅰ,对三因素弹性衬套替换刚性铰接以及下横臂和横向稳定杆的柔化处理的影响进行仿真试验.仿真结果说明:3个因素对车轮定位参数有很大的影响.在模型Ⅰ的基础上综合考虑上述3个因素建立了模型Ⅱ并进行悬架运动学分析,揭示了车轮定位参数的变化特性,为悬架的开发设计奠定了基础.%Based on multi-body dynamics theory, in order to analyze the impact of wheel alignment parameters caused by elastic bushing replacement of rigid hinge, and flexible treatment towards the main parts which bear force and torque in the suspension, the rigid simulation model (Model I) of double-wishbone independent suspension of a certain vehicle is established using Adams/Car module. By means of simulation trials such as replacement of rigid hinge with resilient bushing, as well as flexible treatment towards the upper/lower control arm and the horizontal stabilizer bar in the established rigid suspension model, the results explain that the replacement of rigid hinge with resilient bushing, along with the flexible treatment of the lower control arm and horizontal stabilizer bar, have great impact to wheel alignment parameters. Based on Model I,taking the above three factors into account to establish suspension Model II for kinematics analysis, the results reveal the variation characteristic of wheel alignment parameters, which lays a sound foundation for the development and design for the suspension.

  3. Dynamic Beam Based Calibration of Beam Position Monitors

    CERN Document Server

    Dehning, Bernd; Galbraith, Peter; Mugnai, G; Placidi, Massimo; Sonnemann, F; Tecker, F A; Wenninger, J

    1998-01-01

    The degree of spin polarization at LEP is strongly dependent on the knowledge of the vertical orbit. Quadrupole magnet alignment and beam position monitor (BPM) offsets are the main source of the orbi t uncertainty. The error of the orbit monitor readings can be largely reduced by calibrating the monitor relative to the adjacent quadrupole. At LEP, 16 BPM offsets can be determined in parallel durin g 40 minutes. The error of the measure offset is about 30mm. During the LEP run 1997, more than 500 measurements were made and used for the optimisation of polarization. The method of dynamic beam bas ed calibration will be explained and the results will be shown.

  4. Cycle stability of the electrochemical capacitors patterned with vertically aligned carbon nanotubes in an LiPF6-based electrolyte

    Science.gov (United States)

    Chiou, Yi-Deng; Tsai, Dah-Shyang; Lam, Hoa Hung; Chang, Chuan-Hua; Lee, Kuei-Yi; Huang, Ying-Sheng

    2013-08-01

    The miniature ultracapacitors, with interdigitated electrodes of vertically aligned carbon nanotubes (VACNTs) and an inter-electrode gap of 20 μm, have been prepared in the LiPF6 organic electrolyte with and without PVdF-HFP gel. PVdF-HFP between two opposing electrodes enhances the device reliability, but lessens its power performance because of the extra diffusion resistance. Also noteworthy are the gel influences on the cycle stability. When the applied voltage is 2.0 or 2.5 V, both the LiPF6 and the gel capacitors exhibit excellent stability, typified by a retention ratio of >=95% after 10 000 cycles. Their coulombic efficiencies quickly rise up, and hold steady at 100%. Nonetheless, when the applied voltage is 3.5 or 4.0 V, the cycle stability deteriorates, since the negative electrode potential descends below 0.9 V (vs. Li), leading to electrolyte decomposition and SEI formation. For the LiPF6 capacitor, its retention ratio could be around 60% after 10 000 cycles and the coulombic efficiency of 100% is difficult to reach throughout its cycle life. On the other hand, the gel capacitor cycles energy with a much higher retention ratio, >80% after 10 000 cycles, and a better coulombic efficiency, even though electrolyte decomposition still occurs. We attribute the superior stability of the gel capacitor to its extra diffusion resistance which slows down the performance deterioration.

  5. Machinery running state identification based on discriminant semi-supervised local tangent space alignment for feature fusion and extraction

    Science.gov (United States)

    Su, Zuqiang; Xiao, Hong; Zhang, Yi; Tang, Baoping; Jiang, Yonghua

    2017-04-01

    Extraction of sensitive features is a challenging but key task in data-driven machinery running state identification. Aimed at solving this problem, a method for machinery running state identification that applies discriminant semi-supervised local tangent space alignment (DSS-LTSA) for feature fusion and extraction is proposed. Firstly, in order to extract more distinct features, the vibration signals are decomposed by wavelet packet decomposition WPD, and a mixed-domain feature set consisted of statistical features, autoregressive (AR) model coefficients, instantaneous amplitude Shannon entropy and WPD energy spectrum is extracted to comprehensively characterize the properties of machinery running state(s). Then, the mixed-dimension feature set is inputted into DSS-LTSA for feature fusion and extraction to eliminate redundant information and interference noise. The proposed DSS-LTSA can extract intrinsic structure information of both labeled and unlabeled state samples, and as a result the over-fitting problem of supervised manifold learning and blindness problem of unsupervised manifold learning are overcome. Simultaneously, class discrimination information is integrated within the dimension reduction process in a semi-supervised manner to improve sensitivity of the extracted fusion features. Lastly, the extracted fusion features are inputted into a pattern recognition algorithm to achieve the running state identification. The effectiveness of the proposed method is verified by a running state identification case in a gearbox, and the results confirm the improved accuracy of the running state identification.

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

    Institute of Scientific and Technical Information of China (English)

    徐小俊; 雷秀娟; 郭玲

    2011-01-01

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

  7. H2r: Identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments

    Directory of Open Access Journals (Sweden)

    Zwick Matthias

    2008-03-01

    Full Text Available Abstract Background A multiple sequence alignment (MSA generated for a protein can be used to characterise residues by means of a statistical analysis of single columns. In addition to the examination of individual positions, the investigation of co-variation of amino acid frequencies offers insights into function and evolution of the protein and residues. Results We introduce conn(k, a novel parameter for the characterisation of individual residues. For each residue k, conn(k is the number of most extreme signals of co-evolution. These signals were deduced from a normalised mutual information (MI value U(k, l computed for all pairs of residues k, l. We demonstrate that conn(k is a more robust indicator than an individual MI-value for the prediction of residues most plausibly important for the evolution of a protein. This proposition was inferred by means of statistical methods. It was further confirmed by the analysis of several proteins. A server, which computes conn(k-values is available at http://www-bioinf.uni-regensburg.de. Conclusion The algorithms H2r, which analyses MSAs and computes conn(k-values, characterises a specific class of residues. In contrast to strictly conserved ones, these residues possess some flexibility in the composition of side chains. However, their allocation is sensibly balanced with several other positions, as indicated by conn(k.

  8. PrimerDesign-M: a multiple-alignment based multiple-primer design tool for walking across variable genomes.

    Science.gov (United States)

    Yoon, Hyejin; Leitner, Thomas

    2015-05-01

    Analyses of entire viral genomes or mtDNA requires comprehensive design of many primers across their genomes. Furthermore, simultaneous optimization of several DNA primer design criteria may improve overall experimental efficiency and downstream bioinformatic processing. To achieve these goals, we developed PrimerDesign-M. It includes several options for multiple-primer design, allowing researchers to efficiently design walking primers that cover long DNA targets, such as entire HIV-1 genomes, and that optimizes primers simultaneously informed by genetic diversity in multiple alignments and experimental design constraints given by the user. PrimerDesign-M can also design primers that include DNA barcodes and minimize primer dimerization. PrimerDesign-M finds optimal primers for highly variable DNA targets and facilitates design flexibility by suggesting alternative designs to adapt to experimental conditions. PrimerDesign-M is available as a webtool at http://www.hiv.lanl.gov/content/sequence/PRIMER_DESIGN/primer_design.html tkl@lanl.gov or seq-info@lanl.gov. Published by Oxford University Press 2014. This work is written by US Government employees and is in the public domain in the US.

  9. Dynamic Terrain Visualization Based on ROAM and OGRE

    Institute of Scientific and Technical Information of China (English)

    FU Hui; WANG Quanmin

    2009-01-01

    Terrain Visualization is an important part of visualization systems of battlefield,and the visualization of dynamic terrain is also important for dynamic battle environment.In this paper,special attention has been paid on real-time optimally adapting meshes (ROAM) algorithm,which is a candidate for dynamic terrain,and its mesh representation,mesh continuity algorithm and error metrics are discussed.The DEXTER-ROAM algorithm is discussed and analyzed.By revising the mesh representation of ROAM,a dynamic ROAM algorithm based on partial-regular grid is established.By introducing transition region,mesh discontinuity of dynamic partial-regular grid is resolved.Error metric blocks are removed for computation complexity and culling blocks are introduced to accelerate view frustum culling.The algorithm is implemented in a 3D rendering engine called OGRE.In the end,an example of dynamic crater is given to examine the dynamic ROAM algorithm.

  10. Neural network based dynamic controllers for industrial robots.

    Science.gov (United States)

    Oh, S Y; Shin, W C; Kim, H G

    1995-09-01

    The industrial robot's dynamic performance is frequently measured by positioning accuracy at high speeds and a good dynamic controller is essential that can accurately compute robot dynamics at a servo rate high enough to ensure system stability. A real-time dynamic controller for an industrial robot is developed here using neural networks. First, an efficient time-selectable hidden layer architecture has been developed based on system dynamics localized in time, which lends itself to real-time learning and control along with enhanced mapping accuracy. Second, the neural network architecture has also been specially tuned to accommodate servo dynamics. This not only facilitates the system design through reduced sensing requirements for the controller but also enhances the control performance over the control architecture neglecting servo dynamics. Experimental results demonstrate the controller's excellent learning and control performances compared with a conventional controller and thus has good potential for practical use in industrial robots.

  11. Collective alignment of polar filaments by molecular motors.

    Science.gov (United States)

    Ziebert, F; Vershinin, M; Gross, S P; Aranson, I S

    2009-04-01

    We study the alignment of polar biofilaments, such as microtubules and actin, subject to the action of multiple molecular motors attached simultaneously to more than one filament. Focusing on a paradigm model of only two filaments interacting with multiple motors, we were able to investigate in detail the alignment dynamics. While almost no alignment occurs in the case of a single motor, the filaments become rapidly aligned due to the collective action of the motors. Our analysis shows that the alignment time is governed by the number of bound motors and the magnitude of the motors' stepping fluctuations. We predict that the time scale of alignment is in the order of seconds, much faster than that reported for passive crosslink-induced bundling. In vitro experiments on the alignment of microtubules by multiple-motor covered beads are in qualitative agreement. We also discuss another mode of fast alignment of filaments, namely the cooperation between motors and passive crosslinks.

  12. Alignment and Load Transfer in Carbon Nanotube and Dicyclopentadiene Composites

    Science.gov (United States)

    Severino, Joseph Vincent

    Individual carbon nanotubes (CNTs) are the strongest materials available but their macroscopic assemblies are weak. This work establishes a new thermosetting dicyclopentadiene (DCPD) and CNT composite that increases the strength of CNT assemblies. These high volume fraction and void free structures constitute advanced materials that could one day replace traditional composite systems. To further the understanding of physical interactions between polymer and CNTs, a novel "capstan" load transfer mechanism is also introduced. Self-supporting assemblies of interconnected carbon nanotubes were stretched, twisted and compressed to fashion composites by the infusion and polymerization of low viscosity DCPD based monomeric resins. The properties of the CNTs, polymer and composite were characterized with thermal gravimetric analysis (TGA), dynamic mechanical analysis (DMA) and Raman spectroscopy. The microstructure was analyzed by wide angle X-ray scattering (WAXS), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Sheets were drawn at 15 m/min from a growth furnace to impart alignment then stretched to further modify alignment. The mechanical properties were determined in five orientations with respect to the growth direction. The strength was nearly three times higher along this growth direction than it was perpendicular, and modulus was nearly six times higher. Transverse stretching achieved 1.5 times the elongation but alignment was inferior due to CNT kinking that prevented alignment and consolidation. Composites yarns and sheets were investigated for the mechanical properties, microstructure and load transfer. The DCPD resin was found to wet the CNTs and lubricated deformation. This reduced loads during processing, and curing solidified the aligned and consolidated structure. The stretched and twisted composite yarns increased the failure stress 51%. In aligned composite sheet, the failure stress increased 200%. The increased stresses

  13. Arresting Strategy Based on Dynamic Criminal Networks Changing over Time

    Directory of Open Access Journals (Sweden)

    Junqing Yuan

    2013-01-01

    Full Text Available We investigate a sequence of dynamic criminal networks on a time series based on the dynamic network analysis (DNA. According to the change of networks’ structure, networks’ variation trend is analyzed to forecast its future structure. Finally, an optimal arresting time and priority list are designed based on our analysis. Better results can be expected than that based on social network analysis (SNA.

  14. Sequential Optimization of Global Sequence Alignments Relative to Different Cost Functions

    KAUST Repository

    Odat, Enas M.

    2011-05-01

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

  15. Some aspects of SR beamline alignment

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-09-01

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

  16. Efficient Quantum Private Communication Based on Dynamic Control Code Sequence

    Science.gov (United States)

    Cao, Zheng-Wen; Feng, Xiao-Yi; Peng, Jin-Ye; Zeng, Gui-Hua; Qi, Jin

    2016-12-01

    Based on chaos and quantum properties, we propose a quantum private communication scheme with dynamic control code sequence. The initial sequence is obtained via chaotic systems, and the control code sequence is derived by grouping, XOR and extracting. A shift cycle algorithm is designed to enable the dynamic change of control code sequence. Analysis shows that transmission efficiency could reach 100 % with high dynamics and security.

  17. CADLIVE optimizer: web-based parameter estimation for dynamic models

    Directory of Open Access Journals (Sweden)

    Inoue Kentaro

    2012-08-01

    Full Text Available Abstract Computer simulation has been an important technique to capture the dynamics of biochemical networks. In most networks, however, few kinetic parameters have been measured in vivo because of experimental complexity. We develop a kinetic parameter estimation system, named the CADLIVE Optimizer, which comprises genetic algorithms-based solvers with a graphical user interface. This optimizer is integrated into the CADLIVE Dynamic Simulator to attain efficient simulation for dynamic models.

  18. Efficient Quantum Private Communication Based on Dynamic Control Code Sequence

    Science.gov (United States)

    Cao, Zheng-Wen; Feng, Xiao-Yi; Peng, Jin-Ye; Zeng, Gui-Hua; Qi, Jin

    2017-04-01

    Based on chaos and quantum properties, we propose a quantum private communication scheme with dynamic control code sequence. The initial sequence is obtained via chaotic systems, and the control code sequence is derived by grouping, XOR and extracting. A shift cycle algorithm is designed to enable the dynamic change of control code sequence. Analysis shows that transmission efficiency could reach 100 % with high dynamics and security.

  19. Highly improved homopolymer aware nucleotide-protein alignments with 454 data

    Directory of Open Access Journals (Sweden)

    Lysholm Fredrik

    2012-09-01

    Full Text Available Abstract Background Roche 454 sequencing is the leading sequencing technology for producing long read high throughput sequence data. Unlike most methods where sequencing errors translate to base uncertainties, 454 sequencing inaccuracies create nucleotide gaps. These gaps are particularly troublesome for translated search tools such as BLASTx where they introduce frame-shifts and result in regions of decreased identity and/or terminated alignments, which affect further analysis. Results To address this issue, the Homopolymer Aware Cross Alignment Tool (HAXAT was developed. HAXAT uses a novel dynamic programming algorithm for solving the optimal local alignment between a 454 nucleotide and a protein sequence by allowing frame-shifts, guided by 454 flowpeak values. The algorithm is an efficient minimal extension of the Smith-Waterman-Gotoh algorithm that easily fits in into other tools. Experiments using HAXAT demonstrate, through the introduction of 454 specific frame-shift penalties, significantly increased accuracy of alignments spanning homopolymer sequence errors. The full effect of the new parameters introduced with this novel alignment model is explored. Experimental results evaluating homopolymer inaccuracy through alignments show a two to five-fold increase in Matthews Correlation Coefficient over previous algorithms, for 454-derived data. Conclusions This increased accuracy provided by HAXAT does not only result in improved homologue estimations, but also provides un-interrupted reading-frames, which greatly facilitate further analysis of protein space, for example phylogenetic analysis. The alignment tool is available at http://bioinfo.ifm.liu.se/454tools/haxat.

  20. Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci.

    Science.gov (United States)

    Gill, Mandev S; Lemey, Philippe; Faria, Nuno R; Rambaut, Andrew; Shapiro, Beth; Suchard, Marc A

    2013-03-01

    Effective population size is fundamental in population genetics and characterizes genetic diversity. To infer past population dynamics from molecular sequence data, coalescent-based models have been developed for Bayesian nonparametric estimation of effective population size over time. Among the most successful is a Gaussian Markov random field (GMRF) model for a single gene locus. Here, we present a generalization of the GMRF model that allows for the analysis of multilocus sequence data. Using simulated data, we demonstrate the improved performance of our method to recover true population trajectories and the time to the most recent common ancestor (TMRCA). We analyze a multilocus alignment of HIV-1 CRF02_AG gene sequences sampled from Cameroon. Our results are consistent with HIV prevalence data and uncover some aspects of the population history that go undetected in Bayesian parametric estimation. Finally, we recover an older and more reconcilable TMRCA for a classic ancient DNA data set.