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Sample records for alignment method based

  1. A new initial alignment method of MIMU based on CCD

    NASA Astrophysics Data System (ADS)

    Ma, Kai; Ding, Quanxin; Zhang, Qiuzhi; Chen, Shaodong; Wang, Yongsheng

    2014-09-01

    A new initial alignment of MIMU based on CCD is proposed in this article to overcome problems of time consuming and low accuracy of the traditional HMS. By utilize the attitude information provided by CCD, MIMU can achieve initial alignment process and output real-time head attitude to compute line of sight. Simulation results indicated that the CCD measurement system can effectively reduce the wasting time of initial alignment and improve attitude measurement precision.

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

    NASA Technical Reports Server (NTRS)

    Wheeler, Ward C.

    2003-01-01

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

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

    PubMed

    Wheeler, Ward C

    2003-06-01

    A method to align sequence data based on parsimonious synapomorphy schemes generated by direct optimization (DO; earlier termed optimization alignment) is proposed. DO directly diagnoses sequence data on cladograms without an intervening multiple-alignment step, thereby creating topology-specific, dynamic homology statements. Hence, no multiple-alignment is required to generate cladograms. Unlike general and globally optimal multiple-alignment procedures, the method described here, implied alignment (IA), takes these dynamic homologies and traces them back through a single cladogram, linking the unaligned sequence positions in the terminal taxa via DO transformation series. These "lines of correspondence" link ancestor-descendent states and, when displayed as linearly arrayed columns without hypothetical ancestors, are largely indistinguishable from standard multiple alignment. Since this method is based on synapomorphy, the treatment of certain classes of insertion-deletion (indel) events may be different from that of other alignment procedures. As with all alignment methods, results are dependent on parameter assumptions such as indel cost and transversion:transition ratios. Such an IA could be used as a basis for phylogenetic search, but this would be questionable since the homologies derived from the implied alignment depend on its natal cladogram and any variance, between DO and IA + Search, due to heuristic approach. The utility of this procedure in heuristic cladogram searches using DO and the improvement of heuristic cladogram cost calculations are discussed. PMID:12901383

  4. Genome-based phylogeny of dsDNA viruses by a novel alignment-free method.

    PubMed

    Gao, Yang; Luo, Liaofu

    2012-01-15

    Sequence alignment is not directly applicable to whole genome phylogeny since several events such as rearrangements make full length alignments impossible. Here, a novel alignment-free method derived from the standpoint of information theory is proposed and used to construct the whole-genome phylogeny for a population of viruses from 13 viral families comprising 218 dsDNA viruses. The method is based on information correlation (IC) and partial information correlation (PIC). We observe that (i) the IC-PIC tree segregates the population into clades, the membership of each is remarkably consistent with biologist's systematics only with little exceptions; (ii) the IC-PIC tree reveals potential evolutionary relationships among some viral families; and (iii) the IC-PIC tree predicts the taxonomic positions of certain "unclassified" viruses. Our approach provides a new way for recovering the phylogeny of viruses, and has practical applications in developing alignment-free methods for sequence classification. PMID:22100880

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

    PubMed

    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/ . PMID:23659291

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

    PubMed

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

    2015-11-01

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

  7. Multi-feature-based robust face detection and coarse alignment method via multiple kernel learning

    NASA Astrophysics Data System (ADS)

    Sun, Bo; Zhang, Di; He, Jun; Yu, Lejun; Wu, Xuewen

    2015-10-01

    Face detection and alignment are two crucial tasks to face recognition which is a hot topic in the field of defense and security, whatever for the safety of social public, personal property as well as information and communication security. Common approaches toward the treatment of these tasks in recent years are often of three types: template matching-based, knowledge-based and machine learning-based, which are always separate-step, high computation cost or fragile robust. After deep analysis on a great deal of Chinese face images without hats, we propose a novel face detection and coarse alignment method, which is inspired by those three types of methods. It is multi-feature fusion with Simple Multiple Kernel Learning1 (Simple-MKL) algorithm. The proposed method is contrasted with competitive and related algorithms, and demonstrated to achieve promising results.

  8. A Phylogenetic Analysis of the Brassicales Clade Based on an Alignment-Free Sequence Comparison Method

    PubMed Central

    Hatje, Klas; Kollmar, Martin

    2012-01-01

    Phylogenetic analyses reveal the evolutionary derivation of species. A phylogenetic tree can be inferred from multiple sequence alignments of proteins or genes. The alignment of whole genome sequences of higher eukaryotes is a computational intensive and ambitious task as is the computation of phylogenetic trees based on these alignments. To overcome these limitations, we here used an alignment-free method to compare genomes of the Brassicales clade. For each nucleotide sequence a Chaos Game Representation (CGR) can be computed, which represents each nucleotide of the sequence as a point in a square defined by the four nucleotides as vertices. Each CGR is therefore a unique fingerprint of the underlying sequence. If the CGRs are divided by grid lines each grid square denotes the occurrence of oligonucleotides of a specific length in the sequence (Frequency Chaos Game Representation, FCGR). Here, we used distance measures between FCGRs to infer phylogenetic trees of Brassicales species. Three types of data were analyzed because of their different characteristics: (A) Whole genome assemblies as far as available for species belonging to the Malvidae taxon. (B) EST data of species of the Brassicales clade. (C) Mitochondrial genomes of the Rosids branch, a supergroup of the Malvidae. The trees reconstructed based on the Euclidean distance method are in general agreement with single gene trees. The Fitch–Margoliash and Neighbor joining algorithms resulted in similar to identical trees. Here, for the first time we have applied the bootstrap re-sampling concept to trees based on FCGRs to determine the support of the branchings. FCGRs have the advantage that they are fast to calculate, and can be used as additional information to alignment based data and morphological characteristics to improve the phylogenetic classification of species in ambiguous cases. PMID:22952468

  9. Weighted joint sparse representation-based classification method for robust alignment-free face recognition

    NASA Astrophysics Data System (ADS)

    Sun, Bo; Xu, Feng; Zhou, Guoyan; He, Jun; Ge, Fengxiang

    2015-01-01

    This work proposes a weighted joint sparse representation (WJSR)-based classification method for robust alignment-free face recognition, in which an image is represented by a set of scale-invariant feature transform descriptors. The proposed method considers the correlation and the reliability of the query descriptors. The reliability is measured by the similarity information between the query descriptors and the atoms in the dictionary, which is incorporated into the l0∖l2-norm minimization to seek the optimal WJSR. Compared with the related state-of-art methods, the performance is advanced, as verified by the experiments on the benchmark face databases.

  10. Alignment-free analysis of barcode sequences by means of compression-based methods

    PubMed Central

    2013-01-01

    Background The key idea of DNA barcode initiative is to identify, for each group of species belonging to different kingdoms of life, a short DNA sequence that can act as a true taxon barcode. DNA barcode represents a valuable type of information that can be integrated with ecological, genetic, and morphological data in order to obtain a more consistent taxonomy. Recent studies have shown that, for the animal kingdom, the mitochondrial gene cytochrome c oxidase I (COI), about 650 bp long, can be used as a barcode sequence for identification and taxonomic purposes of animals. In the present work we aims at introducing the use of an alignment-free approach in order to make taxonomic analysis of barcode sequences. Our approach is based on the use of two compression-based versions of non-computable Universal Similarity Metric (USM) class of distances. Our purpose is to justify the employ of USM also for the analysis of short DNA barcode sequences, showing how USM is able to correctly extract taxonomic information among those kind of sequences. Results We downloaded from Barcode of Life Data System (BOLD) database 30 datasets of barcode sequences belonging to different animal species. We built phylogenetic trees of every dataset, according to compression-based and classic evolutionary methods, and compared them in terms of topology preservation. In the experimental tests, we obtained scores with a percentage of similarity between evolutionary and compression-based trees between 80% and 100% for the most of datasets (94%). Moreover we carried out experimental tests using simulated barcode datasets composed of 100, 150, 200 and 500 sequences, each simulation replicated 25-fold. In this case, mean similarity scores between evolutionary and compression-based trees span between 83% and 99% for all simulated datasets. Conclusions In the present work we aims at introducing the use of an alignment-free approach in order to make taxonomic analysis of barcode sequences. Our

  11. A nonlinear biomechanical model based registration method for aligning prone and supine MR breast images.

    PubMed

    Han, Lianghao; Hipwell, John H; Eiben, Björn; Barratt, Dean; Modat, Marc; Ourselin, Sebastien; Hawkes, David J

    2014-03-01

    Preoperative diagnostic magnetic resonance (MR) breast images can provide good contrast between different tissues and 3-D information about suspicious tissues. Aligning preoperative diagnostic MR images with a patient in the theatre during breast conserving surgery could assist surgeons in achieving the complete excision of cancer with sufficient margins. Typically, preoperative diagnostic MR breast images of a patient are obtained in the prone position, while surgery is performed in the supine position. The significant shape change of breasts between these two positions due to gravity loading, external forces and related constraints makes the alignment task extremely difficult. Our previous studies have shown that either nonrigid intensity-based image registration or biomechanical modelling alone are limited in their ability to capture such a large deformation. To tackle this problem, we proposed in this paper a nonlinear biomechanical model-based image registration method with a simultaneous optimization procedure for both the material parameters of breast tissues and the direction of the gravitational force. First, finite element (FE) based biomechanical modelling is used to estimate a physically plausible deformation of the pectoral muscle and the major deformation of breast tissues due to gravity loading. Then, nonrigid intensity-based image registration is employed to recover the remaining deformation that FE analyses do not capture due to the simplifications and approximations of biomechanical models and the uncertainties of external forces and constraints. We assess the registration performance of the proposed method using the target registration error of skin fiducial markers and the Dice similarity coefficient (DSC) of fibroglandular tissues. The registration results on prone and supine MR image pairs are compared with those from two alternative nonrigid registration methods for five breasts. Overall, the proposed algorithm achieved the best registration

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

    PubMed

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

    2015-08-01

    A simple method for the location and auto-alignment of sample fiducials for sample registration using widely available MATLAB/LabVIEW software is demonstrated. The method is robust, easily implemented, and applicable to a wide variety of experiment types for improved reproducibility and increased setup speed. The software uses image processing to locate and measure the diameter and center point of circular fiducials for distance self-calibration and iterative alignment and can be used with most imaging systems. The method is demonstrated to be fast and reliable in locating and aligning sample fiducials, provided here by a nanofabricated array, with accuracy within the optical resolution of the imaging system. The software was further demonstrated to register, load, and sample the dynamically wetted array. PMID:26329245

  13. Projection-Based Volume Alignment

    PubMed Central

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

    2013-01-01

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

  14. Fourier transform interferometer alignment method.

    PubMed

    Goldberg, Kenneth A; Naulleau, Patrick; Bokor, Jeffrey

    2002-08-01

    A rapid and convenient method has been developed to facilitate the alignment of the image-plane components of point-diffraction interferometers, including the phase-shifting point-diffraction interferometer. In real time, the Fourier transform of the detected image is used to calculate a pseudoimage of the electric field in the image plane of the test optic where thecritical alignment o f variousoptical components is performed. Reconstruction of the pseudoimage is similar to off-axis, Fourier transform holography. Intermediate steps in the alignment procedure are described. Fine alignment is aided by the introduction and optimization of a global-contrast parameter that is easily calculated from the Fourier transform. Additional applications include the alignment of image-plane apertures in general optical systems, the rapid identification of patterned image-plane alignment marks, and the probing of important image-plane field properties. PMID:12153074

  15. A compensation alignment method for surface irregularity based on Zernike coefficients

    NASA Astrophysics Data System (ADS)

    Li, Lian; Ma, TianMeng

    2014-11-01

    Surface irregularity of optical elements is one of the errors caused in manufacturing process. The primary aberration caused by surface irregularity is astigmatism which can hardly be removed in traditional alignment method. An alignment method by rotating the lens for compensating the deterioration of the image quality caused by surface irregularity is put forward in the paper, and the mathematical model of the method is established. The calculation of the rotate angle is described in detail. A numerical simulation of the method has been performed for a four-lens precision optical system to verify the ability and accuracy of the method. The results show that the astigmatism of the optical system caused by the surface irregularity can completely be removed, and the image quality can be improved effectively. The method is especially suitable for the optical system which demands a very high image quality.

  16. Genetic algorithm based fast alignment method for strap-down inertial navigation system with large azimuth misalignment.

    PubMed

    He, Hongyang; Xu, Jiangning; Qin, Fangjun; Li, Feng

    2015-11-01

    In order to shorten the alignment time and eliminate the small initial misalignment limit for compass alignment of strap-down inertial navigation system (SINS), which is sometimes not easy to satisfy when the ship is moored or anchored, an optimal model based time-varying parameter compass alignment algorithm is proposed in this paper. The contributions of the work presented here are twofold. First, the optimization of compass alignment parameters, which involves a lot of trial-and-error traditionally, is achieved based on genetic algorithm. On this basis, second, the optimal parameter varying model is established by least-square polynomial fitting. Experiments are performed with a navigational grade fiber optical gyroscope SINS, which validate the efficiency of the proposed method. PMID:26628165

  17. Genetic algorithm based fast alignment method for strap-down inertial navigation system with large azimuth misalignment

    NASA Astrophysics Data System (ADS)

    He, Hongyang; Xu, Jiangning; Qin, Fangjun; Li, Feng

    2015-11-01

    In order to shorten the alignment time and eliminate the small initial misalignment limit for compass alignment of strap-down inertial navigation system (SINS), which is sometimes not easy to satisfy when the ship is moored or anchored, an optimal model based time-varying parameter compass alignment algorithm is proposed in this paper. The contributions of the work presented here are twofold. First, the optimization of compass alignment parameters, which involves a lot of trial-and-error traditionally, is achieved based on genetic algorithm. On this basis, second, the optimal parameter varying model is established by least-square polynomial fitting. Experiments are performed with a navigational grade fiber optical gyroscope SINS, which validate the efficiency of the proposed method.

  18. Evaporation-based method for preparing gelatin foams with aligned tubular pore structures.

    PubMed

    Frazier, Shane D; Srubar, Wil V

    2016-05-01

    Gelatin-based foams with aligned tubular pore structures were prepared via liquid-to-gas vaporization of tightly bound water in dehydrated gelatin hydrogels. This study elucidates the mechanism of the foaming process by investigating the secondary (i.e., helical) structure, molecular interactions, and water content of gelatin films before and after foaming using X-ray diffraction, Fourier transform infrared (FTIR) spectroscopy, differential scanning calorimetry and thermogravimetric analysis (TGA), respectively. Experimental data from gelatin samples prepared at various gelatin-to-water concentrations (5-30 wt.%) substantiate that resulting foam structures are similar in pore diameter (approximately 350 μm), shape, and density (0.05-0.22 g/cm(3)) to those fabricated using conventional methods (e.g., freeze-drying). Helical structures were identified in the films but were not evident in the foamed samples after vaporization (~150 °C), suggesting that the primary foaming mechanism is governed by the vaporization of water that is tightly bound in secondary structures (i.e., helices, β-turns, β-sheets) that are present in dehydrated gelatin films. FTIR and TGA data show that the foaming process leads to more disorder and reduced hydrogen bonding to hydroxyl groups in gelatin and that no thermal degradation of gelatin occurs before or after foaming. PMID:26952448

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

    PubMed Central

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

    2014-01-01

    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. PMID:24977504

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

    PubMed

    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. PMID:24977504

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

    PubMed

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

    2013-01-01

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

  2. Computed Tomography Analysis of Postsurgery Femoral Component Rotation Based on a Force Sensing Device Method versus Hypothetical Rotational Alignment Based on Anatomical Landmark Methods: A Pilot Study

    PubMed Central

    Kreuzer, Stefan W.; Pourmoghaddam, Amir; Leffers, Kevin J.; Johnson, Clint W.; Dettmer, Marius

    2016-01-01

    Rotation of the femoral component is an important aspect of knee arthroplasty, due to its effects on postsurgery knee kinematics and associated functional outcomes. It is still debated which method for establishing rotational alignment is preferable in orthopedic surgery. We compared force sensing based femoral component rotation with traditional anatomic landmark methods to investigate which method is more accurate in terms of alignment to the true transepicondylar axis. Thirty-one patients underwent computer-navigated total knee arthroplasty for osteoarthritis with femoral rotation established via a force sensor. During surgery, three alternative hypothetical femoral rotational alignments were assessed, based on transepicondylar axis, anterior-posterior axis, or the utilization of a posterior condyles referencing jig. Postoperative computed tomography scans were obtained to investigate rotation characteristics. Significant differences in rotation characteristics were found between rotation according to DKB and other methods (P < 0.05). Soft tissue balancing resulted in smaller deviation from anatomical epicondylar axis than any other method. 77% of operated knees were within a range of ±3° of rotation. Only between 48% and 52% of knees would have been rotated appropriately using the other methods. The current results indicate that force sensors may be valuable for establishing correct femoral rotation. PMID:26881086

  3. High angular accuracy manufacture method of micro v-grooves based on tool alignment by on-machine measurement.

    PubMed

    Zhang, Xiaodong; Jiang, Lili; Zeng, Zhen; Fang, Fengzhou; Liu, Xianlei

    2015-10-19

    Micro v-groove has found wide applications in optical areas as one of the most important structures. However, its performance is significantly affected by its angular geometry accuracy. The diamond cutting has been commonly used as the fabrication method of micro v-groove, but it is still difficult to guarantee the cutting tool angle, which is limited by the measurement accuracy in the manufacture and mounting of the diamond tool. A cutting tool alignment method based on the on-machine measurement is proposed to improve the fabricated quality of the v-groove angle. An on-machine probe is employed to scan the v-groove geometrical deviation precisely. The system errors model, data processing algorithm and tool alignment methods are analyzed in details. Experimental results show that the measurement standard deviation within 0.01° can be achieved. Retro-reflection mirrors are fabricated and measured finally by the proposed method for verification. PMID:26480443

  4. Rapid shape-based ligand alignment and virtual screening method based on atom/feature-pair similarities and volume overlap scoring.

    PubMed

    Sastry, G Madhavi; Dixon, Steven L; Sherman, Woody

    2011-10-24

    Shape-based methods for aligning and scoring ligands have proven to be valuable in the field of computer-aided drug design. Here, we describe a new shape-based flexible ligand superposition and virtual screening method, Phase Shape, which is shown to rapidly produce accurate 3D ligand alignments and efficiently enrich actives in virtual screening. We describe the methodology, which is based on the principle of atom distribution triplets to rapidly define trial alignments, followed by refinement of top alignments to maximize the volume overlap. The method can be run in a shape-only mode or it can include atom types or pharmacophore feature encoding, the latter consistently producing the best results for database screening. We apply Phase Shape to flexibly align molecules that bind to the same target and show that the method consistently produces correct alignments when compared with crystal structures. We then illustrate the effectiveness of the method for identifying active compounds in virtual screening of eleven diverse targets. Multiple parameters are explored, including atom typing, query structure conformation, and the database conformer generation protocol. We show that Phase Shape performs well in database screening calculations when compared with other shape-based methods using a common set of actives and decoys from the literature. PMID:21870862

  5. Laser beam alignment apparatus and method

    DOEpatents

    Gruhn, Charles R.; Hammond, Robert B.

    1981-01-01

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

  6. Laser beam alignment apparatus and method

    DOEpatents

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

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

  7. Method for protein structure alignment

    DOEpatents

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

    2005-02-22

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

  8. AIMFAST : an alignment tool based on fringe reflection methods applied to dish concentrators.

    SciTech Connect

    Yellowhair, Julius; Stone, Brad; Myer, Brian; Hunt, Kirby; Trapeznikov, Kirill; Andraka, Charles E.; Carlson, Jeffrey J.

    2010-08-01

    The proper alignment of facets on a dish engine concentrated solar power system is critical to the performance of the system. These systems are generally highly concentrating to produce high temperatures for maximum thermal efficiency so there is little tolerance for poor optical alignment. Improper alignment can lead to poor performance and shortened life through excessively high flux on the receiver surfaces, imbalanced power on multicylinder engines, and intercept losses at the aperture. Alignment approaches used in the past are time consuming field operations, typically taking 4-6 h per dish with 40-80 facets on the dish. Production systems of faceted dishes will need rapid, accurate alignment implemented in a fraction of an hour. In this paper, we present an extension to our Sandia Optical Fringe Analysis Slope Technique mirror characterization system that will automatically acquire data, implement an alignment strategy, and provide real-time mirror angle corrections to actuators or labor beneath the dish. The Alignment Implementation for Manufacturing using Fringe Analysis Slope Technique (AIMFAST) has been implemented and tested at the prototype level. In this paper we present the approach used in AIMFAST to rapidly characterize the dish system and provide near-real-time adjustment updates for each facet. The implemented approach can provide adjustment updates every 5 s, suitable for manual or automated adjustment of facets on a dish assembly line.

  9. Alignment method for parabolic trough solar concentrators

    DOEpatents

    Diver, Richard B.

    2010-02-23

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

  10. Methodological Alignment in Design-Based Research

    ERIC Educational Resources Information Center

    Hoadley, Christopher M.

    2004-01-01

    Empirical research is all about trying to model and predict the world. In this article, I discuss how design-based research methods can help do this effectively. In particular, design-based research methods can help with the problem of methodological alignment: ensuring that the research methods we use actually test what we think they are testing.…

  11. Comparison of Beam-Based Alignment Algorithms for the ILC

    SciTech Connect

    Smith, J.C.; Gibbons, L.; Patterson, J.R.; Rubin, D.L.; Sagan, D.; Tenenbaum, P.; /SLAC

    2006-03-15

    The main linac of the International Linear Collider (ILC) requires more sophisticated alignment techniques than those provided by survey alone. Various Beam-Based Alignment (BBA) algorithms have been proposed to achieve the desired low emittance preservation. Dispersion Free Steering, Ballistic Alignment and the Kubo method are compared. Alignment algorithms are also tested in the presence of an Earth-like stray field.

  12. Image correlation method for DNA sequence alignment.

    PubMed

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

    2012-01-01

    The complexity of searches and the volume of genomic data make sequence alignment one of bioinformatics most active research areas. New alignment approaches have incorporated digital signal processing techniques. Among these, correlation methods are highly sensitive. This paper proposes a novel sequence alignment method based on 2-dimensional images, where each nucleic acid base is represented as a fixed gray intensity pixel. Query and known database sequences are coded to their pixel representation and sequence alignment is handled as object recognition in a scene problem. Query and database become object and scene, respectively. An image correlation process is carried out in order to search for the best match between them. Given that this procedure can be implemented in an optical correlator, the correlation could eventually be accomplished at light speed. This paper shows an initial research stage where results were "digitally" obtained by simulating an optical correlation of DNA sequences represented as images. A total of 303 queries (variable lengths from 50 to 4500 base pairs) and 100 scenes represented by 100 x 100 images each (in total, one million base pair database) were considered for the image correlation analysis. The results showed that correlations reached very high sensitivity (99.01%), specificity (98.99%) and outperformed BLAST when mutation numbers increased. However, digital correlation processes were hundred times slower than BLAST. We are currently starting an initiative to evaluate the correlation speed process of a real experimental optical correlator. By doing this, we expect to fully exploit optical correlation light properties. As the optical correlator works jointly with the computer, digital algorithms should also be optimized. The results presented in this paper are encouraging and support the study of image correlation methods on sequence alignment. PMID:22761742

  13. Alignment method for solar collector arrays

    DOEpatents

    Driver, Jr., Richard B

    2012-10-23

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

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

    PubMed Central

    Katoh, Kazutaka; Standley, Daron M.

    2016-01-01

    Motivation: 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. Results: 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. Availability and implementation: The new feature is available in MAFFT versions 7.263 and higher. http://mafft.cbrc.jp/alignment/software/ Contact: katoh@ifrec.osaka-u.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153688

  15. A New Analytic Alignment Method for a SINS

    PubMed Central

    Tan, Caiming; Zhu, Xinhua; Su, Yan; Wang, Yu; Wu, Zhiqiang; Gu, Dongbing

    2015-01-01

    Analytic alignment is a type of self-alignment for a Strapdown inertial navigation system (SINS) that is based solely on two non-collinear vectors, which are the gravity and rotational velocity vectors of the Earth at a stationary base on the ground. The attitude of the SINS with respect to the Earth can be obtained directly using the TRIAD algorithm given two vector measurements. For a traditional analytic coarse alignment, all six outputs from the inertial measurement unit (IMU) are used to compute the attitude. In this study, a novel analytic alignment method called selective alignment is presented. This method uses only three outputs of the IMU and a few properties from the remaining outputs such as the sign and the approximate value to calculate the attitude. Simulations and experimental results demonstrate the validity of this method, and the precision of yaw is improved using the selective alignment method compared to the traditional analytic coarse alignment method in the vehicle experiment. The selective alignment principle provides an accurate relationship between the outputs and the attitude of the SINS relative to the Earth for a stationary base, and it is an extension of the TRIAD algorithm. The selective alignment approach has potential uses in applications such as self-alignment, fault detection, and self-calibration. PMID:26556353

  16. A New Analytic Alignment Method for a SINS.

    PubMed

    Tan, Caiming; Zhu, Xinhua; Su, Yan; Wang, Yu; Wu, Zhiqiang; Gu, Dongbing

    2015-01-01

    Analytic alignment is a type of self-alignment for a Strapdown inertial navigation system (SINS) that is based solely on two non-collinear vectors, which are the gravity and rotational velocity vectors of the Earth at a stationary base on the ground. The attitude of the SINS with respect to the Earth can be obtained directly using the TRIAD algorithm given two vector measurements. For a traditional analytic coarse alignment, all six outputs from the inertial measurement unit (IMU) are used to compute the attitude. In this study, a novel analytic alignment method called selective alignment is presented. This method uses only three outputs of the IMU and a few properties from the remaining outputs such as the sign and the approximate value to calculate the attitude. Simulations and experimental results demonstrate the validity of this method, and the precision of yaw is improved using the selective alignment method compared to the traditional analytic coarse alignment method in the vehicle experiment. The selective alignment principle provides an accurate relationship between the outputs and the attitude of the SINS relative to the Earth for a stationary base, and it is an extension of the TRIAD algorithm. The selective alignment approach has potential uses in applications such as self-alignment, fault detection, and self-calibration. PMID:26556353

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

    ERIC Educational Resources Information Center

    Nasstrom, Gunilla; Henriksson, Widar

    2008-01-01

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

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

    SciTech Connect

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

    2015-11-01

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

  19. Combining Multiple Pairwise Structure-based Alignments

    SciTech Connect

    2014-11-12

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

  20. Fiber alignment apparatus and method

    DOEpatents

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

    1997-01-01

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

  1. Fiber alignment apparatus and method

    DOEpatents

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

    1997-08-19

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

  2. Automatic alignment method for calibration of hydrometers

    NASA Astrophysics Data System (ADS)

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

    2004-04-01

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

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

    PubMed

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

    2015-01-01

    In this paper, an improved inertial frame alignment algorithm for a marine SINS under mooring conditions is proposed, which significantly improves accuracy. Since the horizontal alignment is easy to complete, and a characteristic of gravity is that its component in the horizontal plane is zero, we use a clever method to improve the conventional inertial alignment algorithm. Firstly, a large misalignment angle model and a dimensionality reduction Gauss-Hermite filter are employed to establish the fine horizontal reference frame. Based on this, the projection of the gravity in the body inertial coordinate frame can be calculated easily. Then, the initial alignment algorithm is accomplished through an inertial frame alignment algorithm. The simulation and experiment results show that the improved initial alignment algorithm performs better than the conventional inertial alignment algorithm, and meets the accuracy requirements of a medium-accuracy marine SINS. PMID:26445048

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

    PubMed Central

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

    2015-01-01

    In this paper, an improved inertial frame alignment algorithm for a marine SINS under mooring conditions is proposed, which significantly improves accuracy. Since the horizontal alignment is easy to complete, and a characteristic of gravity is that its component in the horizontal plane is zero, we use a clever method to improve the conventional inertial alignment algorithm. Firstly, a large misalignment angle model and a dimensionality reduction Gauss-Hermite filter are employed to establish the fine horizontal reference frame. Based on this, the projection of the gravity in the body inertial coordinate frame can be calculated easily. Then, the initial alignment algorithm is accomplished through an inertial frame alignment algorithm. The simulation and experiment results show that the improved initial alignment algorithm performs better than the conventional inertial alignment algorithm, and meets the accuracy requirements of a medium-accuracy marine SINS. PMID:26445048

  5. Graph-based molecular alignment (GMA).

    PubMed

    Marialke, J; Körner, R; Tietze, S; Apostolakis, Joannis

    2007-01-01

    We describe a combined 2D/3D approach for the superposition of flexible chemical structures, which is based on recent progress in the efficient identification of common subgraphs and a gradient-based torsion space optimization algorithm. The simplicity of the approach is reflected in its generality and computational efficiency: the suggested approach neither requires precalculated statistics on the conformations of the molecules nor does it make simplifying assumptions on the topology of the molecules being compared. Furthermore, graph-based molecular alignment produces alignments that are consistent with the chemistry of the molecules as well as their general structure, as it depends on both the local connectivities between atoms and the overall topology of the molecules. We validate this approach on benchmark sets taken from the literature and show that it leads to good results compared to computationally and algorithmically more involved methods. The results suggest that, for most practical purposes, graph-based molecular alignment is a viable alternative to molecular field alignment with respect to structural superposition and leads to structures of comparable quality in a fraction of the time. PMID:17381175

  6. Combining Multiple Pairwise Structure-based Alignments

    2014-11-12

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

  7. Effective Electrocardiogram Steganography Based on Coefficient Alignment.

    PubMed

    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. PMID:26711443

  8. HubAlign: an accurate and efficient method for global alignment of protein–protein interaction networks

    PubMed Central

    Hashemifar, Somaye; Xu, Jinbo

    2014-01-01

    Motivation: High-throughput experimental techniques have produced a large amount of protein–protein interaction (PPI) data. The study of PPI networks, such as comparative analysis, shall benefit the understanding of life process and diseases at the molecular level. One way of comparative analysis is to align PPI networks to identify conserved or species-specific subnetwork motifs. A few methods have been developed for global PPI network alignment, but it still remains challenging in terms of both accuracy and efficiency. Results: This paper presents a novel global network alignment algorithm, denoted as HubAlign, that makes use of both network topology and sequence homology information, based upon the observation that topologically important proteins in a PPI network usually are much more conserved and thus, more likely to be aligned. HubAlign uses a minimum-degree heuristic algorithm to estimate the topological and functional importance of a protein from the global network topology information. Then HubAlign aligns topologically important proteins first and gradually extends the alignment to the whole network. Extensive tests indicate that HubAlign greatly outperforms several popular methods in terms of both accuracy and efficiency, especially in detecting functionally similar proteins. Availability: HubAlign is available freely for non-commercial purposes at http://ttic.uchicago.edu/∼hashemifar/software/HubAlign.zip Contact: jinboxu@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25161231

  9. Aligning a reflection cavity by Anderson's method.

    PubMed

    Reasenberg, Robert D

    2012-06-01

    The sounding rocket principle of equivalence measurement uses a set of four laser gauges operating in Fabry-Perot cavities to determine the relative acceleration of two test masses that are chemically different. One end of each cavity is a flat mirror on a test mass. Because the test masses are unconstrained and thus expected to rotate slightly during measurement, and because the distance measurements are made at the sub-picometer level, it is essential to have real-time alignment of the beam entering the cavity. However, the cavity must be used in reflection and space is limited. We show that Anderson's alignment method can be used in reflection, but that it requires that the Fabry-Perot cavity have mirrors with significantly unequal reflectivities. PMID:22695543

  10. Local alignment of two-base encoded DNA sequence

    PubMed Central

    Homer, Nils; Merriman, Barry; Nelson, Stanley F

    2009-01-01

    Background DNA sequence comparison is based on optimal local alignment of two sequences using a similarity score. However, some new DNA sequencing technologies do not directly measure the base sequence, but rather an encoded form, such as the two-base encoding considered here. In order to compare such data to a reference sequence, the data must be decoded into sequence. The decoding is deterministic, but the possibility of measurement errors requires searching among all possible error modes and resulting alignments to achieve an optimal balance of fewer errors versus greater sequence similarity. Results We present an extension of the standard dynamic programming method for local alignment, which simultaneously decodes the data and performs the alignment, maximizing a similarity score based on a weighted combination of errors and edits, and allowing an affine gap penalty. We also present simulations that demonstrate the performance characteristics of our two base encoded alignment method and contrast those with standard DNA sequence alignment under the same conditions. Conclusion The new local alignment algorithm for two-base encoded data has substantial power to properly detect and correct measurement errors while identifying underlying sequence variants, and facilitating genome re-sequencing efforts based on this form of sequence data. PMID:19508732

  11. A novel alignment-free method for detection of lateral genetic transfer based on TF-IDF

    PubMed Central

    Cong, Yingnan; Chan, Yao-ban; Ragan, Mark A.

    2016-01-01

    Lateral genetic transfer (LGT) plays an important role in the evolution of microbes. Existing computational methods for detecting genomic regions of putative lateral origin scale poorly to large data. Here, we propose a novel method based on TF-IDF (Term Frequency-Inverse Document Frequency) statistics to detect not only regions of lateral origin, but also their origin and direction of transfer, in sets of hierarchically structured nucleotide or protein sequences. This approach is based on the frequency distributions of k-mers in the sequences. If a set of contiguous k-mers appears sufficiently more frequently in another phyletic group than in its own, we infer that they have been transferred from the first group to the second. We performed rigorous tests of TF-IDF using simulated and empirical datasets. With the simulated data, we tested our method under different parameter settings for sequence length, substitution rate between and within groups and post-LGT, deletion rate, length of transferred region and k size, and found that we can detect LGT events with high precision and recall. Our method performs better than an established method, ALFY, which has high recall but low precision. Our method is efficient, with runtime increasing approximately linearly with sequence length. PMID:27453035

  12. To develop a geometric matching method for precision mold alignment

    NASA Astrophysics Data System (ADS)

    Chen, Chun-Jen; Chang, Chun-Li; Jywe, Wenyuh

    2014-09-01

    In order to develop a high accuracy optical alignment system for precision molding machine, a geometric matching method was developed in this paper. The alignment system includes 4 high magnification lenses, 4 CCD cameras and 4 LED light sources. In the precision molding machine, a bottom metal mold and a top glass mold are used to produce a micro lens. The two molds combination does not use any pin or alignment part. They only use the optical alignment system to alignment. In this optical alignment system, the off-axis alignment method was used. The alignment accuracy of the alignment system is about 0.5 μm. There are 2 cross marks on the top glass mold and 2 cross marks on the bottom metal mod. In this paper did not use edge detection to recognize the mask center because the mask easy wears when the combination times increased. Therefore, this paper develops a geometric matching method to recognize mask center.

  13. An Accurate Scalable Template-based Alignment Algorithm.

    PubMed

    Gardner, David P; Xu, Weijia; Miranker, Daniel P; Ozer, Stuart; Cannone, Jamie J; Gutell, Robin R

    2012-12-31

    The rapid determination of nucleic acid sequences is increasing the number of sequences that are available. Inherent in a template or seed alignment is the culmination of structural and functional constraints that are selecting those mutations that are viable during the evolution of the RNA. While we might not understand these structural and functional, template-based alignment programs utilize the patterns of sequence conservation to encapsulate the characteristics of viable RNA sequences that are aligned properly. We have developed a program that utilizes the different dimensions of information in rCAD, a large RNA informatics resource, to establish a profile for each position in an alignment. The most significant include sequence identity and column composition in different phylogenetic taxa. We have compared our methods with a maximum of eight alternative alignment methods on different sets of 16S and 23S rRNA sequences with sequence percent identities ranging from 50% to 100%. The results showed that CRWAlign outperformed the other alignment methods in both speed and accuracy. A web-based alignment server is available at http://www.rna.ccbb.utexas.edu/SAE/2F/CRWAlign. PMID:24772376

  14. Image-based temporal alignment of echocardiographic sequences

    NASA Astrophysics Data System (ADS)

    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.

  15. Refining Methods for Estimating Critical Values for an Alignment Index

    ERIC Educational Resources Information Center

    Polikoff, Morgan S.; Fulmer, Gavin W.

    2013-01-01

    The alignment among standards, assessments, and teachers' instruction is an essential element of standards-based educational reforms. The Surveys of Enacted Curriculum (SEC) is the only common tool that can be used to measure the alignment among all three of these sources (Martone & Sireci, 2009). Prior SEC alignment work has been limited…

  16. Alignment Content Analysis of NAEP 2009 Reading Assessment Analysis Based on Method of Surveys of Enacted Curriculum

    ERIC Educational Resources Information Center

    Blank, Rolf K.; Smithson, John

    2010-01-01

    Beginning in summer 2009, the complete set of NAEP student assessment items for grades 4 and 8 Science and Reading 2009 assessments were analyzed for comparison to the National Assessment of Educational Progress (NAEP) Item Specifications which are based on the NAEP Assessment Frameworks for these subjects (National Assessment Governing Board,…

  17. Aligned, short-fiber composites by novel flow processing methods

    SciTech Connect

    Guell, D.C.; Graham, A.L.; Papathanasiou, T.; Petrovic, J.J.

    1993-01-01

    A hydrodynamic method has been employed to align short, reinforcing fibers in polymer matrix composite materials. Samples of composite materials were prepared and tested two at a time (one with randomly oriented fibers and the other with aligned fibers) to isolate and directly measure the effect on mechanical properties of aligning the fibers. Data were collected for the ultimate tensile strength, modulus of elasticity, and ultimate tensile strain of the composite samples prepared. Results show that the aligned fibers were approximately twice as effective (as randomly oriented fibers) at stiffening and strengthening the composite in the alignment direction. 5 figs, 20 refs.

  18. Aligned, short-fiber composites by novel flow processing methods

    SciTech Connect

    Guell, D.C.; Graham, A.L.; Papathanasiou, T.; Petrovic, J.J.

    1993-03-01

    A hydrodynamic method has been employed to align short, reinforcing fibers in polymer matrix composite materials. Samples of composite materials were prepared and tested two at a time (one with randomly oriented fibers and the other with aligned fibers) to isolate and directly measure the effect on mechanical properties of aligning the fibers. Data were collected for the ultimate tensile strength, modulus of elasticity, and ultimate tensile strain of the composite samples prepared. Results show that the aligned fibers were approximately twice as effective (as randomly oriented fibers) at stiffening and strengthening the composite in the alignment direction. 5 figs, 20 refs.

  19. SUMONA: A supervised method for optimizing network alignment.

    PubMed

    Tuncay, Erhun Giray; Can, Tolga

    2016-08-01

    This study focuses on improving the multi-objective memetic algorithm for protein-protein interaction (PPI) network alignment, Optimizing Network Aligner - OptNetAlign, via integration with other existing network alignment methods such as SPINAL, NETAL and HubAlign. The output of this algorithm is an elite set of aligned networks all of which are optimal with respect to multiple user-defined criteria. However, OptNetAlign is an unsupervised genetic algorithm that initiates its search with completely random solutions and it requires substantial running times to generate an elite set of solutions that have high scores with respect to the given criteria. In order to improve running time, the search space of the algorithm can be narrowed down by focusing on remarkably qualified alignments and trying to optimize the most desired criteria on a more limited set of solutions. The method presented in this study improves OptNetAlign in a supervised fashion by utilizing the alignment results of different network alignment algorithms with varying parameters that depend upon user preferences. Therefore, the user can prioritize certain objectives upon others and achieve better running time performance while optimizing the secondary objectives. PMID:27177812

  20. Receptor-based 3D QSAR analysis of estrogen receptor ligands--merging the accuracy of receptor-based alignments with the computational efficiency of ligand-based methods.

    PubMed

    Sippl, W

    2000-08-01

    One of the major challenges in computational approaches to drug design is the accurate prediction of binding affinity of biomolecules. In the present study several prediction methods for a published set of estrogen receptor ligands are investigated and compared. The binding modes of 30 ligands were determined using the docking program AutoDock and were compared with available X-ray structures of estrogen receptor-ligand complexes. On the basis of the docking results an interaction energy-based model, which uses the information of the whole ligand-receptor complex, was generated. Several parameters were modified in order to analyze their influence onto the correlation between binding affinities and calculated ligand-receptor interaction energies. The highest correlation coefficient (r2 = 0.617, q2Loo = 0.570) was obtained considering protein flexibility during the interaction energy evaluation. The second prediction method uses a combination of receptor-based and 3D quantitative structure-activity relationships (3D QSAR) methods. The ligand alignment obtained from the docking simulations was taken as basis for a comparative field analysis applying the GRID/GOLPE program. Using the interaction field derived with a water probe and applying the smart region definition (SRD) variable selection, a significant and robust model was obtained (r2 = 0.991, q2LOO = 0.921). The predictive ability of the established model was further evaluated by using a test set of six additional compounds. The comparison with the generated interaction energy-based model and with a traditional CoMFA model obtained using a ligand-based alignment (r2 = 0.951, q2L00 = 0.796) indicates that the combination of receptor-based and 3D QSAR methods is able to improve the quality of the underlying model. PMID:10921772

  1. Spent fuel container alignment device and method

    DOEpatents

    Jones, Stewart D.; Chapek, George V.

    1996-01-01

    An alignment device is used with a spent fuel shipping container including a plurality of fuel pockets for spent fuel arranged in an annular array and having a rotatable cover including an access opening therein. The alignment device includes a lightweight plate which is installed over the access opening of the cover. A laser device is mounted on the plate so as to emit a laser beam through a laser admittance window in the cover into the container in the direction of a pre-established target associated with a particular fuel pocket. An indexing arrangement on the container provides an indication of the angular position of the rotatable cover when the laser beam produced by the laser is brought into alignment with the target of the associated fuel pocket.

  2. Multiple Sequence Alignment Based on Chaotic PSO

    NASA Astrophysics Data System (ADS)

    Lei, Xiu-Juan; Sun, Jing-Jing; Ma, Qian-Zhi

    This paper introduces a new improved algorithm called chaotic PSO (CPSO) based on the thought of chaos optimization to solve multiple sequence alignment. For one thing, the chaotic variables are generated between 0 and 1 when initializing the population so that the particles are distributed uniformly in the solution space. For another thing, the chaotic sequences are generated using the Logistic mapping function in order to make chaotic search and strengthen the diversity of the population. The simulation results of several benchmark data sets of BAliBase show that the improved algorithm is effective and has good performances for the data sets with different similarity.

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

    NASA Astrophysics Data System (ADS)

    Parc, Yong Woon; Hwang, Ilmoon; Han, Jang-Hui; Ko, In Soo

    2015-05-01

    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.

  4. Alignment of the magnet and a positioning method

    NASA Astrophysics Data System (ADS)

    Kim, Dae-Il

    2015-10-01

    The 100-MeV proton linac and magnets for the KOMAC (Korea Multi-purpose Accelerator Complex) were installed in the tunnel and the beamlines. The fiducialization process was accomplished with the measurement of mechanical shape and the transfer of the coordinates to the fiducial points that are used in two laser-trackers based alignments. The reference points called the alignment network were set up on the wall inside tunnel. The linac and the beam transport magnets were aligned based on the survey results of the alignment networks. In this paper, the alignment procedure and the alignment results are presented, and an algorithm that was developed to manipulate the adjusters of the magnetsis introduced.

  5. QUADRUPOLE BEAM-BASED ALIGNMENT AT RHIC.

    SciTech Connect

    NIEDZIELA, J.; MONTAG, C.; SATOGATA, T.

    2005-05-16

    Successful implementation of a beam-based alignment algorithm, tailored to different types of quadrupoles at RHIC, provides significant benefits to machine operations for heavy ions and polarized protons. This algorithm was used to calibrate beam position monitor centers relative to interaction region quadrupoles to maximize aperture. This approach was also used to determine the optimal orbit through transition jump quadrupoles to minimize orbit changes during the transition jump for heavy ion acceleration. This paper provides background discussion and results from first measurements during the RHIC 2005 run.

  6. Graphics processing unit-based alignment of protein interaction networks.

    PubMed

    Xie, Jiang; Zhou, Zhonghua; Ma, Jin; Xiang, Chaojuan; Nie, Qing; Zhang, Wu

    2015-08-01

    Network alignment is an important bridge to understanding human protein-protein interactions (PPIs) and functions through model organisms. However, the underlying subgraph isomorphism problem complicates and increases the time required to align protein interaction networks (PINs). Parallel computing technology is an effective solution to the challenge of aligning large-scale networks via sequential computing. In this study, the typical Hungarian-Greedy Algorithm (HGA) is used as an example for PIN alignment. The authors propose a HGA with 2-nearest neighbours (HGA-2N) and implement its graphics processing unit (GPU) acceleration. Numerical experiments demonstrate that HGA-2N can find alignments that are close to those found by HGA while dramatically reducing computing time. The GPU implementation of HGA-2N optimises the parallel pattern, computing mode and storage mode and it improves the computing time ratio between the CPU and GPU compared with HGA when large-scale networks are considered. By using HGA-2N in GPUs, conserved PPIs can be observed, and potential PPIs can be predicted. Among the predictions based on 25 common Gene Ontology terms, 42.8% can be found in the Human Protein Reference Database. Furthermore, a new method of reconstructing phylogenetic trees is introduced, which shows the same relationships among five herpes viruses that are obtained using other methods. PMID:26243827

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

    PubMed

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

    2012-01-01

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

  8. Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference

    PubMed Central

    Tan, Ge; Muffato, Matthieu; Ledergerber, Christian; Herrero, Javier; Goldman, Nick; Gil, Manuel; Dessimoz, Christophe

    2015-01-01

    Phylogenetic inference is generally performed on the basis of multiple sequence alignments (MSA). Because errors in an alignment can lead to errors in tree estimation, there is a strong interest in identifying and removing unreliable parts of the alignment. In recent years several automated filtering approaches have been proposed, but despite their popularity, a systematic and comprehensive comparison of different alignment filtering methods on real data has been lacking. Here, we extend and apply recently introduced phylogenetic tests of alignment accuracy on a large number of gene families and contrast the performance of unfiltered versus filtered alignments in the context of single-gene phylogeny reconstruction. Based on multiple genome-wide empirical and simulated data sets, we show that the trees obtained from filtered MSAs are on average worse than those obtained from unfiltered MSAs. Furthermore, alignment filtering often leads to an increase in the proportion of well-supported branches that are actually wrong. We confirm that our findings hold for a wide range of parameters and methods. Although our results suggest that light filtering (up to 20% of alignment positions) has little impact on tree accuracy and may save some computation time, contrary to widespread practice, we do not generally recommend the use of current alignment filtering methods for phylogenetic inference. By providing a way to rigorously and systematically measure the impact of filtering on alignments, the methodology set forth here will guide the development of better filtering algorithms. PMID:26031838

  9. Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference.

    PubMed

    Tan, Ge; Muffato, Matthieu; Ledergerber, Christian; Herrero, Javier; Goldman, Nick; Gil, Manuel; Dessimoz, Christophe

    2015-09-01

    Phylogenetic inference is generally performed on the basis of multiple sequence alignments (MSA). Because errors in an alignment can lead to errors in tree estimation, there is a strong interest in identifying and removing unreliable parts of the alignment. In recent years several automated filtering approaches have been proposed, but despite their popularity, a systematic and comprehensive comparison of different alignment filtering methods on real data has been lacking. Here, we extend and apply recently introduced phylogenetic tests of alignment accuracy on a large number of gene families and contrast the performance of unfiltered versus filtered alignments in the context of single-gene phylogeny reconstruction. Based on multiple genome-wide empirical and simulated data sets, we show that the trees obtained from filtered MSAs are on average worse than those obtained from unfiltered MSAs. Furthermore, alignment filtering often leads to an increase in the proportion of well-supported branches that are actually wrong. We confirm that our findings hold for a wide range of parameters and methods. Although our results suggest that light filtering (up to 20% of alignment positions) has little impact on tree accuracy and may save some computation time, contrary to widespread practice, we do not generally recommend the use of current alignment filtering methods for phylogenetic inference. By providing a way to rigorously and systematically measure the impact of filtering on alignments, the methodology set forth here will guide the development of better filtering algorithms. PMID:26031838

  10. Dosimetric comparison of four target alignment methods for prostate cancer radiotherapy

    SciTech Connect

    O'Daniel, Jennifer C.; Dong Lei . E-mail: ldong@mdanderson.org; Zhang Lifei; Crevoisier, Renaud de; Wang He; Lee, Andrew K.; Cheung, Rex; Tucker, Susan L.; Kudchadker, Rajat J.; Bonnen, Mark D.; Cox, James D.; Mohan, Radhe; Kuban, Deborah A.

    2006-11-01

    Purpose: The aim of this study was to compare the dosimetric consequences of 4 treatment delivery techniques for prostate cancer patients treated with intensity-modulated radiotherapy (IMRT). Methods and Materials: During an 8-week course of radiotherapy, 10 patients underwent computed tomography (CT) scans 3 times per week (243 total) before daily treatment with a CT-linear accelerator. Treatment delivery was simulated by realigning a fixed-margin treatment plan on each CT scan and calculating doses. The alignment methods were those based on the following: skin marks, bony registration, ultrasonography (United States), and in-room CT. For the last two methods, prostate was the alignment target. The dosimetric effects of these alignment methods on the prostate, seminal vesicles, rectum, and bladder were compared. The average daily minimum dose to 0.1 cm{sup 3} was used as the metric for target coverage. Results: Skin and bone alignments provided acceptable prostate coverage for only 70% of patients, US alignment for 90%, and CT alignment for 100%. CT-based alignment of the prostate provided seminal vesicle (SV) coverage of {>=}69 Gy for all patients; US and bone alignments provided SV coverage of {>=}60 Gy. This SV coverage may be acceptable for early-stage cancer (equivalent SV dose = 55.8 Gy at 1.8 Gy per fraction), but unacceptable for late-stage cancer (SV dose = 75.6 Gy). At 75.6 Gy, the acceptable rate for SV coverage was 40% for skin and bone alignments, 70% for US, and 80% for CT. Conclusions: Direct target alignment methods (US and CT) provided better target coverage. CT-guided alignment provided the best and most consistent dosimetric coverage. A larger planning target volume margin is needed for SV coverage when the alignment target is the prostate.

  11. Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have developed Look-Align, an interactive web-based viewer to display pre-computed multiple sequence alignments. Although initially developed to support the visualization needs of the maize diversity website Panzea (http://www.panzea.org), the viewer is a generic stand-alone tool that can be easi...

  12. Exploring Dance Movement Data Using Sequence Alignment Methods

    PubMed Central

    Chavoshi, Seyed Hossein; De Baets, Bernard; Neutens, Tijs; De Tré, Guy; Van de Weghe, Nico

    2015-01-01

    Despite the abundance of research on knowledge discovery from moving object databases, only a limited number of studies have examined the interaction between moving point objects in space over time. This paper describes a novel approach for measuring similarity in the interaction between moving objects. The proposed approach consists of three steps. First, we transform movement data into sequences of successive qualitative relations based on the Qualitative Trajectory Calculus (QTC). Second, sequence alignment methods are applied to measure the similarity between movement sequences. Finally, movement sequences are grouped based on similarity by means of an agglomerative hierarchical clustering method. The applicability of this approach is tested using movement data from samba and tango dancers. PMID:26181435

  13. Initial alignment method for free space optics laser beam

    NASA Astrophysics Data System (ADS)

    Shimada, Yuta; Tashiro, Yuki; Izumi, Kiyotaka; Yoshida, Koichi; Tsujimura, Takeshi

    2016-08-01

    The authors have newly proposed and constructed an active free space optics transmission system. It is equipped with a motor driven laser emitting mechanism and positioning photodiodes, and it transmits a collimated thin laser beam and accurately steers the laser beam direction. It is necessary to introduce the laser beam within sensible range of the receiver in advance of laser beam tracking control. This paper studies an estimation method of laser reaching point for initial laser beam alignment. Distributed photodiodes detect laser luminescence at respective position, and the optical axis of laser beam is analytically presumed based on the Gaussian beam optics. Computer simulation evaluates the accuracy of the proposed estimation methods, and results disclose that the methods help us to guide the laser beam to a distant receiver.

  14. Upcoming challenges for multiple sequence alignment methods in the high-throughput era

    PubMed Central

    Kemena, Carsten; Notredame, Cedric

    2009-01-01

    This review focuses on recent trends in multiple sequence alignment tools. It describes the latest algorithmic improvements including the extension of consistency-based methods to the problem of template-based multiple sequence alignments. Some results are presented suggesting that template-based methods are significantly more accurate than simpler alternative methods. The validation of existing methods is also discussed at length with the detailed description of recent results and some suggestions for future validation strategies. The last part of the review addresses future challenges for multiple sequence alignment methods in the genomic era, most notably the need to cope with very large sequences, the need to integrate large amounts of experimental data, the need to accurately align non-coding and non-transcribed sequences and finally, the need to integrate many alternative methods and approaches. Contact: cedric.notredame@crg.es PMID:19648142

  15. Alignathon: a competitive assessment of whole-genome alignment methods.

    PubMed

    Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Harris, Robert S; Fitzgerald, Stephen; Beal, Kathryn; Seledtsov, Igor; Molodtsov, Vladimir; Raney, Brian J; Clawson, Hiram; Kim, Jaebum; Kemena, Carsten; Chang, Jia-Ming; Erb, Ionas; Poliakov, Alexander; Hou, Minmei; Herrero, Javier; Kent, William James; Solovyev, Victor; Darling, Aaron E; Ma, Jian; Notredame, Cedric; Brudno, Michael; Dubchak, Inna; Haussler, David; Paten, Benedict

    2014-12-01

    Multiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary analyses. Published assessments and benchmark data sets for protein and, to a lesser extent, global nucleotide MSAs are available, but less effort has been made to establish benchmarks in the more general problem of whole-genome alignment (WGA). Using the same model as the successful Assemblathon competitions, we organized a competitive evaluation in which teams submitted their alignments and then assessments were performed collectively after all the submissions were received. Three data sets were used: Two were simulated and based on primate and mammalian phylogenies, and one was comprised of 20 real fly genomes. In total, 35 submissions were assessed, submitted by 10 teams using 12 different alignment pipelines. We found agreement between independent simulation-based and statistical assessments, indicating that there are substantial accuracy differences between contemporary alignment tools. We saw considerable differences in the alignment quality of differently annotated regions and found that few tools aligned the duplications analyzed. We found that many tools worked well at shorter evolutionary distances, but fewer performed competitively at longer distances. We provide all data sets, submissions, and assessment programs for further study and provide, as a resource for future benchmarking, a convenient repository of code and data for reproducing the simulation assessments. PMID:25273068

  16. Alignathon: a competitive assessment of whole-genome alignment methods

    PubMed Central

    Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Harris, Robert S.; Fitzgerald, Stephen; Beal, Kathryn; Seledtsov, Igor; Molodtsov, Vladimir; Raney, Brian J.; Clawson, Hiram; Kim, Jaebum; Kemena, Carsten; Chang, Jia-Ming; Erb, Ionas; Poliakov, Alexander; Hou, Minmei; Herrero, Javier; Kent, William James; Solovyev, Victor; Darling, Aaron E.; Ma, Jian; Notredame, Cedric; Brudno, Michael; Dubchak, Inna; Haussler, David; Paten, Benedict

    2014-01-01

    Multiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary analyses. Published assessments and benchmark data sets for protein and, to a lesser extent, global nucleotide MSAs are available, but less effort has been made to establish benchmarks in the more general problem of whole-genome alignment (WGA). Using the same model as the successful Assemblathon competitions, we organized a competitive evaluation in which teams submitted their alignments and then assessments were performed collectively after all the submissions were received. Three data sets were used: Two were simulated and based on primate and mammalian phylogenies, and one was comprised of 20 real fly genomes. In total, 35 submissions were assessed, submitted by 10 teams using 12 different alignment pipelines. We found agreement between independent simulation-based and statistical assessments, indicating that there are substantial accuracy differences between contemporary alignment tools. We saw considerable differences in the alignment quality of differently annotated regions and found that few tools aligned the duplications analyzed. We found that many tools worked well at shorter evolutionary distances, but fewer performed competitively at longer distances. We provide all data sets, submissions, and assessment programs for further study and provide, as a resource for future benchmarking, a convenient repository of code and data for reproducing the simulation assessments. PMID:25273068

  17. Fourier-transform and global contrast interferometer alignment methods

    DOEpatents

    Goldberg, Kenneth A.

    2001-01-01

    Interferometric methods are presented to facilitate alignment of image-plane components within an interferometer and for the magnified viewing of interferometer masks in situ. Fourier-transforms are performed on intensity patterns that are detected with the interferometer and are used to calculate pseudo-images of the electric field in the image plane of the test optic where the critical alignment of various components is being performed. Fine alignment is aided by the introduction and optimization of a global contrast parameter that is easily calculated from the Fourier-transform.

  18. LSST Telescope Alignment Plan Based on Nodal Aberration Theory

    NASA Astrophysics Data System (ADS)

    Sebag, J.; Gressler, W.; Schmid, T.; Rolland, J. P.; Thompson, K. P.

    2012-04-01

    The optical alignment of the Large Synoptic Survey Telescope (LSST) is potentially challenging, due to its fast three-mirror optical design and its large 3.5° field of view (FOV). It is highly advantageous to align the three-mirror optical system prior to the integration of the complex science camera on the telescope, which corrects the FOV via three refractive elements and includes the operational wavefront sensors. A telescope alignment method based on nodal aberration theory (NAT) is presented here to address this challenge. Without the science camera installed on the telescope, the on-axis imaging performance of the telescope is diffraction-limited, but the field of view is not corrected. The nodal properties of the three-mirror telescope design have been analyzed and an alignment approach has been developed using the intrinsically linear nodal behavior, which is linked via sensitivities to the misalignment parameters. Since mirror figure errors will exist in any real application, a methodology to introduce primary-mirror figure errors into the analysis has been developed and is also presented.

  19. Physically motivated global alignment method for electron tomography

    DOE PAGESBeta

    Sanders, Toby; Prange, Micah; Akatay, Cem; Binev, Peter

    2015-04-08

    Electron tomography is widely used for nanoscale determination of 3-D structures in many areas of science. Determining the 3-D structure of a sample from electron tomography involves three major steps: acquisition of sequence of 2-D projection images of the sample with the electron microscope, alignment of the images to a common coordinate system, and 3-D reconstruction and segmentation of the sample from the aligned image data. The resolution of the 3-D reconstruction is directly influenced by the accuracy of the alignment, and therefore, it is crucial to have a robust and dependable alignment method. In this paper, we develop amore » new alignment method which avoids the use of markers and instead traces the computed paths of many identifiable ‘local’ center-of-mass points as the sample is rotated. Compared with traditional correlation schemes, the alignment method presented here is resistant to cumulative error observed from correlation techniques, has very rigorous mathematical justification, and is very robust since many points and paths are used, all of which inevitably improves the quality of the reconstruction and confidence in the scientific results.« less

  20. Physically motivated global alignment method for electron tomography

    SciTech Connect

    Sanders, Toby; Prange, Micah; Akatay, Cem; Binev, Peter

    2015-04-08

    Electron tomography is widely used for nanoscale determination of 3-D structures in many areas of science. Determining the 3-D structure of a sample from electron tomography involves three major steps: acquisition of sequence of 2-D projection images of the sample with the electron microscope, alignment of the images to a common coordinate system, and 3-D reconstruction and segmentation of the sample from the aligned image data. The resolution of the 3-D reconstruction is directly influenced by the accuracy of the alignment, and therefore, it is crucial to have a robust and dependable alignment method. In this paper, we develop a new alignment method which avoids the use of markers and instead traces the computed paths of many identifiable ‘local’ center-of-mass points as the sample is rotated. Compared with traditional correlation schemes, the alignment method presented here is resistant to cumulative error observed from correlation techniques, has very rigorous mathematical justification, and is very robust since many points and paths are used, all of which inevitably improves the quality of the reconstruction and confidence in the scientific results.

  1. A Rank-Based Sequence Aligner with Applications in Phylogenetic Analysis

    PubMed Central

    2014-01-01

    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 -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. PMID:25133391

  2. Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies.

    PubMed

    Joseph, Agnel Praveen; Srinivasan, Narayanaswamy; de Brevern, Alexandre G

    2012-09-01

    Comparison of multiple protein structures has a broad range of applications in the analysis of protein structure, function and evolution. Multiple structure alignment tools (MSTAs) are necessary to obtain a simultaneous comparison of a family of related folds. In this study, we have developed a method for multiple structure comparison largely based on sequence alignment techniques. A widely used Structural Alphabet named Protein Blocks (PBs) was used to transform the information on 3D protein backbone conformation as a 1D sequence string. A progressive alignment strategy similar to CLUSTALW was adopted for multiple PB sequence alignment (mulPBA). Highly similar stretches identified by the pairwise alignments are given higher weights during the alignment. The residue equivalences from PB based alignments are used to obtain a three dimensional fit of the structures followed by an iterative refinement of the structural superposition. Systematic comparisons using benchmark datasets of MSTAs underlines that the alignment quality is better than MULTIPROT, MUSTANG and the alignments in HOMSTRAD, in more than 85% of the cases. Comparison with other rigid-body and flexible MSTAs also indicate that mulPBA alignments are superior to most of the rigid-body MSTAs and highly comparable to the flexible alignment methods. PMID:22676903

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

    SciTech Connect

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

    2011-04-01

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

  4. Effect of 25(OH) vitamin D reference method procedure (RMP) alignment on clinical measurements obtained with the IDS-iSYS chemiluminescent-based automated analyzer.

    PubMed

    Simpson, Christine A; Cusano, Anna Maria; Bihuniak, Jessica; Walker, Joanne; Insogna, Karl L

    2015-04-01

    The Vitamin D Standardization Program (VDSP) has identified ID-LC/MS/MS as the reference method procedure (RMP) for 25(OH) vitamin D and NIST Standard SRM2972 as the standard reference material (SRM). As manufacturers align their products to the RMP and NIST standard, a concern is that results obtained in aligned assays will be divergent from those obtained with pre-alignment assays. The Immunodiagnostic Systems Ltd., chemiluminescent, 25(OH) vitamin D iSYS platform assay, was recently harmonized to the RMP. To determine the impact of standardization on results obtained with iSYS reagents, 119 single donor serum samples from eight different disease categories were analyzed in four non-standardized and two standardized iSYS assays. There were strong correlations between the four non-standardized and two standardized assays with Spearman's rank r values between 0.975 and 0.961 and four of the eight r values were >0.97. R(2) values for the eight best-fit linear regression equations ranging between 0.947 and 0.916. None of the slopes were found to be significantly different from one another. Bland-Altman plots showed that the bias was comparable when each of the four non-standardized assays was compared to either of the standardized assays. When the data were segregated in values between 6 and 49ng/mL (15-122nmol/L) or between 50 and 100ng/mL (125-250nmol/L) significant associations remained between results obtained with non-standardized and standardized calibrators regardless of the absolute value. When five recent DEQAS unknowns were analyzed in one non-standardized and one standardized assay the mean percent difference from the NIST target in values obtained using standardized vs. non-standardized calibrators were not significantly different. Finally, strong and statistically significant associations between the results were obtained using non-standardized and standardized assays for six of eight clinical conditions. The only exceptions were hypocalcemia and breast

  5. A Topologically-Informed Hyperstreamline Seeding Method for Alignment Tensor Fields.

    PubMed

    Fu, Fred; Abukhdeir, Nasser Mohieddin

    2015-03-01

    A topologically-informed hyperstreamline seeding method is presented for visualization of alignment tensor fields. The method is inspired by and applied to visualization of nematic liquid crystal (LC) orientation dynamics simulations. The method distributes hyperstreamlines along domain boundaries and edges of a nearest-neighbor graph whose vertices are degenerate regions of the alignment tensor field, which correspond to orientational defects in a nematic LC domain. This is accomplished without iteration while conforming to a user-specified spacing between hyperstreamlines and avoids possible failure modes associated with hyperstreamline integration in the vicinity of degeneracies in alignment (orientational defects). It is shown that the presented seeding method enables automated hyperstreamline-based visualization of a broad range of alignment tensor fields which enhances the ability of researchers to interpret these fields and provides an alternative to using glyph-based techniques. PMID:26357072

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

    PubMed

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

    2014-01-01

    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. PMID:25513826

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

    PubMed Central

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

    2014-01-01

    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. PMID:25513826

  8. PHASE CORRELATION METHOD FOR THE ALIGNMENT OF TOTAL SOLAR ECLIPSE IMAGES

    SciTech Connect

    Druckmueller, M.

    2009-12-01

    A modified phase correlation method, based on Fourier transform, which enables the alignment of solar coronal images taken during the total solar eclipses, is presented. The method enables the measurement of translation, rotation, and scaling factor between two images. With the application of this technique, pairs of images with different exposure times, different brightness scale, such as linear for CCD and nonlinear for images taken with photographic film, and even images from different emission lines can be aligned with sub-pixel precision.

  9. Dual AFM probes alignment based on vision guidance

    NASA Astrophysics Data System (ADS)

    Zhang, Hua-kun; Gao, Si-tian; Lu, Ming-zhen; Wang, Long-long

    2013-10-01

    Atomic force microscope (AFM) with dual probes that operate together can measure both side walls excellently at the same time, which virtually eliminates the prevalent effect of probe width that contributes a large component of uncertainty in measurement results and finally obtains the critical dimension (CD)(e.g. the linewidth) through data synthesis. In calibration process, the dual probes must contact each other in advance, which realizes the alignment in the three dimensions, to establish a zero reference point and ensure the accuracy of measurement. Because nowadays the optical resolution of advanced lens have exceeded micrometer range, and the size of probes is within micro level, it is possible to acquire dual probes images in both horizontal and vertical directions, through which the movement of the probes can be controlled in time. In order to further enhance the alignment precision, sub-pixel edge detection method based on Zernike orthogonal moment is used to obtain relative position between these two probes, which helps the tips alignment attains sub-micron range. Piezoelectric nanopositioning stages calibrated by laser interferometer are used to implement fine movement of the probes to verify the accuracy of the experimental results. To simplify the system, novel self-sensing and self-actuating probe based on a quartz tuning fork combined with a micromachined cantilever is used for dynamic mode AFM. In this case, an external optical detection system is not needed, so the system is simple and small.

  10. Evaluating the Accuracy and Efficiency of Multiple Sequence Alignment Methods

    PubMed Central

    Pervez, Muhammad Tariq; Babar, Masroor Ellahi; Nadeem, Asif; Aslam, Muhammad; Awan, Ali Raza; Aslam, Naeem; Hussain, Tanveer; Naveed, Nasir; Qadri, Salman; Waheed, Usman; Shoaib, Muhammad

    2014-01-01

    A comparison of 10 most popular Multiple Sequence Alignment (MSA) tools, namely, MUSCLE, MAFFT(L-INS-i), MAFFT (FFT-NS-2), T-Coffee, ProbCons, SATe, Clustal Omega, Kalign, Multalin, and Dialign-TX is presented. We also focused on the significance of some implementations embedded in algorithm of each tool. Based on 10 simulated trees of different number of taxa generated by R, 400 known alignments and sequence files were constructed using indel-Seq-Gen. A total of 4000 test alignments were generated to study the effect of sequence length, indel size, deletion rate, and insertion rate. Results showed that alignment quality was highly dependent on the number of deletions and insertions in the sequences and that the sequence length and indel size had a weaker effect. Overall, ProbCons was consistently on the top of list of the evaluated MSA tools. SATe, being little less accurate, was 529.10% faster than ProbCons and 236.72% faster than MAFFT(L-INS-i). Among other tools, Kalign and MUSCLE achieved the highest sum of pairs. We also considered BALiBASE benchmark datasets and the results relative to BAliBASE- and indel-Seq-Gen-generated alignments were consistent in the most cases. PMID:25574120

  11. Method for Providing Semiconductors Having Self-Aligned Ion Implant

    NASA Technical Reports Server (NTRS)

    Neudeck, Philip G. (Inventor)

    2014-01-01

    A method is disclosed that provides a self-aligned nitrogen-implant particularly suited for a Junction Field Effect Transistor (JFET) semiconductor device preferably comprised of a silicon carbide (SiC). This self-aligned nitrogen-implant allows for the realization of durable and stable electrical functionality of high temperature transistors such as JFETs. The method implements the self-aligned nitrogen-implant having predetermined dimensions, at a particular step in the fabrication process, so that the SiC junction field effect transistors are capable of being electrically operating continuously at 500.degree. C. for over 10,000 hours in an air ambient with less than a 10% change in operational transistor parameters.

  12. Method for Providing Semiconductors Having Self-Aligned Ion Implant

    NASA Technical Reports Server (NTRS)

    Neudeck, Philip G. (Inventor)

    2011-01-01

    A method is disclosed that provides a self-aligned nitrogen-implant particularly suited for a Junction Field Effect Transistor (JFET) semiconductor device preferably comprised of a silicon carbide (SiC). This self-aligned nitrogen-implant allows for the realization of durable and stable electrical functionality of high temperature transistors such as JFETs. The method implements the self-aligned nitrogen-implant having predetermined dimensions, at a particular step in the fabrication process, so that the SiC junction field effect transistors are capable of being electrically operating continuously at 500.degree. C. for over 10,000 hours in an air ambient with less than a 10% change in operational transistor parameters.

  13. Compensation method for the alignment angle error of a gear axis in profile deviation measurement

    NASA Astrophysics Data System (ADS)

    Fang, Suping; Liu, Yongsheng; Wang, Huiyi; Taguchi, Tetsuya; Takeda, Ryuhei

    2013-05-01

    In the precision measurement of involute helical gears, the alignment angle error of a gear axis, which was caused by the assembly error of a gear measuring machine, will affect the measurement accuracy of profile deviation. A model of the involute helical gear is established under the condition that the alignment angle error of the gear axis exists. Based on the measurement theory of profile deviation, without changing the initial measurement method and data process of the gear measuring machine, a compensation method is proposed for the alignment angle error of the gear axis that is included in profile deviation measurement results. Using this method, the alignment angle error of the gear axis can be compensated for precisely. Some experiments that compare the residual alignment angle error of a gear axis after compensation for the initial alignment angle error were performed to verify the accuracy and feasibility of this method. Experimental results show that the residual alignment angle error of a gear axis included in the profile deviation measurement results is decreased by more than 85% after compensation, and this compensation method significantly improves the measurement accuracy of the profile deviation of involute helical gear.

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

    NASA Astrophysics Data System (ADS)

    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.

  15. Beam-based alignment of the final focus test beam

    SciTech Connect

    Tenenbaum, P.; Burke, D.; Helm, R.; Irwin, J.; Raimondi, P.; Oide, K.; Floettmann, K.

    1995-12-01

    Beam-based alignment of quadrupole and sextupole magnets is crucial for the overall performance of linear collider final focus systems, especially for elimination of backgrounds and higher-order aberrations. At the Final Focus Test Beam (FFTB), alignment tolerances required for achieving the desired spot size are 100 microns in the horizontal and 30 microns in the vertical. Using a combination of independent magnet power supplies, hi-h-resolution stripline beam position monitors and precision magnet movers, the FFTB can be aligned to these tolerances in about 8 hours. Description of the algorithm, presentation of alignment results, and possible improvements to the system are discussed.

  16. Evaluation of Eight Methods for Aligning Orientation of Two Coordinate Systems.

    PubMed

    Mecheri, Hakim; Robert-Lachaine, Xavier; Larue, Christian; Plamondon, André

    2016-08-01

    The aim of this study was to evaluate eight methods for aligning the orientation of two different local coordinate systems. Alignment is very important when combining two different systems of motion analysis. Two of the methods were developed specifically for biomechanical studies, and because there have been at least three decades of algorithm development in robotics, it was decided to include six methods from this field. To compare these methods, an Xsens sensor and two Optotrak clusters were attached to a Plexiglas plate. The first optical marker cluster was fixed on the sensor and 20 trials were recorded. The error of alignment was calculated for each trial, and the mean, the standard deviation, and the maximum values of this error over all trials were reported. One-way repeated measures analysis of variance revealed that the alignment error differed significantly across the eight methods. Post-hoc tests showed that the alignment error from the methods based on angular velocities was significantly lower than for the other methods. The method using angular velocities performed the best, with an average error of 0.17 ± 0.08 deg. We therefore recommend this method, which is easy to perform and provides accurate alignment. PMID:27245737

  17. A new method and device of aligning patient setup lasers in radiation therapy.

    PubMed

    Hwang, Ui-Jung; Jo, Kwanghyun; Lim, Young Kyung; Kwak, Jung Won; Choi, Sang Hyuon; Jeong, Chiyoung; Kim, Mi Young; Jeong, Jong Hwi; Shin, Dongho; Lee, Se Byeong; Park, Jeong-Hoon; Park, Sung Yong; Kim, Siyong

    2016-01-01

    The aim of this study is to develop a new method to align the patient setup lasers in a radiation therapy treatment room and examine its validity and efficiency. The new laser alignment method is realized by a device composed of both a metallic base plate and a few acrylic transparent plates. Except one, every plate has either a crosshair line (CHL) or a single vertical line that is used for alignment. Two holders for radiochromic film insertion are prepared in the device to find a radiation isocenter. The right laser positions can be found optically by matching the shadows of all the CHLs in the gantry head and the device. The reproducibility, accuracy, and efficiency of laser alignment and the dependency on the position error of the light source were evaluated by comparing the means and the standard deviations of the measured laser positions. After the optical alignment of the lasers, the radiation isocenter was found by the gantry and collimator star shots, and then the lasers were translated parallel to the isocenter. In the laser position reproducibility test, the mean and standard deviation on the wall of treatment room were 32.3 ± 0.93 mm for the new method whereas they were 33.4 ± 1.49 mm for the conventional method. The mean alignment accuracy was 1.4 mm for the new method, and 2.1 mm for the conventional method on the walls. In the test of the dependency on the light source position error, the mean laser position was shifted just by a similar amount of the shift of the light source in the new method, but it was greatly magnified in the conventional method. In this study, a new laser alignment method was devised and evaluated successfully. The new method provided more accurate, more reproducible, and faster alignment of the lasers than the conventional method. PMID:26894331

  18. Aligning Transition and Standards-Based Education: Issues and Strategies.

    ERIC Educational Resources Information Center

    Kochhar-Bryant, Carol, Ed.; Bassett, Diane S., Ed.

    Eleven papers address issues in the alignment of standards-based education and individualized transition planning and service development for students with disabilities including differences in assumptions and principles, the transition planning model as a framework for achieving this alignment, and educational practices resulting from this…

  19. Chunk Alignment for Corpus-Based Machine Translation

    ERIC Educational Resources Information Center

    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…

  20. SU-E-T-484: A New Method of Aligning Patient Setup Lasers in Radiation Therapy

    SciTech Connect

    Hwang, U; Lim, Y; Cho, K; Jeong, C; Kim, M; Jeong, J; Park, J; Shin, D; Lee, S; Kim, J; Choi, S; Kwak, J; Yoon, K; Park, S; Kim, S

    2014-06-01

    Purpose: To develop a new method to align the patient setup lasers in radiation therapy and examine its validity and effectiveness. Methods: The new laser alignment method was realized by a device composed of both a metallic base plate and few acrylic transparent plates with a cross hair line on each of them. The holders of radiochromic films were prepared in the device to find a radiation isocenter. The right laser positions could be found optically by matching the shadows of all the cross hairs in the gantry head and the device. The repeatability and reproducibility (R and R) of laser alignments and the dependency of the alignment on the position error of the light source were evaluated by comparing the standard deviations and the means of the measured laser positions. After aligning the lasers optically, a radiation isocenter was found by a collimator spoke shot and the gantry spoke shot, and then the lasers were parallely translated to the isocenter. Results: In the R and R test, the standard deviation was 1.14 mm for the new method whereas it was 1.49 mm or 2.76 mm for the conventional method with either high- or low-precision levels. In the test of the dependency on the position error of the light source, the mean laser position was shifted by 5.3 mm corresponding to the shift of the light source, 4.8 mm for the new method, but for the conventional method the laser position was shifted more than 7 times than that. The positional shift could be corrected by a parallel translation to the isocenter in the new method. Conclusion: A new laser alignment method was devised for radiation therapy and tested successfully. The method enabled us to align the lasers easily and accurately without repetition, and all lasers could be finally aligned to the radiation isocenter.

  1. Boresight alignment method for mobile laser scanning systems

    NASA Astrophysics Data System (ADS)

    Rieger, P.; Studnicka, N.; Pfennigbauer, M.; Zach, G.

    2010-06-01

    Mobile laser scanning (MLS) is the latest approach towards fast and cost-efficient acquisition of 3-dimensional spatial data. Accurately evaluating the boresight alignment in MLS systems is an obvious necessity. However, recent systems available on the market may lack of suitable and efficient practical workflows on how to perform this calibration. This paper discusses an innovative method for accurately determining the boresight alignment of MLS systems by employing 3D laser scanners. Scanning objects using a 3D laser scanner operating in a 2D line-scan mode from various different runs and scan directions provides valuable scan data for determining the angular alignment between inertial measurement unit and laser scanner. Field data is presented demonstrating the final accuracy of the calibration and the high quality of the point cloud acquired during an MLS campaign.

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

    PubMed

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

    2015-01-01

    Ontology Matching aims at identifying a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, alignments produced for large ontologies are often logically incoherent. It was only recently that the use of repair techniques to improve the coherence of ontology alignments began to be explored. This paper presents a novel modularization technique for ontology alignment repair which extracts fragments of the input ontologies that only contain the necessary classes and relations to resolve all detectable incoherences. The paper presents also an alignment repair algorithm that uses a global repair strategy to minimize both the degree of incoherence and the number of mappings removed from the alignment, while overcoming the scalability problem by employing the proposed modularization technique. Our evaluation shows that our modularization technique produces significantly small fragments of the ontologies and that our repair algorithm produces more complete alignments than other current alignment repair systems, while obtaining an equivalent degree of incoherence. Additionally, we also present a variant of our repair algorithm that makes use of the confidence values of the mappings to improve alignment repair. Our repair algorithm was implemented as part of AgreementMakerLight, a free and open-source ontology matching system. PMID:26710335

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

    PubMed Central

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

    2015-01-01

    Ontology Matching aims at identifying a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, alignments produced for large ontologies are often logically incoherent. It was only recently that the use of repair techniques to improve the coherence of ontology alignments began to be explored. This paper presents a novel modularization technique for ontology alignment repair which extracts fragments of the input ontologies that only contain the necessary classes and relations to resolve all detectable incoherences. The paper presents also an alignment repair algorithm that uses a global repair strategy to minimize both the degree of incoherence and the number of mappings removed from the alignment, while overcoming the scalability problem by employing the proposed modularization technique. Our evaluation shows that our modularization technique produces significantly small fragments of the ontologies and that our repair algorithm produces more complete alignments than other current alignment repair systems, while obtaining an equivalent degree of incoherence. Additionally, we also present a variant of our repair algorithm that makes use of the confidence values of the mappings to improve alignment repair. Our repair algorithm was implemented as part of AgreementMakerLight, a free and open-source ontology matching system. PMID:26710335

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

    DOEpatents

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

    2013-06-18

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

  5. Method of fabricating vertically aligned group III-V nanowires

    DOEpatents

    Wang, George T; Li, Qiming

    2014-11-25

    A top-down method of fabricating vertically aligned Group III-V micro- and nanowires uses a two-step etch process that adds a selective anisotropic wet etch after an initial plasma etch to remove the dry etch damage while enabling micro/nanowires with straight and smooth faceted sidewalls and controllable diameters independent of pitch. The method enables the fabrication of nanowire lasers, LEDs, and solar cells.

  6. Beam based alignment of C-shaped quadrupole magnets

    SciTech Connect

    Portmann, G.; Robin, D.

    1998-06-01

    Many storage rings have implemented a method of finding the positional offset between the electrical center of the beam position monitors (BPM) and the magnetic center of the adjacent quadrupole magnets. The algorithm for accomplishing this is usually based on modulating the current in the quadrupole magnet and finding the beam position that minimizes the orbit perturbation. When the quadrupole magnet is C-shaped, as it is for many light sources, the modulation method can produce an erroneous measurement of the magnetic center in the horizontal plane. When the current in a C-shaped quadrupole is changed, there is an additional dipole component in the vertical field. Due to nonlinearities in the hysteresis cycle of the C-magnet geometry, the beam-based alignment technique at the Advanced Light Source (ALS) deviated horizontally by .5 mm from the actual magnetic center. By modifying the technique, the offsets were measured to an accuracy of better than 50 {micro}m.

  7. Structure based 3D-QSAR studies of Interleukin-2 inhibitors: Comparing the quality and predictivity of 3D-QSAR models obtained from different alignment methods and charge calculations.

    PubMed

    Halim, Sobia Ahsan; Zaheer-ul-Haq

    2015-08-01

    Interleukin-2 is an essential cytokine in an innate immune response, and is a promising drug target for several immunological disorders. In the present study, structure-based 3D-QSAR modeling was carried out via Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Index Analysis (CoMSIA) methods. Six different partial charge calculation methods were used in combination with two different alignment methods to scrutinize their effects on the predictive power of 3D-QSAR models. The best CoMFA and CoMSIA models were obtained with the AM1 charges when used with co-conformer based substructure alignment (CCBSA) method. The obtained models posses excellent correlation coefficient value and also exhibited good predictive power (for CoMFA: q(2)=0.619; r(2)=0.890; r(2)Pred=0.765 and for CoMSIA: q(2)=0.607; r(2)=0.884; r(2)Pred=0.655). The developed models were further validated by using a set of another sixteen compounds as external test set 2 and both models showed strong predictive power with r(2)Pred=>0.8. The contour maps obtained from these models better interpret the structure activity relationship; hence the developed models would help to design and optimize more potent IL-2 inhibitors. The results might have implications for rational design of specific anti-inflammatory compounds with improved affinity and selectivity. PMID:26051521

  8. A Self-Alignment Algorithm for SINS Based on Gravitational Apparent Motion and Sensor Data Denoising

    PubMed Central

    Liu, Yiting; Xu, Xiaosu; Liu, Xixiang; Yao, Yiqing; Wu, Liang; Sun, Jin

    2015-01-01

    Initial alignment is always a key topic and difficult to achieve in an inertial navigation system (INS). In this paper a novel self-initial alignment algorithm is proposed using gravitational apparent motion vectors at three different moments and vector-operation. Simulation and analysis showed that this method easily suffers from the random noise contained in accelerometer measurements which are used to construct apparent motion directly. Aiming to resolve this problem, an online sensor data denoising method based on a Kalman filter is proposed and a novel reconstruction method for apparent motion is designed to avoid the collinearity among vectors participating in the alignment solution. Simulation, turntable tests and vehicle tests indicate that the proposed alignment algorithm can fulfill initial alignment of strapdown INS (SINS) under both static and swinging conditions. The accuracy can either reach or approach the theoretical values determined by sensor precision under static or swinging conditions. PMID:25923932

  9. A Self-Alignment Algorithm for SINS Based on Gravitational Apparent Motion and Sensor Data Denoising.

    PubMed

    Liu, Yiting; Xu, Xiaosu; Liu, Xixiang; Yao, Yiqing; Wu, Liang; Sun, Jin

    2015-01-01

    Initial alignment is always a key topic and difficult to achieve in an inertial navigation system (INS). In this paper a novel self-initial alignment algorithm is proposed using gravitational apparent motion vectors at three different moments and vector-operation. Simulation and analysis showed that this method easily suffers from the random noise contained in accelerometer measurements which are used to construct apparent motion directly. Aiming to resolve this problem, an online sensor data denoising method based on a Kalman filter is proposed and a novel reconstruction method for apparent motion is designed to avoid the collinearity among vectors participating in the alignment solution. Simulation, turntable tests and vehicle tests indicate that the proposed alignment algorithm can fulfill initial alignment of strapdown INS (SINS) under both static and swinging conditions. The accuracy can either reach or approach the theoretical values determined by sensor precision under static or swinging conditions. PMID:25923932

  10. Applications of alignment-free methods in epigenomics

    PubMed Central

    Pinello, Luca

    2014-01-01

    Epigenetic mechanisms play an important role in the regulation of cell type-specific gene activities, yet how epigenetic patterns are established and maintained remains poorly understood. Recent studies have supported a role of DNA sequences in recruitment of epigenetic regulators. Alignment-free methods have been applied to identify distinct sequence features that are associated with epigenetic patterns and to predict epigenomic profiles. Here, we review recent advances in such applications, including the methods to map DNA sequence to feature space, sequence comparison and prediction models. Computational studies using these methods have provided important insights into the epigenetic regulatory mechanisms. PMID:24197932

  11. ALFRED: A Practical Method for Alignment-Free Distance Computation.

    PubMed

    Thankachan, Sharma V; Chockalingam, Sriram P; Liu, Yongchao; Apostolico, Alberto; Aluru, Srinivas

    2016-06-01

    Alignment-free approaches are gaining persistent interest in many sequence analysis applications such as phylogenetic inference and metagenomic classification/clustering, especially for large-scale sequence datasets. Besides the widely used k-mer methods, the average common substring (ACS) approach has emerged to be one of the well-known alignment-free approaches. Two recent works further generalize this ACS approach by allowing a bounded number k of mismatches in the common substrings, relying on approximation (linear time) and exact computation, respectively. Albeit having a good worst-case time complexity [Formula: see text], the exact approach is complex and unlikely to be efficient in practice. Herein, we present ALFRED, an alignment-free distance computation method, which solves the generalized common substring search problem via exact computation. Compared to the theoretical approach, our algorithm is easier to implement and more practical to use, while still providing highly competitive theoretical performances with an expected run-time of [Formula: see text]. By applying our program to phylogenetic inference as a case study, we find that our program facilitates to exactly reconstruct the topology of the reference phylogenetic tree for a set of 27 primate mitochondrial genomes, at reasonably acceptable speed. ALFRED is implemented in C++ programming language and the source code is freely available online. PMID:27138275

  12. System and method for 2D workpiece alignment

    SciTech Connect

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

    2015-07-14

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

  13. A Robust Self-Alignment Method for Ship's Strapdown INS Under Mooring Conditions

    PubMed Central

    Sun, Feng; Lan, Haiyu; Yu, Chunyang; El-Sheimy, Naser; Zhou, Guangtao; Cao, Tong; Liu, Hang

    2013-01-01

    Strapdown inertial navigation systems (INS) need an alignment process to determine the initial attitude matrix between the body frame and the navigation frame. The conventional alignment process is to compute the initial attitude matrix using the gravity and Earth rotational rate measurements. However, under mooring conditions, the inertial measurement unit (IMU) employed in a ship's strapdown INS often suffers from both the intrinsic sensor noise components and the external disturbance components caused by the motions of the sea waves and wind waves, so a rapid and precise alignment of a ship's strapdown INS without any auxiliary information is hard to achieve. A robust solution is given in this paper to solve this problem. The inertial frame based alignment method is utilized to adapt the mooring condition, most of the periodical low-frequency external disturbance components could be removed by the mathematical integration and averaging characteristic of this method. A novel prefilter named hidden Markov model based Kalman filter (HMM-KF) is proposed to remove the relatively high-frequency error components. Different from the digital filters, the HMM-KF barely cause time-delay problem. The turntable, mooring and sea experiments favorably validate the rapidness and accuracy of the proposed self-alignment method and the good de-noising performance of HMM-KF. PMID:23799492

  14. A robust self-alignment method for ship's strapdown INS under mooring conditions.

    PubMed

    Sun, Feng; Lan, Haiyu; Yu, Chunyang; El-Sheimy, Naser; Zhou, Guangtao; Cao, Tong; Liu, Hang

    2013-01-01

    Strapdown inertial navigation systems (INS) need an alignment process to determine the initial attitude matrix between the body frame and the navigation frame. The conventional alignment process is to compute the initial attitude matrix using the gravity and Earth rotational rate measurements. However, under mooring conditions, the inertial measurement unit (IMU) employed in a ship's strapdown INS often suffers from both the intrinsic sensor noise components and the external disturbance components caused by the motions of the sea waves and wind waves, so a rapid and precise alignment of a ship's strapdown INS without any auxiliary information is hard to achieve. A robust solution is given in this paper to solve this problem. The inertial frame based alignment method is utilized to adapt the mooring condition, most of the periodical low-frequency external disturbance components could be removed by the mathematical integration and averaging characteristic of this method. A novel prefilter named hidden Markov model based Kalman filter (HMM-KF) is proposed to remove the relatively high-frequency error components. Different from the digital filters, the HMM-KF barely cause time-delay problem. The turntable, mooring and sea experiments favorably validate the rapidness and accuracy of the proposed self-alignment method and the good de-noising performance of HMM-KF. PMID:23799492

  15. Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification

    PubMed Central

    Borozan, Ivan; Watt, Stuart; Ferretti, Vincent

    2015-01-01

    Motivation: Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature of alignment-based and alignment-free similarity measures with the aim to improve the accuracy with which DNA and protein sequences are characterized. Results: Our model classifies sequences using a combined sequence similarity score calculated by adaptively weighting the contribution of different sequence similarity measures. Weights are determined independently for each sequence in the test set and reflect the discriminatory ability of individual similarity measures in the training set. Because the similarity between some sequences is determined more accurately with one type of measure rather than another, our classifier allows different sets of weights to be associated with different sequences. Using five different similarity measures, we show that our model significantly improves the classification accuracy over the current composition- and alignment-based models, when predicting the taxonomic lineage for both short viral sequence fragments and complete viral sequences. We also show that our model can be used effectively for the classification of reads from a real metagenome dataset as well as protein sequences. Availability and implementation: All the datasets and the code used in this study are freely available at https://collaborators.oicr.on.ca/vferretti/borozan_csss/csss.html. Contact: ivan.borozan@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25573913

  16. TS-AMIR: a topology string alignment method for intensive rapid protein structure comparison

    PubMed Central

    2012-01-01

    Background In structural biology, similarity analysis of protein structure is a crucial step in studying the relationship between proteins. Despite the considerable number of techniques that have been explored within the past two decades, the development of new alternative methods is still an active research area due to the need for high performance tools. Results In this paper, we present TS-AMIR, a Topology String Alignment Method for Intensive Rapid comparison of protein structures. The proposed method works in two stages: In the first stage, the method generates a topology string based on the geometric details of secondary structure elements, and then, utilizes an n-gram modelling technique over entropy concept to capture similarities in these strings. This initial correspondence map between secondary structure elements is submitted to the second stage in order to obtain the alignment at the residue level. Applying the Kabsch method, a heuristic step-by-step algorithm is adopted in the second stage to align the residues, resulting in an optimal rotation matrix and minimized RMSD. The performance of the method was assessed in different information retrieval tests and the results were compared with those of CE and TM-align, representing two geometrical tools, and YAKUSA, 3D-BLAST and SARST as three representatives of linear encoding schemes. It is shown that the method obtains a high running speed similar to that of the linear encoding schemes. In addition, the method runs about 800 and 7200 times faster than TM-align and CE respectively, while maintaining a competitive accuracy with TM-align and CE. Conclusions The experimental results demonstrate that linear encoding techniques are capable of reaching the same high degree of accuracy as that achieved by geometrical methods, while generally running hundreds of times faster than conventional programs. PMID:22336468

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

    PubMed

    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. PMID:26939754

  18. Cryo-EM Image Alignment Based on Nonuniform Fast Fourier Transform

    PubMed Central

    Yang, Zhengfan; Penczek, Pawel A.

    2008-01-01

    In single particle analysis, two-dimensional (2-D) alignment is a fundamental step intended to put into register various particle projections of biological macromolecules collected at the electron microscope. The efficiency and quality of three-dimensional (3-D) structure reconstruction largely depends on the computational speed and alignment accuracy of this crucial step. In order to improve the performance of alignment, we introduce a new method that takes advantage of the highly accurate interpolation scheme based on the gridding method, a version of the nonuniform Fast Fourier Transform, and utilizes a multi-dimensional optimization algorithm for the refinement of the orientation parameters. Using simulated data, we demonstrate that by using less than half of the sample points and taking twice the runtime, our new 2-D alignment method achieves dramatically better alignment accuracy than that based on quadratic interpolation. We also apply our method to image to volume registration, the key step in the single particle EM structure refinement protocol. We find that in this case the accuracy of the method not only surpasses the accuracy of the commonly used real-space implementation, but results are achieved in much shorter time, making gridding-based alignment a perfect candidate for efficient structure determination in single particle analysis. PMID:18499351

  19. An active alignment method for post launch co-alignment of laser beam combiner systems

    NASA Technical Reports Server (NTRS)

    Yu, A. W.; Green, J. W.; Maynard, W. L.; Minott, P. O.; Krainak, M. A.

    1992-01-01

    A laser transmitter for high bandwidth geosynchronous satellite communications is described. High optical power is achieved by combining semiconductor laser diodes. An active alignment scheme is proposed for achieving the +/- 20 microrad post launch multiple laser angular co-alignment requirement.

  20. Compensation method for the alignment angle error in pitch deviation measurement

    NASA Astrophysics Data System (ADS)

    Liu, Yongsheng; Fang, Suping; Wang, Huiyi; Taguchi, Tetsuya; Takeda, Ryohei

    2016-05-01

    When measuring the tooth flank of an involute helical gear by gear measuring center (GMC), the alignment angle error of a gear axis, which was caused by the assembly error and manufacturing error of the GMC, will affect the measurement accuracy of pitch deviation of the gear tooth flank. Based on the model of the involute helical gear and the tooth flank measurement theory, a method is proposed to compensate the alignment angle error that is included in the measurement results of pitch deviation, without changing the initial measurement method of the GMC. Simulation experiments are done to verify the compensation method and the results show that after compensation, the alignment angle error of the gear axis included in measurement results of pitch deviation declines significantly, more than 90% of the alignment angle errors are compensated, and the residual alignment angle errors in pitch deviation measurement results are less than 0.1 μm. It shows that the proposed method can improve the measurement accuracy of the GMC when measuring the pitch deviation of involute helical gear.

  1. Fast multiple alignment of ungapped DNA sequences using information theory and a relaxation method.

    PubMed

    Schneider, Thomas D; Mastronarde, David N

    1996-12-01

    An information theory based multiple alignment ("Malign") method was used to align the DNA binding sequences of the OxyR and Fis proteins, whose sequence conservation is so spread out that it is difficult to identify the sites. In the algorithm described here, the information content of the sequences is used as a unique global criterion for the quality of the alignment. The algorithm uses look-up tables to avoid recalculating computationally expensive functions such as the logarithm. Because there are no arbitrary constants and because the results are reported in absolute units (bits), the best alignment can be chosen without ambiguity. Starting from randomly selected alignments, a hill-climbing algorithm can track through the immense space of s(n) combinations where s is the number of sequences and n is the number of positions possible for each sequence. Instead of producing a single alignment, the algorithm is fast enough that one can afford to use many start points and to classify the solutions. Good convergence is indicated by the presence of a single well-populated solution class having higher information content than other classes. The existence of several distinct classes for the Fis protein indicates that those binding sites have self-similar features. PMID:19953199

  2. Method and system for aligning fibers during electrospinning

    NASA Technical Reports Server (NTRS)

    Scott-Carnell, Lisa A. (Inventor); Stephens, Ralph M (Inventor); Holloway, Nancy M. (Inventor); Rhim, Caroline (Inventor); Niklason, Laura (Inventor); Clark, Robert L. (Inventor); Siochi, Emilie J. (Inventor)

    2011-01-01

    A method and system are provided for aligning fibers in an electrospinning process. A jet of a fiberizable material is directed towards an uncharged collector from a dispensing location that is spaced apart from the collector. While the fiberizable material is directed towards the collector, an elliptical electric field is generated via the electrically charged dispenser and an oppositely-charged control location. The field spans between the dispensing location and the control location that is within line-of-sight of the dispensing location, and impinges upon at least a portion of the collector. Various combinations of numbers and geometries of dispensers, collectors, and electrodes can be used.

  3. BEAM-BASED ALIGNMENT IN THE RHIC E-COOLING SOLENOIDS.

    SciTech Connect

    CAMERON, P.; BEN-ZVI, I.; DAWSON, W.C.; ET AL.

    2005-05-16

    Accurate alignment of the electron and ion beams in the RHIC electron cooling solenoids is crucial for well-optimized cooling. Because of the greatly differing rigidities of the electron and ion beams, to achieve the specified alignment accuracy it is required that transverse magnetic fields resulting from imperfections in solenoid fabrication be down by five orders of magnitude relative to the pure solenoid fields. Shimming the solenoid field to this accuracy might be accomplished by survey techniques prior to operation with beam, or by methods of beam-based alignment. We report on the details of a method of beam-based alignment, as well as the results of preliminary measurements with the ion beam at RHIC.

  4. Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer.

    PubMed

    Bromberg, Raquel; Grishin, Nick V; Otwinowski, Zbyszek

    2016-06-01

    Advances in sequencing have generated a large number of complete genomes. Traditionally, phylogenetic analysis relies on alignments of orthologs, but defining orthologs and separating them from paralogs is a complex task that may not always be suited to the large datasets of the future. An alternative to traditional, alignment-based approaches are whole-genome, alignment-free methods. These methods are scalable and require minimal manual intervention. We developed SlopeTree, a new alignment-free method that estimates evolutionary distances by measuring the decay of exact substring matches as a function of match length. SlopeTree corrects for horizontal gene transfer, for composition variation and low complexity sequences, and for branch-length nonlinearity caused by multiple mutations at the same site. We tested SlopeTree on 495 bacteria, 73 archaea, and 72 strains of Escherichia coli and Shigella. We compared our trees to the NCBI taxonomy, to trees based on concatenated alignments, and to trees produced by other alignment-free methods. The results were consistent with current knowledge about prokaryotic evolution. We assessed differences in tree topology over different methods and settings and found that the majority of bacteria and archaea have a core set of proteins that evolves by descent. In trees built from complete genomes rather than sets of core genes, we observed some grouping by phenotype rather than phylogeny, for instance with a cluster of sulfur-reducing thermophilic bacteria coming together irrespective of their phyla. The source-code for SlopeTree is available at: http://prodata.swmed.edu/download/pub/slopetree_v1/slopetree.tar.gz. PMID:27336403

  5. Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer

    PubMed Central

    Grishin, Nick V.; Otwinowski, Zbyszek

    2016-01-01

    Advances in sequencing have generated a large number of complete genomes. Traditionally, phylogenetic analysis relies on alignments of orthologs, but defining orthologs and separating them from paralogs is a complex task that may not always be suited to the large datasets of the future. An alternative to traditional, alignment-based approaches are whole-genome, alignment-free methods. These methods are scalable and require minimal manual intervention. We developed SlopeTree, a new alignment-free method that estimates evolutionary distances by measuring the decay of exact substring matches as a function of match length. SlopeTree corrects for horizontal gene transfer, for composition variation and low complexity sequences, and for branch-length nonlinearity caused by multiple mutations at the same site. We tested SlopeTree on 495 bacteria, 73 archaea, and 72 strains of Escherichia coli and Shigella. We compared our trees to the NCBI taxonomy, to trees based on concatenated alignments, and to trees produced by other alignment-free methods. The results were consistent with current knowledge about prokaryotic evolution. We assessed differences in tree topology over different methods and settings and found that the majority of bacteria and archaea have a core set of proteins that evolves by descent. In trees built from complete genomes rather than sets of core genes, we observed some grouping by phenotype rather than phylogeny, for instance with a cluster of sulfur-reducing thermophilic bacteria coming together irrespective of their phyla. The source-code for SlopeTree is available at: http://prodata.swmed.edu/download/pub/slopetree_v1/slopetree.tar.gz. PMID:27336403

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

    PubMed

    Xia, Xuhua

    2016-09-01

    While pairwise sequence alignment (PSA) by dynamic programming is guaranteed to generate one of the optimal alignments, multiple sequence alignment (MSA) of highly divergent sequences often results in poorly aligned sequences, plaguing all subsequent phylogenetic analysis. One way to avoid this problem is to use only PSA to reconstruct phylogenetic trees, which can only be done with distance-based methods. I compared the accuracy of this new computational approach (named PhyPA for phylogenetics by pairwise alignment) against the maximum likelihood method using MSA (the ML+MSA approach), based on nucleotide, amino acid and codon sequences simulated with different topologies and tree lengths. I present a surprising discovery that the fast PhyPA method consistently outperforms the slow ML+MSA approach for highly diverged sequences even when all optimization options were turned on for the ML+MSA approach. Only when sequences are not highly diverged (i.e., when a reliable MSA can be obtained) does the ML+MSA approach outperforms PhyPA. The true topologies are always recovered by ML with the true alignment from the simulation. However, with MSA derived from alignment programs such as MAFFT or MUSCLE, the recovered topology consistently has higher likelihood than that for the true topology. Thus, the failure to recover the true topology by the ML+MSA is not because of insufficient search of tree space, but by the distortion of phylogenetic signal by MSA methods. I have implemented in DAMBE PhyPA and two approaches making use of multi-gene data sets to derive phylogenetic support for subtrees equivalent to resampling techniques such as bootstrapping and jackknifing. PMID:27377322

  7. Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison

    SciTech Connect

    Ovacik, Meric A.; Androulakis, Ioannis P.

    2013-09-15

    Pathway-based information has become an important source of information for both establishing evolutionary relationships and understanding the mode of action of a chemical or pharmaceutical among species. Cross-species comparison of pathways can address two broad questions: comparison in order to inform evolutionary relationships and to extrapolate species differences used in a number of different applications including drug and toxicity testing. Cross-species comparison of metabolic pathways is complex as there are multiple features of a pathway that can be modeled and compared. Among the various methods that have been proposed, reaction alignment has emerged as the most successful at predicting phylogenetic relationships based on NCBI taxonomy. We propose an improvement of the reaction alignment method by accounting for sequence similarity in addition to reaction alignment method. Using nine species, including human and some model organisms and test species, we evaluate the standard and improved comparison methods by analyzing glycolysis and citrate cycle pathways conservation. In addition, we demonstrate how organism comparison can be conducted by accounting for the cumulative information retrieved from nine pathways in central metabolism as well as a more complete study involving 36 pathways common in all nine species. Our results indicate that reaction alignment with enzyme sequence similarity results in a more accurate representation of pathway specific cross-species similarities and differences based on NCBI taxonomy.

  8. Analyses of the radiation of birnaviruses from diverse host phyla and of their evolutionary affinities with other double-stranded RNA and positive strand RNA viruses using robust structure-based multiple sequence alignments and advanced phylogenetic methods

    PubMed Central

    2013-01-01

    Background Birnaviruses form a distinct family of double-stranded RNA viruses infecting animals as different as vertebrates, mollusks, insects and rotifers. With such a wide host range, they constitute a good model for studying the adaptation to the host. Additionally, several lines of evidence link birnaviruses to positive strand RNA viruses and suggest that phylogenetic analyses may provide clues about transition. Results We characterized the genome of a birnavirus from the rotifer Branchionus plicalitis. We used X-ray structures of RNA-dependent RNA polymerases and capsid proteins to obtain multiple structure alignments that allowed us to obtain reliable multiple sequence alignments and we employed “advanced” phylogenetic methods to study the evolutionary relationships between some positive strand and double-stranded RNA viruses. We showed that the rotifer birnavirus genome exhibited an organization remarkably similar to other birnaviruses. As this host was phylogenetically very distant from the other known species targeted by birnaviruses, we revisited the evolutionary pathways within the Birnaviridae family using phylogenetic reconstruction methods. We also applied a number of phylogenetic approaches based on structurally conserved domains/regions of the capsid and RNA-dependent RNA polymerase proteins to study the evolutionary relationships between birnaviruses, other double-stranded RNA viruses and positive strand RNA viruses. Conclusions We show that there is a good correlation between the phylogeny of the birnaviruses and that of their hosts at the phylum level using the RNA-dependent RNA polymerase (genomic segment B) on the one hand and a concatenation of the capsid protein, protease and ribonucleoprotein (genomic segment A) on the other hand. This correlation tends to vanish within phyla. The use of advanced phylogenetic methods and robust structure-based multiple sequence alignments allowed us to obtain a more accurate picture (in terms of

  9. A method for small-animal PET/CT alignment calibration

    NASA Astrophysics Data System (ADS)

    Pascau, J.; Vaquero, J. J.; Chamorro-Servent, J.; Rodríguez-Ruano, A.; Desco, M.

    2012-06-01

    Small-animal positron-emission tomography/computed tomography (PET/CT) scanners provide anatomical and molecular imaging, which enables the joint visualization and analysis of both types of data. A proper alignment calibration procedure is essential for small-animal imaging since resolution is much higher than that in human devices. This work presents an alignment phantom and two different calibration methods that provide a reliable and repeatable measurement of the spatial geometrical alignment between the PET and the CT subsystems of a hybrid scanner. The phantom can be built using laboratory materials, and it is meant to estimate the rigid spatial transformation that aligns both modalities. It consists of three glass capillaries filled with a positron-emitter solution and positioned in a non-coplanar triangular geometry inside the system field of view. The calibration methods proposed are both based on automatic line detection, but with different approaches to calculate the transformation of the lines between both modalities. Our results show an average accuracy of the alignment estimation of 0.39 mm over the whole field of view.

  10. A line-source method for aligning on-board and other pinhole SPECT systems

    PubMed Central

    Yan, Susu; Bowsher, James; Yin, Fang-Fang

    2013-01-01

    Purpose: In order to achieve functional and molecular imaging as patients are in position for radiation therapy, a robotic multipinhole SPECT system is being developed. Alignment of the SPECT system—to the linear accelerator (LINAC) coordinate frame and to the coordinate frames of other on-board imaging systems such as cone-beam CT (CBCT)—is essential for target localization and image reconstruction. An alignment method that utilizes line sources and one pinhole projection is proposed and investigated to achieve this goal. Potentially, this method could also be applied to the calibration of the other pinhole SPECT systems. Methods: An alignment model consisting of multiple alignment parameters was developed which maps line sources in three-dimensional (3D) space to their two-dimensional (2D) projections on the SPECT detector. In a computer-simulation study, 3D coordinates of line-sources were defined in a reference room coordinate frame, such as the LINAC coordinate frame. Corresponding 2D line-source projections were generated by computer simulation that included SPECT blurring and noise effects. The Radon transform was utilized to detect angles (α) and offsets (ρ) of the line-source projections. Alignment parameters were then estimated by a nonlinear least squares method, based on the α and ρ values and the alignment model. Alignment performance was evaluated as a function of number of line sources, Radon transform accuracy, finite line-source width, intrinsic camera resolution, Poisson noise, and acquisition geometry. Experimental evaluations were performed using a physical line-source phantom and a pinhole-collimated gamma camera attached to a robot. Results: In computer-simulation studies, when there was no error in determining angles (α) and offsets (ρ) of the measured projections, six alignment parameters (three translational and three rotational) were estimated perfectly using three line sources. When angles (α) and offsets (ρ) were provided by

  11. A line-source method for aligning on-board and other pinhole SPECT systems

    SciTech Connect

    Yan, Susu; Bowsher, James; Yin, Fang-Fang

    2013-12-15

    Purpose: In order to achieve functional and molecular imaging as patients are in position for radiation therapy, a robotic multipinhole SPECT system is being developed. Alignment of the SPECT system—to the linear accelerator (LINAC) coordinate frame and to the coordinate frames of other on-board imaging systems such as cone-beam CT (CBCT)—is essential for target localization and image reconstruction. An alignment method that utilizes line sources and one pinhole projection is proposed and investigated to achieve this goal. Potentially, this method could also be applied to the calibration of the other pinhole SPECT systems.Methods: An alignment model consisting of multiple alignment parameters was developed which maps line sources in three-dimensional (3D) space to their two-dimensional (2D) projections on the SPECT detector. In a computer-simulation study, 3D coordinates of line-sources were defined in a reference room coordinate frame, such as the LINAC coordinate frame. Corresponding 2D line-source projections were generated by computer simulation that included SPECT blurring and noise effects. The Radon transform was utilized to detect angles (α) and offsets (ρ) of the line-source projections. Alignment parameters were then estimated by a nonlinear least squares method, based on the α and ρ values and the alignment model. Alignment performance was evaluated as a function of number of line sources, Radon transform accuracy, finite line-source width, intrinsic camera resolution, Poisson noise, and acquisition geometry. Experimental evaluations were performed using a physical line-source phantom and a pinhole-collimated gamma camera attached to a robot.Results: In computer-simulation studies, when there was no error in determining angles (α) and offsets (ρ) of the measured projections, six alignment parameters (three translational and three rotational) were estimated perfectly using three line sources. When angles (α) and offsets (ρ) were provided by

  12. Paramagnetic alignment of small grains: A novel method for measuring interstellar magnetic fields

    SciTech Connect

    Hoang, Thiem; Martin, P. G.; Lazarian, A.

    2014-07-20

    We present a novel method to measure the strength of interstellar magnetic fields using ultraviolet (UV) polarization of starlight that is in part produced by weakly aligned, small dust grains. We begin with calculating the degrees of the paramagnetic alignment of small (size a ∼ 0.01 μm) and very small (a ∼ 0.001 μm) grains in the interstellar magnetic field due to the Davis-Greenstein relaxation and resonance relaxation. To calculate the degrees of paramagnetic alignment, we use Langevin equations and take into account various interaction processes essential for the rotational dynamics of small grains. 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 infrared (IR) wavelengths. Based on fitting theoretical models to observed extinction and polarization curves, we find that the best-fit model for the case with the peak wavelength of polarization λ{sub max} < 0.55 μm requires a higher degree of alignment of small grains than for the typical case with λ{sub max} = 0.55 μm. We interpret the correlation between the systematic increase of the UV polarization relative to maximum polarization (i.e., of p(6 μm{sup –1})/p{sub max}) with λ{sub max}{sup −1} for cases of low λ{sub max} by appealing to the higher degree of alignment of small grains. We utilize the correlation of the paramagnetic alignment of small grains with the magnetic field strength B to suggest a new way to measure B using the observable parameters λ{sub max} and p(6 μm{sup –1})/p{sub max}.

  13. Prokaryotic Phylogeny Based on Complete Genomes Without Sequence Alignment

    NASA Astrophysics Data System (ADS)

    Hao, Bailin; Qi, Ji; Wang, Bin

    We present a brief review of a series of on-going work on bacterial phylogeny. We propose a new method to infer relatedness of prokaryotes from their complete genome data without using sequence alignment, leading to results comparable with the bacteriologist's systematics as reflected in the latest 2001 edition of Bergey's Manual of Systematic Bacteriology.1 We only touch on the mathematical aspects of the method. The biological implications of our results will be published elsewhere.

  14. Enhancement of initial equivalency for protein structure alignment based on encoded local structures.

    PubMed

    Hung, Kenneth; Wang, Jui-Chih; Chen, Cheng-Wei; Chuang, Cheng-Long; Tsai, Kun-Nan; Chen, Chung-Ming

    2012-11-01

    Most alignment algorithms find an initial equivalent residue pair followed by an iterative optimization process to explore better near-optimal alignments in the surrounding solution space of the initial alignment. It plays a decisive role in determining the alignment quality since a poor initial alignment may make the final alignment trapped in an undesirable local optimum even with an iterative optimization. We proposed a vector-based alignment algorithm with a new initial alignment approach accounting for local structure features called MIRAGE-align. The new idea is to enhance the quality of the initial alignment based on encoded local structural alphabets to identify the protein structure pair whose sequence identity falls in or below twilight zone. The statistical analysis of alignment quality based on Match Index (MI) and computation time demonstrated that MIRAGE-align algorithm outperformed four previously published algorithms, i.e., the residue-based algorithm (CE), the vector-based algorithm (SSM), TM-align, and Fr-TM-align. MIRAGE-align yields a better estimate of initial solution to enhance the quality of initial alignment and enable the employment of a non-iterative optimization process to achieve a better alignment. PMID:22717522

  15. Word aligned bitmap compression method, data structure, and apparatus

    DOEpatents

    Wu, Kesheng; Shoshani, Arie; Otoo, Ekow

    2004-12-14

    The Word-Aligned Hybrid (WAH) bitmap compression method and data structure is a relatively efficient method for searching and performing logical, counting, and pattern location operations upon large datasets. The technique is comprised of a data structure and methods that are optimized for computational efficiency by using the WAH compression method, which typically takes advantage of the target computing system's native word length. WAH is particularly apropos to infrequently varying databases, including those found in the on-line analytical processing (OLAP) industry, due to the increased computational efficiency of the WAH compressed bitmap index. Some commercial database products already include some version of a bitmap index, which could possibly be replaced by the WAH bitmap compression techniques for potentially increased operation speed, as well as increased efficiencies in constructing compressed bitmaps. Combined together, this technique may be particularly useful for real-time business intelligence. Additional WAH applications may include scientific modeling, such as climate and combustion simulations, to minimize search time for analysis and subsequent data visualization.

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

    PubMed

    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. PMID:24979431

  17. Terahertz detectors arrays based on orderly aligned InN nanowires

    PubMed Central

    Chen, Xuechen; Liu, Huiqiang; Li, Qiuguo; Chen, Hao; Peng, Rufang; Chu, Sheng; Cheng, Binbin

    2015-01-01

    Nanostructured terahertz detectors employing a single semiconducting nanowire or graphene sheet have recently generated considerable interest as an alternative to existing THz technologies, for their merit on the ease of fabrication and above-room-temperature operation. However, the lack of alignment in nanostructure device hindered their potential toward practical applications. The present work reports ordered terahertz detectors arrays based on neatly aligned InN nanowires. The InN nanostructures (nanowires and nano-necklaces) were achieved by chemical vapor deposition growth, and then InN nanowires were successfully transferred and aligned into micrometer-sized groups by a “transfer-printing” method. Field effect transistors on aligned nanowires were fabricated and tested for terahertz detection purpose. The detector showed good photoresponse as well as low noise level. Besides, dense arrays of such detectors were also fabricated, which rendered a peak responsivity of 1.1 V/W from 7 detectors connected in series. PMID:26289498

  18. Development of a method of alignment between various SOLAR MAXIMUM MISSION experiments

    NASA Technical Reports Server (NTRS)

    1977-01-01

    Results of an engineering study of the methods of alignment between various experiments for the solar maximum mission are described. The configuration studied consists of the instruments, mounts and instrument support platform located within the experiment module. Hardware design, fabrication methods and alignment techniques were studied with regard to optimizing the coalignment between the experiments and the fine sun sensor. The proposed hardware design was reviewed with regard to loads, stress, thermal distortion, alignment error budgets, fabrication techniques, alignment techniques and producibility. Methods of achieving comparable alignment accuracies on previous projects were also reviewed.

  19. A General Assignment Method for Oriented Sample (OS) Solid-state NMR of Proteins Based on The Correlation of Resonances through Heteronuclear Dipolar Couplings in Samples Aligned Parallel and Perpendicular to the Magnetic Field

    PubMed Central

    Lu, George J.; Son, Woo Sung; Opella, Stanley J.

    2011-01-01

    A general method for assigning oriented sample (OS) solid-state NMR spectra of proteins is demonstrated. In principle, this method requires only a single sample of a uniformly 15N-labeled membrane protein in magnetically aligned bilayers, and a previously assigned isotropic chemical shift spectrum obtained either from solution NMR on micelle or isotropic bicelle samples or from magic angle spinning (MAS) solid-state NMR on unoriented proteoliposomes. The sequential isotropic resonance assignments are transferred to the OS solid-state NMR spectra of aligned samples by correlating signals from the same residue observed in protein-containing bilayers aligned with their normals parallel and perpendicular to the magnetic field. The underlying principle is that the resonances from the same residue have heteronuclear dipolar couplings that differ by exactly a factor of two between parallel and perpendicular alignments. The method is demonstrated on the membrane-bound form of Pf1 coat protein in phospholipid bilayers, whose assignments have been previously made using an earlier generation of methods that relied on the preparation of many selectively labeled (by residue type) samples. The new method provides the correct resonance assignments using only a single uniformly 15N-labeled sample, two solid-state NMR spectra, and a previously assigned isotropic spectrum. Significantly, this approach is equally applicable to residues in alpha helices, beta sheets, loops, and any other elements of tertiary structure. Moreover, the strategy bridges between OS solid-state NMR of aligned samples and solution NMR or MAS solid-state NMR of unoriented samples. In combination with the development of complementary experimental methods, it provides a step towards unifying these apparently different NMR approaches. PMID:21316275

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

    SciTech Connect

    Jena, Saroj Kumar; Husain, Riyasat; Gandhi, M. L.; Agrawal, R. K.; Yadav, S.; Ghodke, A. D.

    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.

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

    NASA Astrophysics Data System (ADS)

    Jena, Saroj Kumar; Husain, Riyasat; Gandhi, M. L.; Agrawal, R. K.; Yadav, S.; Ghodke, A. D.

    2015-09-01

    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.

  2. Quadrupole beam-based alignment in the RHIC interaction regions

    SciTech Connect

    Ziegler, J.; Satogata, T.

    2011-03-28

    Continued beam-based alignment (BBA) efforts have provided significant benefit to both heavy ion and polarized proton operations at RHIC. Recent studies demonstrated previously unknown systematic beam position monitor (BPM) offset errors and produced accurate measurements of individual BPM offsets in the experiment interaction regions. Here we describe the algorithm used to collect and analyze data during the 2010 and early 2011 RHIC runs and the results of these measurements. BBA data has been collected over the past two runs for all three of the active experimental IRs at RHIC, updating results from the 2005 run which were taken with incorrectly installed offsets. The technique was successfully applied to expose a systematic misuse of the BPM survey offsets in the control system. This is likely to benefit polarized proton operations as polarization transmission through acceleration ramps depends on RMS orbit control in the arcs, but a quantitative understanding of its impact is still under active investigation. Data taking is ongoing as are refinements to the BBA technique aimed at reducing systematic errors and properly accounting for dispersive effects. Further development may focus on non-triplet BPMs such as those located near snakes, or arc quadrupoles that do not have individually shunted power supplies (a prerequisite for the current method) and as such, will require a modified procedure.

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

    PubMed

    Jena, Saroj Kumar; Husain, Riyasat; Gandhi, M L; Agrawal, R K; Yadav, S; Ghodke, A D

    2015-09-01

    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. PMID:26429436

  4. Quadrupole Beam-Based Alignment in the RHIC Interaction Regions

    SciTech Connect

    T. Satogata, J. Ziegler

    2011-03-01

    Continued beam-based alignment (BBA) efforts have provided significant benefit to both heavy ion and polarized proton operations at RHIC. Recent studies demonstrated previously unknown systematic beam position monitor (BPM) offset errors and produced accurate measurements of individual BPM offsets in the experiment interaction regions. Here we describe the algorithm used to collect and analyze data during the 2010 and early 2011 RHIC runs and the results of these measurements.

  5. Optimal alignment of mirror based pentaprisms for scanning deflectometric devices

    SciTech Connect

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

    2011-03-04

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

  6. Beam-based alignment measurements of the LANSCE linac

    SciTech Connect

    McCrady, R. C.; Rybarcyk, L. J.

    2004-01-01

    We have made measurements of the alignment of the Los Alamos Neutron Science Center (LANSCE) Drift Tube linac (DTL) and Side Coupled linac (SCL) using beam position measurements and analyzing them with linear models. In the DTL, we varied the injection steering and focusing lattice strengths, measured the beam position after each DTL tank, and analyzed the data with a linear model using R-matrices that were either computed by the Trace-3D computer program or extracted from analysis of the data. The analysis model allowed for tank-to-tank misalignments. The measurements were made similarly in the SCL, where the analysis model allowed for misalignments of each quadrupole doublet lens. We present here the analysis techniques and the resulting beam-based alignment measurements.

  7. Prokaryotic Phylogeny Based on Complete Genomes Without Sequence Alignment

    NASA Astrophysics Data System (ADS)

    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.

  8. Method of Deployment of a Space Tethered System Aligned to the Local Vertical

    NASA Astrophysics Data System (ADS)

    Zakrzhevskii, A. E.

    2016-09-01

    The object of this research is a space tether of two bodies connected by a flexible massless string. The research objective is the development and theoretical justification of a novel approach to the solution of the problem of deployment of the space tether in a circular orbit with its alignment to the local vertical. The approach is based on use of the theorem on the angular momentum change. It allows developing the open-loop control of the tether length that provides desired change of the angular momentum of the tether under the effect of the gravitational torque to the value, which corresponds to the angular momentum of the deployed tether aligned to the local vertical. The given example of application of the approach to a case of deployment of a tether demonstrates the simplicity of use of the method in practice, and also the method of validation of the mathematical model.

  9. Method of Deployment of a Space Tethered System Aligned to the Local Vertical

    NASA Astrophysics Data System (ADS)

    Zakrzhevskii, A. E.

    2016-04-01

    The object of this research is a space tether of two bodies connected by a flexible massless string. The research objective is the development and theoretical justification of a novel approach to the solution of the problem of deployment of the space tether in a circular orbit with its alignment to the local vertical. The approach is based on use of the theorem on the angular momentum change. It allows developing the open-loop control of the tether length that provides desired change of the angular momentum of the tether under the effect of the gravitational torque to the value, which corresponds to the angular momentum of the deployed tether aligned to the local vertical. The given example of application of the approach to a case of deployment of a tether demonstrates the simplicity of use of the method in practice, and also the method of validation of the mathematical model.

  10. Amplitude differences least squares method applied to temporal cardiac beat alignment

    NASA Astrophysics Data System (ADS)

    Correa, R. O.; Laciar, E.; Valentinuzzi, M. E.

    2007-11-01

    High resolution averaged ECG is an important diagnostic technique in post-infarcted and/or chagasic patients with high risk of ventricular tachycardia (VT). It calls for precise determination of the synchronism point (fiducial point) in each beat to be averaged. Cross-correlation (CC) between each detected beat and a reference beat is, by and large, the standard alignment procedure. However, the fiducial point determination is not precise in records contaminated with high levels of noise. Herein, we propose an alignment procedure based on the least squares calculation of the amplitude differences (LSAD) between the ECG samples and a reference or template beat. Both techniques, CC and LSAD, were tested in high resolution ECG's corrupted with white noise and 50 Hz line interference of varying amplitudes (RMS range: 0-100μV). Results point out that LSDA produced a lower alignment error in all contaminated records while in those blurred by power line interference better results were found only within the 0-40 μV range. It is concluded that the proposed method represents a valid alignment alternative.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

  13. Globally Optimal Base Station Clustering in Interference Alignment-Based Multicell Networks

    NASA Astrophysics Data System (ADS)

    Brandt, Rasmus; Mochaourab, Rami; Bengtsson, Mats

    2016-04-01

    Coordinated precoding based on interference alignment is a promising technique for improving the throughputs in future wireless multicell networks. In small networks, all base stations can typically jointly coordinate their precoding. In large networks however, base station clustering is necessary due to the otherwise overwhelmingly high channel state information (CSI) acquisition overhead. In this work, we provide a branch and bound algorithm for finding the globally optimal base station clustering. The algorithm is mainly intended for benchmarking existing suboptimal clustering schemes. We propose a general model for the user throughputs, which only depends on the long-term CSI statistics. The model assumes intracluster interference alignment and is able to account for the CSI acquisition overhead. By enumerating a search tree using a best-first search and pruning sub-trees in which the optimal solution provably cannot be, the proposed method converges to the optimal solution. The pruning is done using specifically derived bounds, which exploit some assumed structure in the throughput model. It is empirically shown that the proposed method has an average complexity which is orders of magnitude lower than that of exhaustive search.

  14. Intrinsic alignments of BOSS LOWZ galaxies - II. Impact of shape measurement methods

    NASA Astrophysics Data System (ADS)

    Singh, Sukhdeep; Mandelbaum, Rachel

    2016-04-01

    Measurements of intrinsic alignments of galaxy shapes with the large-scale density field, and the inferred intrinsic alignments model parameters, are sensitive to the shape measurement methods used. In this paper, we measure the intrinsic alignments of the Sloan Digital Sky Survey-III (SDSS-III) Baryon Oscillation Spectroscopic Survey (BOSS) low redshift (LOWZ) galaxies using three different shape measurement methods (re-Gaussianization, isophotal, and de Vaucouleurs), identifying a variation in the inferred intrinsic alignments amplitude at the 40 per cent level between these methods, independent of the galaxy luminosity or other properties. We also carry out a suite of systematics tests on the shapes and their two-point correlation functions, identifying a pronounced contribution from additive point spread function systematics in the de Vaucouleurs shapes. Since different methods measure galaxy shapes at different effective radii, the trends we identify in the intrinsic alignments amplitude are consistent with the interpretation that the outer regions of galaxy shapes are more responsive to tidal fields, resulting in isophote twisting and stronger alignments for isophotal shapes. We observe environment dependence of ellipticity, with brightest galaxies in groups being rounder on average compared to satellite and field galaxies. We also study the anisotropy in intrinsic alignments measurements introduced by projected shapes, finding effects consistent with predictions of the non-linear alignment model and hydrodynamic simulations. The large variations seen using the different shape measurement methods have important implications for intrinsic alignments forecasting and mitigation with future surveys.

  15. Automated alignment method for coherence-controlled holographic microscope

    NASA Astrophysics Data System (ADS)

    Dostal, Zbynek; Slaby, Tomas; Kvasnica, Lukas; Lostak, Martin; Krizova, Aneta; Chmelik, Radim

    2015-11-01

    A coherence-controlled holographic microscope (CCHM) was developed particularly for quantitative phase imaging and measurement of live cell dynamics, which is the proper subject of digital holographic microscopy (DHM). CCHM in low-coherence mode extends DHM in the study of living cells. However, this advantage is compensated by sensitivity of the system to easily become misaligned, which is a serious hindrance to wanted performance. Therefore, it became clear that introduction of a self-correcting system is inevitable. Accordingly, we had to devise a theory of a suitable control and design an automated alignment system for CCHM. The modulus of the reconstructed holographic signal was identified as a significant variable for guiding the alignment procedures. From this, we derived the original basic realignment three-dimensional algorithm, which encompasses a unique set of procedures for automated alignment that contains processes for initial and advanced alignment as well as long-term maintenance of microscope tuning. All of these procedures were applied to a functioning microscope and the tested processes were successfully validated. Finally, in such a way, CCHM is enabled to substantially contribute to study of biology, particularly of cancer cells in vitro.

  16. Comprehensive Evaluation of Protein Structure Alignment Methods: Scoring by Geometric Measures

    PubMed Central

    Kolodny, Rachel; Koehl, Patrice; Levitt, Michael

    2009-01-01

    We report the largest and most comprehensive comparison of protein structural alignment methods. Specifically, we evaluate six publicly available structure alignment programs: SSAP, STRUCTAL, DALI, LSQMAN, CE and SSM by aligning all 8,581,970 protein structure pairs in a test set of 2930 protein domains specially selected from CATH v.2.4 to ensure sequence diversity. We consider an alignment good if it matches many residues, and the two substructures are geometrically similar. Even with this definition, evaluating structural alignment methods is not straightforward. At first, we compared the rates of true and false positives using receiver operating characteristic (ROC) curves with the CATH classification taken as a gold standard. This proved unsatisfactory in that the quality of the alignments is not taken into account: sometimes a method that finds less good alignments scores better than a method that finds better alignments. We correct this intrinsic limitation by using four different geometric match measures (SI, MI, SAS, and GSAS) to evaluate the quality of each structural alignment. With this improved analysis we show that there is a wide variation in the performance of different methods; the main reason for this is that it can be difficult to find a good structural alignment between two proteins even when such an alignment exists. We find that STRUCTAL and SSM perform best, followed by LSQMAN and CE. Our focus on the intrinsic quality of each alignment allows us to propose a new method, called “Best-of-All” that combines the best results of all methods. Many commonly used methods miss 10–50% of the good Best-of-All alignments. By putting existing structural alignments into proper perspective, our study allows better comparison of protein structures. By highlighting limitations of existing methods, it will spur the further development of better structural alignment methods. This will have significant biological implications now that structural

  17. Comparison of Two Automatic Signal Correlation Methods to Align Relative Paleointensity Data

    NASA Astrophysics Data System (ADS)

    Lee, D. B.; Channell, J. E. T.

    2012-04-01

    Sedimentary relative paleointensity (RPI) data are often believed to represent a global signal at >103 yr timescales. The development of chronologies independent of oxygen isotope data (and orbital tuning) has important implications in paleoclimate science. Age models derived from RPI data could ultimately be used to better understand the climate signal in oxygen/carbon isotope data, the true link between orbital cycles and climate variations, and test for leads and lags in the climate system. As a first step, a method of accurately and reliably correlating RPI data from different sites must be developed. Automated correlations using algorithms have great advantage over visual correlations as they are based on firm criteria and repeatable, although a comparison of how various methods perform when aligning RPI or δ18O data (or both signals in tandem) has not been undertaken. Here we compare the performance of two automatic correlation techniques when used to align RPI or δ18O data. One is the dynamic programming method developed by Lisiecki and Lisiecki (2002) to align δ18O. records, the other is the simulated annealing method proposed by Huybers and Wunsch (2004). RPI and δ18O data collected from the North Atlantic are used to examine the differences in how these algorithms cope with different levels of inter-site variation in both RPI and δ18O data, and fluctuations in sedimentation rate. The algorithms are also evaluated using synthetic datasets obtained using Monte Carlo simulations of RPI and δ18O data. Multiple simulations are used to test the accuracy of the algorithms when handling different levels of signal to noise, variations in sedimentation rate, and differences in RPI resolution that are encountered when aligning RPI data collected from sediments with variable or differing sedimentation rates. Once data from the North Atlantic have been fully aligned using both methods, stacking techniques are employed to develop stacks of RPI and δ18O data for

  18. A novel fully automatic scheme for fiducial marker-based alignment in electron tomography.

    PubMed

    Han, Renmin; Wang, Liansan; Liu, Zhiyong; Sun, Fei; Zhang, Fa

    2015-12-01

    Although the topic of fiducial marker-based alignment in electron tomography (ET) has been widely discussed for decades, alignment without human intervention remains a difficult problem. Specifically, the emergence of subtomogram averaging has increased the demand for batch processing during tomographic reconstruction; fully automatic fiducial marker-based alignment is the main technique in this process. However, the lack of an accurate method for detecting and tracking fiducial markers precludes fully automatic alignment. In this paper, we present a novel, fully automatic alignment scheme for ET. Our scheme has two main contributions: First, we present a series of algorithms to ensure a high recognition rate and precise localization during the detection of fiducial markers. Our proposed solution reduces fiducial marker detection to a sampling and classification problem and further introduces an algorithm to solve the parameter dependence of marker diameter and marker number. Second, we propose a novel algorithm to solve the tracking of fiducial markers by reducing the tracking problem to an incomplete point set registration problem. Because a global optimization of a point set registration occurs, the result of our tracking is independent of the initial image position in the tilt series, allowing for the robust tracking of fiducial markers without pre-alignment. The experimental results indicate that our method can achieve an accurate tracking, almost identical to the current best one in IMOD with half automatic scheme. Furthermore, our scheme is fully automatic, depends on fewer parameters (only requires a gross value of the marker diameter) and does not require any manual interaction, providing the possibility of automatic batch processing of electron tomographic reconstruction. PMID:26433028

  19. Study on the technology of mutual alignment based on the four-quadrant photo electric detector

    NASA Astrophysics Data System (ADS)

    Hu, Ya-bin; Wang, Miao

    2015-11-01

    Panoramic stereo cameras and laser radars have their own coordinate system in the dynamic spatial sensing area and they have to determine the position relationship between each other through joint calibration. As using the traditional technology of mutual alignment based on the telescope cross wire is tedious and requires high operating skills, a new method of mutual alignment using lasers and four-quadrant photo electric detectors is provided after analyzing the working principle of four-quadrant photo electric detectors. Firstly make the laser beam irradiate the active area of the four-quadrant photo electric detector through coarse aiming. Then the center of a light spot offset relative to the center of the active area can be obtained according to the output voltage of four quadrants. The pose of two instruments can be adjusted properly to realize mutual alignment. The experimental results indicate that the alignment accuracy of four-quadrant detectors can meet the requirements of mutual alignment, which provides a new idea for joint calibration.

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

    PubMed Central

    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.

  1. Nanogenerators based on vertically aligned InN nanowires.

    PubMed

    Liu, Guocheng; Zhao, Songrui; Henderson, Robert D E; Leonenko, Zoya; Abdel-Rahman, Eihab; Mi, Zetian; Ban, Dayan

    2016-01-28

    Piezoelectric nanogenerators (NGs) based on vertically aligned InN nanowires (NWs) are fabricated, characterized, and evaluated. In these NGs, arrays of p-type and intrinsic InN NWs prepared by plasma-assisted molecular beam epitaxy (MBE) demonstrate similar piezoelectric properties. The p-type NGs show 160% more output current and 70% more output power product than the intrinsic NGs. The features driving performance enhancement are reduced electrostatic losses due to better NW array morphology, improved electromechanical energy conversion efficiency due to smaller NW diameters, and the higher impedance of intrinsic NGs due to elevated NW surface charge levels. These findings highlight the potential of InN based NGs as a power source for self-powered systems and the importance of NW morphology and surface state in overall NG performance. PMID:26700694

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

    SciTech Connect

    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

  3. Avalanche for shape and feature-based virtual screening with 3D alignment.

    PubMed

    Diller, David J; Connell, Nancy D; Welsh, William J

    2015-11-01

    This report introduces a new ligand-based virtual screening tool called Avalanche that incorporates both shape- and feature-based comparison with three-dimensional (3D) alignment between the query molecule and test compounds residing in a chemical database. Avalanche proceeds in two steps. The first step is an extremely rapid shape/feature based comparison which is used to narrow the focus from potentially millions or billions of candidate molecules and conformations to a more manageable number that are then passed to the second step. The second step is a detailed yet still rapid 3D alignment of the remaining candidate conformations to the query conformation. Using the 3D alignment, these remaining candidate conformations are scored, re-ranked and presented to the user as the top hits for further visualization and evaluation. To provide further insight into the method, the results from two prospective virtual screens are presented which show the ability of Avalanche to identify hits from chemical databases that would likely be missed by common substructure-based or fingerprint-based search methods. The Avalanche method is extended to enable patent landscaping, i.e., structural refinements to improve the patentability of hits for deployment in drug discovery campaigns. PMID:26458937

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

    SciTech Connect

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

    2015-07-21

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

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

    SciTech Connect

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

    2011-03-23

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

  6. A Fast and Specific Alignment Method for Minisatellite Maps

    PubMed Central

    Bérard, Sèverine; Nicolas, François; Buard, Jérôme; Gascuel, Olivier; Rivals, Eric

    2007-01-01

    Background Variable minisatellites count among the most polymorphic markers of eukaryotic and prokaryotic genomes. This variability can affect gene coding regions, like in the prion protein gene, or gene regulation regions, like for the cystatin B gene, and be associated or implicated in diseases: the Creutzfeld-Jakob disease and the myoclonus epilepsy type 1, for our examples. When it affects neutrally evolving regions, the polymorphism in length (i.e., in number of copies) of minisatellites proved useful in population genetics. Motivation In these tandem repeat sequences, different mutational mechanisms let the number of copies, as well as the copies themselves, vary. Especially, the interspersion of events of tandem duplication/contraction and of punctual mutation makes the succession of variant repeats much more informative than the sole allele length. To exploit this information requires the ability to align minisatellite alleles by accounting for both punctual mutations and tandem duplications. Results We propose a minisatellite maps alignment program that improves on previous solutions. Our new program is faster, simpler, considers an extended evolutionary model, and is available to the community. We test it on the data set of 609 alleles of the MSY1 (DYF155S1) human minisatellite and confirm its ability to recover known evolutionary signals. Our experiments highlight that the informativeness of minisatellites resides in their length and composition polymorphisms. Exploiting both simultaneously is critical to unravel the implications of variable minisatellites in the control of gene expression and diseases. PMID:19455224

  7. Curve aligning approach for gait authentication based on a wearable accelerometer.

    PubMed

    Sun, Hu; Yuao, Tao

    2012-06-01

    Gait authentication based on a wearable accelerometer is a novel biometric which can be used for identity identification, medical rehabilitation and early detection of neurological disorders. The method for matching gait patterns tells heavily on authentication performances. In this paper, curve aligning is introduced as a new method for matching gait patterns and it is compared with correlation and dynamic time warping (DTW). A support vector machine (SVM) is proposed to fuse pattern-matching methods in a decision level. Accelerations collected from ankles of 22 walking subjects are processed for authentications in our experiments. The fusion of curve aligning with backward-forward accelerations and DTW with vertical accelerations promotes authentication performances substantially and consistently. This fusion algorithm is tested repeatedly. Its mean and standard deviation of equal error rates are 0.794% and 0.696%, respectively, whereas among all presented non-fusion algorithms, the best one shows an EER of 3.03%. PMID:22621972

  8. Alignment of high resolution magic angle spinning magnetic resonance spectra using warping methods.

    PubMed

    Giskeødegård, Guro F; Bloemberg, Tom G; Postma, Geert; Sitter, Beathe; Tessem, May-Britt; Gribbestad, Ingrid S; Bathen, Tone F; Buydens, Lutgarde M C

    2010-12-17

    The peaks of magnetic resonance (MR) spectra can be shifted due to variations in physiological and experimental conditions, and correcting for misaligned peaks is an important part of data processing prior to multivariate analysis. In this paper, five warping algorithms (icoshift, COW, fastpa, VPdtw and PTW) are compared for their feasibility in aligning spectral peaks in three sets of high resolution magic angle spinning (HR-MAS) MR spectra with different degrees of misalignments, and their merits are discussed. In addition, extraction of information that might be present in the shifts is examined, both for simulated data and the real MR spectra. The generic evaluation methodology employs a number of frequently used quality criteria for evaluation of the alignments, together with PLS-DA to assess the influence of alignment on the classification outcome. Peak alignment greatly improved the internal similarity of the data sets. Especially icoshift and COW seem suitable for aligning HR-MAS MR spectra, possibly because they perform alignment segment-wise. The choice of reference spectrum can influence the alignment result, and it is advisable to test several references. Information from the peak shifts was extracted, and in one case cancer samples were successfully discriminated from normal tissue based on shift information only. Based on these findings, general recommendations for alignment of HR-MAS MRS data are presented. Where possible, observations are generalized to other data types (e.g. chromatographic data). PMID:21094376

  9. GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution

    PubMed Central

    Kinjo, Akira R.; Nakamura, Haruki

    2012-01-01

    Comparison and classification of protein structures are fundamental means to understand protein functions. Due to the computational difficulty and the ever-increasing amount of structural data, however, it is in general not feasible to perform exhaustive all-against-all structure comparisons necessary for comprehensive classifications. To efficiently handle such situations, we have previously proposed a method, now called GIRAF. We herein describe further improvements in the GIRAF protein structure search and alignment method. The GIRAF method achieves extremely efficient search of similar structures of ligand binding sites of proteins by exploiting database indexing of structural features of local coordinate frames. In addition, it produces refined atom-wise alignments by iterative applications of the Hungarian method to the bipartite graph defined for a pair of superimposed structures. By combining the refined alignments based on different local coordinate frames, it is made possible to align structures involving domain movements. We provide detailed accounts for the database design, the search and alignment algorithms as well as some benchmark results.

  10. Multidimensional mutual information methods for the analysis of covariation in multiple sequence alignments

    PubMed Central

    2014-01-01

    Background Several methods are available for the detection of covarying positions from a multiple sequence alignment (MSA). If the MSA contains a large number of sequences, information about the proximities between residues derived from covariation maps can be sufficient to predict a protein fold. However, in many cases the structure is already known, and information on the covarying positions can be valuable to understand the protein mechanism and dynamic properties. Results In this study we have sought to determine whether a multivariate (multidimensional) extension of traditional mutual information (MI) can be an additional tool to study covariation. The performance of two multidimensional MI (mdMI) methods, designed to remove the effect of ternary/quaternary interdependencies, was tested with a set of 9 MSAs each containing <400 sequences, and was shown to be comparable to that of the newest methods based on maximum entropy/pseudolikelyhood statistical models of protein sequences. However, while all the methods tested detected a similar number of covarying pairs among the residues separated by < 8 Å in the reference X-ray structures, there was on average less than 65% overlap between the top scoring pairs detected by methods that are based on different principles. Conclusions Given the large variety of structure and evolutionary history of different proteins it is possible that a single best method to detect covariation in all proteins does not exist, and that for each protein family the best information can be derived by merging/comparing results obtained with different methods. This approach may be particularly valuable in those cases in which the size of the MSA is small or the quality of the alignment is low, leading to significant differences in the pairs detected by different methods. PMID:24886131

  11. Alignment-Free Methods for the Detection and Specificity Prediction of Adenylation Domains.

    PubMed

    Agüero-Chapin, Guillermin; Pérez-Machado, Gisselle; Sánchez-Rodríguez, Aminael; Santos, Miguel Machado; Antunes, Agostinho

    2016-01-01

    Identifying adenylation domains (A-domains) and their substrate specificity can aid the detection of nonribosomal peptide synthetases (NRPS) at genome/proteome level and allow inferring the structure of oligopeptides with relevant biological activities. However, that is challenging task due to the high sequence diversity of A-domains (~10-40 % of amino acid identity) and their selectivity for 50 different natural/unnatural amino acids. Altogether these characteristics make their detection and the prediction of their substrate specificity a real challenge when using traditional sequence alignment methods, e.g., BLAST searches. In this chapter we describe two workflows based on alignment-free methods intended for the identification and substrate specificity prediction of A-domains. To identify A-domains we introduce a graphical-numerical method, implemented in TI2BioP version 2.0 (topological indices to biopolymers), which in a first step uses protein four-color maps to represent A-domains. In a second step, simple topological indices (TIs), called spectral moments, are derived from the graphical representations of known A-domains (positive dataset) and of unrelated but well-characterized sequences (negative set). Spectral moments are then used as input predictors for statistical classification techniques to build alignment-free models. Finally, the resulting alignment-free models can be used to explore entire proteomes for unannotated A-domains. In addition, this graphical-numerical methodology works as a sequence-search method that can be ensemble with homology-based tools to deeply explore the A-domain signature and cope with the diversity of this class (Aguero-Chapin et al., PLoS One 8(7):e65926, 2013). The second workflow for the prediction of A-domain's substrate specificity is based on alignment-free models constructed by transductive support vector machines (TSVMs) that incorporate information of uncharacterized A-domains. The construction of the models was

  12. A facile method to align carbon nanotubes on polymeric membrane substrate

    PubMed Central

    Zhao, Haiyang; Zhou, Zhijun; Dong, Hang; Zhang, Lin; Chen, Huanlin; Hou, Lian

    2013-01-01

    The alignment of carbon nanotubes (CNT) is the fundamental requirement to ensure their excellent functions but seems to be desolated in recent years. A facile method, hot-press combined with peel-off (HPPO), is introduced here, through which CNT can be successfully vertically aligned on the polymeric membrane substrate. Shear force and mechanical stretch are proposed to be the main forces to align the tubes perpendicular to the substrate surface during the peel-off process. The alignment of CNT keeps its orientation in a thin hybrid membrane by dip-coating cellulose acetate dope solution. It is expected that the stable alignment of CNT by HPPO would contribute to the realization of its potential applications. PMID:24326297

  13. A facile method to align carbon nanotubes on polymeric membrane substrate

    NASA Astrophysics Data System (ADS)

    Zhao, Haiyang; Zhou, Zhijun; Dong, Hang; Zhang, Lin; Chen, Huanlin; Hou, Lian

    2013-12-01

    The alignment of carbon nanotubes (CNT) is the fundamental requirement to ensure their excellent functions but seems to be desolated in recent years. A facile method, hot-press combined with peel-off (HPPO), is introduced here, through which CNT can be successfully vertically aligned on the polymeric membrane substrate. Shear force and mechanical stretch are proposed to be the main forces to align the tubes perpendicular to the substrate surface during the peel-off process. The alignment of CNT keeps its orientation in a thin hybrid membrane by dip-coating cellulose acetate dope solution. It is expected that the stable alignment of CNT by HPPO would contribute to the realization of its potential applications.

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

    PubMed Central

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

    2009-01-01

    Motivation: The most accurate way to determine the intron–exon structures in a genome is to align spliced cDNA sequences to the genome. Thus, cDNA-to-genome alignment programs are a key component of most annotation pipelines. The scoring system used to choose the best alignment is a primary determinant of alignment accuracy, while heuristics that prevent consideration of certain alignments are a primary determinant of runtime and memory usage. Both accuracy and speed are important considerations in choosing an alignment algorithm, but scoring systems have received much less attention than 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’ simulated cDNA sequences by splicing the sequences of exons in the reference genome sequences of fly and human. The complete reference genome sequences were then mutated to various degrees using a realistic mutation simulator and the perfect cDNAs were aligned to them using Pairagon and 12 other aligners. To validate these results with natural sequences, we performed cross-species alignment using orthologous transcripts from human, mouse and rat. We found that aligner accuracy is heavily dependent on sequence identity. For sequences with 100% identity, Pairagon achieved accuracy levels of >99.6%, with one quarter of the errors of any other aligner. Furthermore, for human/mouse alignments, which are only 85% identical, Pairagon achieved 87% accuracy, higher than any other aligner. Availability: Pairagon source and executables are freely available at http://mblab.wustl.edu/software/pairagon/ Contact: davidlu@wustl.edu; brent@cse.wustl.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19414532

  15. Initial Alignment of Large Azimuth Misalignment Angles in SINS Based on Adaptive UPF

    PubMed Central

    Sun, Jin; Xu, Xiao-Su; Liu, Yi-Ting; Zhang, Tao; Li, Yao

    2015-01-01

    The case of large azimuth misalignment angles in a strapdown inertial navigation system (SINS) is analyzed, and a method of using the adaptive UPF for the initial alignment is proposed. The filter is based on the idea of a strong tracking filter; through the introduction of the attenuation memory factor to effectively enhance the corrections of the current information residual error on the system, it reduces the influence on the system due to the system simplification, and the uncertainty of noise statistical properties to a certain extent; meanwhile, the UPF particle degradation phenomenon is better overcome. Finally, two kinds of non-linear filters, UPF and adaptive UPF, are adopted in the initial alignment of large azimuth misalignment angles in SINS, and the filtering effects of the two kinds of nonlinear filter on the initial alignment were compared by simulation and turntable experiments. The simulation and turntable experiment results show that the speed and precision of the initial alignment using adaptive UPF for a large azimuth misalignment angle in SINS under the circumstance that the statistical properties of the system noise are certain or not have been improved to some extent. PMID:26334277

  16. A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications.

    PubMed

    Tyagi, Manoj; Gowri, Venkataraman S; Srinivasan, Narayanaswamy; de Brevern, Alexandre G; Offmann, Bernard

    2006-10-01

    Analysis of protein structures based on backbone structural patterns known as structural alphabets have been shown to be very useful. Among them, a set of 16 pentapeptide structural motifs known as protein blocks (PBs) has been identified and upon which backbone model of most protein structures can be built. PBs allows simplification of 3D space onto 1D space in the form of sequence of PBs. Here, for the first time, substitution probabilities of PBs in a large number of aligned homologous protein structures have been studied and are expressed as a simplified 16 x 16 substitution matrix. The matrix was validated by benchmarking how well it can align sequences of PBs rather like amino acid alignment to identify structurally equivalent regions in closely or distantly related proteins using dynamic programming approach. The alignment results obtained are very comparable to well established structure comparison methods like DALI and STAMP. Other interesting applications of the matrix have been investigated. We first show that, in variable regions between two superimposed homologous proteins, one can distinguish between local conformational differences and rigid-body displacement of a conserved motif by comparing the PBs and their substitution scores. Second, we demonstrate, with the example of aspartic proteinases, that PBs can be efficiently used to detect the lobe/domain flexibility in the multidomain proteins. Lastly, using protein kinase as an example, we identify regions of conformational variations and rigid body movements in the enzyme as it is changed to the active state from an inactive state. PMID:16894618

  17. Initial Alignment of Large Azimuth Misalignment Angles in SINS Based on Adaptive UPF.

    PubMed

    Sun, Jin; Xu, Xiao-Su; Liu, Yi-Ting; Zhang, Tao; Li, Yao

    2015-01-01

    The case of large azimuth misalignment angles in a strapdown inertial navigation system (SINS) is analyzed, and a method of using the adaptive UPF for the initial alignment is proposed. The filter is based on the idea of a strong tracking filter; through the introduction of the attenuation memory factor to effectively enhance the corrections of the current information residual error on the system, it reduces the influence on the system due to the system simplification, and the uncertainty of noise statistical properties to a certain extent; meanwhile, the UPF particle degradation phenomenon is better overcome. Finally, two kinds of non-linear filters, UPF and adaptive UPF, are adopted in the initial alignment of large azimuth misalignment angles in SINS, and the filtering effects of the two kinds of nonlinear filter on the initial alignment were compared by simulation and turntable experiments. The simulation and turntable experiment results show that the speed and precision of the initial alignment using adaptive UPF for a large azimuth misalignment angle in SINS under the circumstance that the statistical properties of the system noise are certain or not have been improved to some extent. PMID:26334277

  18. Solution-based electric-field-assisted assembly of vertically aligned CNT membranes

    NASA Astrophysics Data System (ADS)

    Castellano, Richard; Akin, Cevat; Shan, Jerry

    2014-11-01

    Carbon-nanotube (CNT) membranes are of interest due to experiments and simulations showing flow through nanotubes to be 3 to 5 orders of magnitude faster than predicted by viscous flow theory. Thus, membranes incorporating vertically aligned CNTs (VACNTs) as through-pores offer promise as highly efficient and permeable membranes for a variety of filter and separation processes. However, current membrane-fabrication techniques utilizing CVD-grown VACNT arrays are costly and difficult to scale up. We are developing a solution-based, electric-field-assisted approach as a cost-effective and scalable method to producing large-area VACNT membranes and composites. Post-growth nanotubes are first dispersed in a polymeric matrix and then aligned with an AC electric field. A DC component induces electrophoresis to the CNTs to significantly increase the VACNT number density. This composite field also introduces complex fluid motion caused by induced-charge electro-osmosis and the electrochemistry of the fluid/electrode interface. We experimentally probe all of these effects and consider factors affecting the number density and spatial uniformity of VACNT membranes. We also consider the basic electrokinetics of nanotube alignment under spatially uniform AC electric fields, making quantitative comparison with classical models of the dynamics of polarizable, 1D particles under the combined effects of electric fields, hydrodynamic drag, and Brownian motion. We conclude by discussing the implications of these fundamental electrohydrodynamic studies for producing large-area membranes containing aligned CNTs.

  19. Fast statistical alignment.

    PubMed

    Bradley, Robert K; Roberts, Adam; Smoot, Michael; Juvekar, Sudeep; Do, Jaeyoung; Dewey, Colin; Holmes, Ian; Pachter, Lior

    2009-05-01

    We describe a new program for the alignment of multiple biological sequences that is both statistically motivated and fast enough for problem sizes that arise in practice. Our Fast Statistical Alignment program is based on pair hidden Markov models which approximate an insertion/deletion process on a tree and uses a sequence annealing algorithm to combine the posterior probabilities estimated from these models into a multiple alignment. FSA uses its explicit statistical model to produce multiple alignments which are accompanied by estimates of the alignment accuracy and uncertainty for every column and character of the alignment--previously available only with alignment programs which use computationally-expensive Markov Chain Monte Carlo approaches--yet can align thousands of long sequences. Moreover, FSA utilizes an unsupervised query-specific learning procedure for parameter estimation which leads to improved accuracy on benchmark reference alignments in comparison to existing programs. The centroid alignment approach taken by FSA, in combination with its learning procedure, drastically reduces the amount of false-positive alignment on biological data in comparison to that given by other methods. The FSA program and a companion visualization tool for exploring uncertainty in alignments can be used via a web interface at http://orangutan.math.berkeley.edu/fsa/, and the source code is available at http://fsa.sourceforge.net/. PMID:19478997

  20. Nanoelectrode Arrays Based on Low Site Density Aligned Carbon Nanotubes

    SciTech Connect

    Yi, Tu; Lin, Yuehe ); Ren, Zhifeng N.

    2003-01-29

    Nanoelectrode arrays (NEAs) were fabricated from the low site density aligned carbon nanotubes (CNTs). The CNTs were grown by plasma enhanced chemical vapor deposition (PECVD) on Ni nanoparticles made by the electrochemical deposition.

  1. A rapid protein structure alignment algorithm based on a text modeling technique

    PubMed Central

    Razmara, Jafar; Deris, Safaai; Parvizpour, Sepideh

    2011-01-01

    Structural alignment of proteins is widely used in various fields of structural biology. In order to further improve the quality of alignment, we describe an algorithm for structural alignment based on text modelling techniques. The technique firstly superimposes secondary structure elements of two proteins and then, models the 3D-structure of the protein in a sequence of alphabets. These sequences are utilized by a step-by-step sequence alignment procedure to align two protein structures. A benchmark test was organized on a set of 200 non-homologous proteins to evaluate the program and compare it to state of the art programs, e.g. CE, SAL, TM-align and 3D-BLAST. On average, the results of all-against-all structure comparison by the program have a competitive accuracy with CE and TM-align where the algorithm has a high running speed like 3D-BLAST. PMID:21814392

  2. Littrow angle method to remove alignment errors in grating pulse compressors.

    PubMed

    Guardalben, M J

    2008-09-20

    An alignment method for pulse-compression gratings that obviates the need to place the gratings at normal incidence to remove grating-tip error is proposed. Grating-tip and groove-orientation errors are removed using two alignment wavelengths in a manner analogous to a laser-beam pointing and centering procedure entirely at the respective Littrow angles for the two wavelengths. By choosing wavelengths with Littrow angles close to the use angle of the grating, the residual tip and groove-orientation errors that may be introduced when the grating mount is tilted to its use angle are reduced. This method has greatly facilitated the alignment of the OMEGA Extended Performance (EP) large-aperture pulse compressors, thereby reducing residual pulse-front tilt caused by nonparallel gratings. OMEGA EP is a high-energy, petawatt-class laser at the University of Rochester's Laboratory for Laser Energetics. A numerical simulation of the alignment procedure is presented. PMID:18806858

  3. Littrow Angle Method to Remove Alignment Errors in Grating Pulse Compressors

    SciTech Connect

    Guardalben, M.J.

    2008-09-16

    An alignment method for pulse-compression gratings that obviates the need to place the gratings at normal incidence to remove grating-tip error is proposed. Grating-tip and groove-orientation errors are removed using two alignment wavelengths in a manner analogous to a laser-beam pointing and centering procedure entirely at the respective Littrow angles for the two wavelengths. By choosing wavelengths with Littrow angles close to the use angle of the grating, the residual tip and groove-orientation errors that may be introduced when the grating mount is tilted to its use angle are reduced. This method has greatly facilitated the alignment of the OMEGA Extended Performance (EP) large-aperture pulse compressors, thereby reducing residual pulse-front tilt caused by nonparallel gratings. OMEGA EP is a highenergy, petawatt-class laser at the University of Rochester’s Laboratory for Laser Energetics. A numerical simulation of the alignment procedure is presented.

  4. Littrow angle method to remove alignment errors in grating pulse compressors

    SciTech Connect

    Guardalben, M. J

    2008-09-20

    An alignment method for pulse-compression gratings that obviates the need to place the gratings at normal incidence to remove grating-tip error is proposed. Grating-tip and groove-orientation errors are removed using two alignment wavelengths in a manner analogous to a laser-beam pointing and centering procedure entirely at the respective Littrow angles for the two wavelengths. By choosing wavelengths with Littrow angles close to the use angle of the grating, the residual tip and groove-orientation errors that may be introduced when the grating mount is tilted to its use angle are reduced. This method has greatly facilitated the alignment of the OMEGA Extended Performance (EP) large-aperture pulse compressors, thereby reducing residual pulse-front tilt caused by nonparallel gratings. OMEGA EP is a high-energy, petawatt-class laser at the University of Rochester's Laboratory for Laser Energetics. A numerical simulation of the alignment procedure is presented.

  5. An alignment-free method to find and visualise rearrangements between pairs of DNA sequences

    PubMed Central

    Pratas, Diogo; Silva, Raquel M.; Pinho, Armando J.; Ferreira, Paulo J.S.G.

    2015-01-01

    Species evolution is indirectly registered in their genomic structure. The emergence and advances in sequencing technology provided a way to access genome information, namely to identify and study evolutionary macro-events, as well as chromosome alterations for clinical purposes. This paper describes a completely alignment-free computational method, based on a blind unsupervised approach, to detect large-scale and small-scale genomic rearrangements between pairs of DNA sequences. To illustrate the power and usefulness of the method we give complete chromosomal information maps for the pairs human-chimpanzee and human-orangutan. The tool by means of which these results were obtained has been made publicly available and is described in detail. PMID:25984837

  6. An alignment-free method to find and visualise rearrangements between pairs of DNA sequences.

    PubMed

    Pratas, Diogo; Silva, Raquel M; Pinho, Armando J; Ferreira, Paulo J S G

    2015-01-01

    Species evolution is indirectly registered in their genomic structure. The emergence and advances in sequencing technology provided a way to access genome information, namely to identify and study evolutionary macro-events, as well as chromosome alterations for clinical purposes. This paper describes a completely alignment-free computational method, based on a blind unsupervised approach, to detect large-scale and small-scale genomic rearrangements between pairs of DNA sequences. To illustrate the power and usefulness of the method we give complete chromosomal information maps for the pairs human-chimpanzee and human-orangutan. The tool by means of which these results were obtained has been made publicly available and is described in detail. PMID:25984837

  7. An Advanced Electrospinning Method of Fabricating Nanofibrous Patterned Architectures with Controlled Deposition and Desired Alignment

    NASA Astrophysics Data System (ADS)

    Rasel, Sheikh Md

    We introduce a versatile advanced method of electrospinning for fabricating various kinds of nanofibrous patterns along with desired alignment, controlled amount of deposition and locally variable density into the architectures. In this method, we employed multiple electrodes whose potentials have been altered in milliseconds with the help of microprocessor based control system. Therefore, key success of this method was that the electrical field as well as charge carrying fibers could be switched shortly from one electrode's location to another, as a result, electrospun fibers could be deposited on the designated areas with desired alignment. A wide range of nanofibrous patterned architectures were constructed using proper arrangement of multiple electrodes. By controlling the concurrent activation time of two adjacent electrodes, we demonstrated that amount of fibers going into the pattern can be adjusted and desired alignment in electrospun fibers can be obtained. We also revealed that the deposition density of electrospun fibers in different areas of patterned architectures can be varied. We showed that by controlling the deposition time between two adjacent electrodes, a number of functionally graded patterns can be generated with uniaxial alignment. We also demonstrated that this handy method was capable of producing random, aligned, and multidirectional nanofibrous mats by engaging a number of electrodes and switching them in desired patterns. A comprehensive study using finite element method was carried out to understand the effects of electrical field. Simulation results revealed that electrical field strength alters shortly based on electrode control switch patterns. Nanofibrous polyvinyl alcohol (PVA) scaffolds and its composite reinforced with wollastonite and wood flour were fabricated using rotating drum electrospinning technique. Morphological, mechanical, and thermal, properties were characterized on PVA/wollastonite and PVA/wood flour nanocomposites

  8. Semiellipsoid microlens fabrication method using the lift-off and alignment exposure processes

    NASA Astrophysics Data System (ADS)

    Hung, Chien-Hsin; Hung, Shih-Yu; Shen, Ming-Ho; Yang, Hsiharng

    2012-10-01

    We present a new semiellipsoid microlens fabrication method using the lift-off and alignment exposure processes. The lift-off method is used to create an elliptical base before the thermal reflow process. During the photoresist thermal reflow process, the elliptical base can precisely define the bottom shape of the liquid photoresist, and fabricate the semiellipsoid microlens array with a large height and small radius of curvature. The prolate spheroid approximation method is developed to estimate the thickness of the elliptic photoresist column required by the semiellipsoid microlens of a certain height, with the error being controlled within ±3%. Electroforming technology is then used to convert the photoresist patterns into a metallic mold for a PDMS ellipsoidal microlens. The experiment results show that the geometries of a semiellipsoid microlens can be accurately defined by three parameters: the length of the major axis of the elliptical base, the length of the minor axis of the elliptical base and the thickness of the elliptical photoresist column. The proposed fabrication method facilitates mass production to achieve a high-yield and high-coupling semiellipsoid microlens that is suitable for use in commercial fiber transmission systems

  9. Virtual plate pre-bending for the long bone fracture based on axis pre-alignment.

    PubMed

    Liu, Bin; Luo, Xinjian; Huang, Rui; Wan, Chao; Zhang, Bingbing; Hu, Weihua; Yue, Zongge

    2014-06-01

    In this paper, a modeling and visualizing system for assisting surgeons in correctly registering for the closed fracture reduction surgery is presented. By using this system, the geometric parameters of the target fixation plate before the long bone fracture operation can be obtained. The main processing scheme consists of following steps: firstly (image data process), utilize the Curvelet transform to denoise the CT images of fracture part and then reconstruct the 3D models of the broken bones. Secondly (pre-alignment), extract the axial lines of the broken bones and spatially align them. Then drive the broken bone models to be pre-aligned. Thirdly (mesh segmentation), a method based on vertex normal feature is utilized to obtain the broken bone cross-sections mesh models. Fourthly (fine registration), the ICP (Iterative Closest Point) algorithm is used to register the cross-sections and the broken bone models are driven to achieve the fine registration posture. Lastly (plate fitting), an accurate NURBS surface fitting method is used to construct the virtual plate. The experiment proved that the obtained models of the pre-bended plates were closely bonded to the surface of the registered long bone models. Finally, the lengths, angles and other interested geometric parameters can be measured on the plate models. PMID:24598409

  10. In vitro cardiomyocyte-driven biogenerator based on aligned piezoelectric nanofibers

    NASA Astrophysics Data System (ADS)

    Liu, Xia; Zhao, Hui; Lu, Yingxian; Li, Song; Lin, Liwei; Du, Yanan; Wang, Xiaohong

    2016-03-01

    Capturing the body's mechanical energy from the heart, lungs, and diaphragm can probably meet the requirements for in vivo applications of implantable biomedical devices. In this work, we present a novel contractile cardiomyocyte (CM)-driven biogenerator based on piezoelectric nanofibers (NFs) uniaxially aligned on a PDMS thin film. Flexible nanostructures interact with the CMs, as a physical cue to guide the CMs to align in a specific way, and create mechanical interfaces of contractile CMs and piezoelectric NFs. As such, the cellular construct features specific alignment and synchronous contraction, which realizes the maximal resultant force to drive the NFs to bend periodically. Studies on contraction mapping show that neonatal rat CMs self-assemble into a functional bio-bot film with well-defined axes of force generation. Consequently, the biogenerator produces an average voltage of 200 mV and current of 45 nA at the cell concentration of 1.0 million per ml, offering a biocompatible and scalable platform for biological energy conversion.Capturing the body's mechanical energy from the heart, lungs, and diaphragm can probably meet the requirements for in vivo applications of implantable biomedical devices. In this work, we present a novel contractile cardiomyocyte (CM)-driven biogenerator based on piezoelectric nanofibers (NFs) uniaxially aligned on a PDMS thin film. Flexible nanostructures interact with the CMs, as a physical cue to guide the CMs to align in a specific way, and create mechanical interfaces of contractile CMs and piezoelectric NFs. As such, the cellular construct features specific alignment and synchronous contraction, which realizes the maximal resultant force to drive the NFs to bend periodically. Studies on contraction mapping show that neonatal rat CMs self-assemble into a functional bio-bot film with well-defined axes of force generation. Consequently, the biogenerator produces an average voltage of 200 mV and current of 45 nA at the cell

  11. Genomic signal processing methods for computation of alignment-free distances from DNA sequences.

    PubMed

    Borrayo, Ernesto; Mendizabal-Ruiz, E Gerardo; Vélez-Pérez, Hugo; Romo-Vázquez, Rebeca; Mendizabal, Adriana P; Morales, J Alejandro

    2014-01-01

    Genomic signal processing (GSP) refers to the use of digital signal processing (DSP) tools for analyzing genomic data such as DNA sequences. A possible application of GSP that has not been fully explored is the computation of the distance between a pair of sequences. In this work we present GAFD, a novel GSP alignment-free distance computation method. We introduce a DNA sequence-to-signal mapping function based on the employment of doublet values, which increases the number of possible amplitude values for the generated signal. Additionally, we explore the use of three DSP distance metrics as descriptors for categorizing DNA signal fragments. Our results indicate the feasibility of employing GAFD for computing sequence distances and the use of descriptors for characterizing DNA fragments. PMID:25393409

  12. Genomic Signal Processing Methods for Computation of Alignment-Free Distances from DNA Sequences

    PubMed Central

    Borrayo, Ernesto; Mendizabal-Ruiz, E. Gerardo; Vélez-Pérez, Hugo; Romo-Vázquez, Rebeca; Mendizabal, Adriana P.; Morales, J. Alejandro

    2014-01-01

    Genomic signal processing (GSP) refers to the use of digital signal processing (DSP) tools for analyzing genomic data such as DNA sequences. A possible application of GSP that has not been fully explored is the computation of the distance between a pair of sequences. In this work we present GAFD, a novel GSP alignment-free distance computation method. We introduce a DNA sequence-to-signal mapping function based on the employment of doublet values, which increases the number of possible amplitude values for the generated signal. Additionally, we explore the use of three DSP distance metrics as descriptors for categorizing DNA signal fragments. Our results indicate the feasibility of employing GAFD for computing sequence distances and the use of descriptors for characterizing DNA fragments. PMID:25393409

  13. Global Alignment System for Large Genomic Sequencing

    2002-03-01

    AVID is a global alignment system tailored for the alignment of large genomic sequences up to megabases in length. Features include the possibility of one sequence being in draft form, fast alignment, robustness and accuracy. The method is an anchor based alignment using maximal matches derived from suffix trees.

  14. Protein structure alignment beyond spatial proximity

    PubMed Central

    Wang, Sheng; Ma, Jianzhu; Peng, Jian; Xu, Jinbo

    2013-01-01

    Protein structure alignment is a fundamental problem in computational structure biology. Many programs have been developed for automatic protein structure alignment, but most of them align two protein structures purely based upon geometric similarity without considering evolutionary and functional relationship. As such, these programs may generate structure alignments which are not very biologically meaningful from the evolutionary perspective. This paper presents a novel method DeepAlign for automatic pairwise protein structure alignment. DeepAlign aligns two protein structures using not only spatial proximity of equivalent residues (after rigid-body superposition), but also evolutionary relationship and hydrogen-bonding similarity. Experimental results show that DeepAlign can generate structure alignments much more consistent with manually-curated alignments than other automatic tools especially when proteins under consideration are remote homologs. These results imply that in addition to geometric similarity, evolutionary information and hydrogen-bonding similarity are essential to aligning two protein structures. PMID:23486213

  15. Judging Alignment of Curriculum-Based Measures in Mathematics and Common Core Standards

    ERIC Educational Resources Information Center

    Morton, Christopher

    2013-01-01

    Measurement literature supports the utility of alignment models for application with state standards and large-scale assessments. However, the literature is lacking in the application of these models to curriculum-based measures (CBMs) and common core standards. In this study, I investigate the alignment of CBMs and standards, with specific…

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

    SciTech Connect

    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.

  17. Beam based alignment of sector-1 of the SLC linac

    SciTech Connect

    Emma, P.

    1992-03-01

    A technique is described which uses the beam to simultaneously measure quadrupole magnet and beam position monitor (BPM) transverse misalignments. The technique is applied to sector-1 of the SLC linac where simultaneous acceleration of electron and positron beams with minimal steering elements and BPMs makes quadrupole alignment critical for high transmission of the large transverse emittance positron beam. Simulation results as well as measurements are presented.

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  19. Effect of Sterilization Methods on Electrospun Poly(lactic acid) (PLA) Fiber Alignment for Biomedical Applications.

    PubMed

    Valente, T A M; Silva, D M; Gomes, P S; Fernandes, M H; Santos, J D; Sencadas, V

    2016-02-10

    Medically approved sterility methods should be a major concern when developing a polymeric scaffold, mainly when commercialization is envisaged. In the present work, poly(lactic acid) (PLA) fiber membranes were processed by electrospinning with random and aligned fiber alignment and sterilized under UV, ethylene oxide (EO), and γ-radiation, the most common ones for clinical applications. It was observed that UV light and γ-radiation do not influence fiber morphology or alignment, while electrospun samples treated with EO lead to fiber orientation loss and morphology changing from cylindrical fibers to ribbon-like structures, accompanied to an increase of polymer crystallinity up to 28%. UV light and γ-radiation sterilization methods showed to be less harmful to polymer morphology, without significant changes in polymer thermal and mechanical properties, but a slight increase of polymer wettability was detected, especially for the samples treated with UV radiation. In vitro results indicate that both UV and γ-radiation treatments of PLA membranes allow the adhesion and proliferation of MG 63 osteoblastic cells in a close interaction with the fiber meshes and with a growth pattern highly sensitive to the underlying random or aligned fiber orientation. These results are suggestive of the potential of both γ-radiation sterilized PLA membranes for clinical applications in regenerative medicine, especially those where customized membrane morphology and fiber alignment is an important issue. PMID:26756809

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

    PubMed

    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. PMID:18586628

  1. Dimensionality Reduction for Hyperspectral Data Based on Class-Aware Tensor Neighborhood Graph and Patch Alignment.

    PubMed

    Gao, Yang; Wang, Xuesong; Cheng, Yuhu; Wang, Z Jane

    2015-08-01

    To take full advantage of hyperspectral information, to avoid data redundancy and to address the curse of dimensionality concern, dimensionality reduction (DR) becomes particularly important to analyze hyperspectral data. Exploring the tensor characteristic of hyperspectral data, a DR algorithm based on class-aware tensor neighborhood graph and patch alignment is proposed here. First, hyperspectral data are represented in the tensor form through a window field to keep the spatial information of each pixel. Second, using a tensor distance criterion, a class-aware tensor neighborhood graph containing discriminating information is obtained. In the third step, employing the patch alignment framework extended to the tensor space, we can obtain global optimal spectral-spatial information. Finally, the solution of the tensor subspace is calculated using an iterative method and low-dimensional projection matrixes for hyperspectral data are obtained accordingly. The proposed method effectively explores the spectral and spatial information in hyperspectral data simultaneously. Experimental results on 3 real hyperspectral datasets show that, compared with some popular vector- and tensor-based DR algorithms, the proposed method can yield better performance with less tensor training samples required. PMID:25222955

  2. Feature-based multiexposure image-sequence fusion with guided filter and image alignment

    NASA Astrophysics Data System (ADS)

    Xu, Liang; Du, Junping; Zhang, Zhenhong

    2015-01-01

    Multiexposure fusion images have a higher dynamic range and reveal more details than a single captured image of a real-world scene. A clear and intuitive feature-based fusion technique for multiexposure image sequences is conceptually proposed. The main idea of the proposed method is to combine three image features [phase congruency (PC), local contrast, and color saturation] to obtain weight maps of the images. Then, the weight maps are further refined using a guided filter which can improve their accuracy. The final fusion result is constructed using the weighted sum of the source image sequence. In addition, for multiexposure image-sequence fusion involving dynamic scenes containing moving objects, ghost artifacts can easily occur if fusion is directly performed. Therefore, an image-alignment method is first used to adjust the input images to correspond to a reference image, after which fusion is performed. Experimental results demonstrate that the proposed method has a superior performance compared to the existing methods.

  3. A study of an alignment-less lithography method as an educational resource

    NASA Astrophysics Data System (ADS)

    Kai, Kazuho; Shiota, Koki; Nagaoka, Shiro; Mahmood, Mohamad Rusop Bin Haji; Kawai, Akira

    2016-07-01

    A simplification of the lithography process was studied. The simplification method of photolithography, named "alignment-less lithography" was proposed by omitting the photomask alignment process in photolithography process using mechanically aligned photomasks and substrate by using a simple jig on which countersinks were formed. Photomasks made of glass and the photomasks made of transparent plastic sheets were prepared for the process. As the result, approximately 5µm in the case of the glass mask, and 20µm in the case of the OHP mask were obtained with repetitive accuracies, respectively. It was confirmed that the alignment-less lithography method was successful. The possibility of the application to an educational program, such as a heuristic for solving problems was suggested using the method with the OHP mask. The nMOS FET fabrication process was successfully demonstrated using this method. The feasibility of this process was confirmed. It is expected that a totally simplified device fabrication process can be achievable when combined with other simplifications, such ass the simplified impurity diffusion processes using PSG and BSG thin film as diffusion source prepared by the Sol-Gel material under normal air environment.

  4. A Multi-Objective Method to Align Human Resource Allocation with University Strategy

    ERIC Educational Resources Information Center

    Bouillard, Philippe

    2016-01-01

    Universities are currently under considerable pressure to reach their stakeholders' expectations. Management tools that use strategic plans, key performance indicators and quality assurance methods are increasingly deployed. This paper aims to demonstrate how resource allocation can be aligned with institutional strategic plans with a very simple…

  5. hst2galign: an Automated Galaxy-based Alignment Routine

    NASA Astrophysics Data System (ADS)

    Anderson, Jay; Ogaz, Sara

    2014-10-01

    This brief document describes the procedure by which the individual images in the Frontier Fields program have been aligned in order to enable the self-calibration procedure (which will be described in a separate document). Along with this document, we will release the FORTRAN source code (hst2galign) that accomplishes the alignment. The source code is provided as-is, with no guarantee that it will work on any particular data set. However, it should work "out of the box" on datasets that are similar to the Frontier Fields. The data products introduced in this ISR are a very early attempt to provide the flt-level pixel constraints in a package that is accessible to more than the handful of experts in HST astrometry. The hope is that users in the community might begin using them and will provide feedback as to what information they might want to see in the bundles and what general analysis packages they might find useful. For that reason, this document is somewhat informally written, since I know that it will be modified and updated as the products and tools are optimized.

  6. A Parallel Non-Alignment Based Approach to Efficient Sequence Comparison using Longest Common Subsequences

    NASA Astrophysics Data System (ADS)

    Bhowmick, S.; Shafiullah, M.; Rai, H.; Bastola, D.

    2010-11-01

    Biological sequence comparison programs have revolutionized the practice of biochemistry, and molecular and evolutionary biology. Pairwise comparison of genomic sequences is a popular method of choice for analyzing genetic sequence data. However the quality of results from most sequence comparison methods are significantly affected by small perturbations in the data and furthermore, there is a dearth of computational tools to compare sequences beyond a certain length. In this paper, we describe a parallel algorithm for comparing genetic sequences using an alignment free-method based on computing the Longest Common Subsequence (LCS) between genetic sequences. We validate the quality of our results by comparing the phylogenetic tress obtained from ClustalW and LCS. We also show through complexity analysis of the isoefficiency and by empirical measurement of the running time that our algorithm is very scalable.

  7. SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation

    PubMed Central

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

    2014-01-01

    The perpetually increasing rate at which viral full-genome sequences are being determined is creating a pressing demand for computational tools that will aid the objective classification of these genome sequences. Taxonomic classification approaches that are based on pairwise genetic identity measures are potentially highly automatable and are progressively gaining favour with the International Committee on Taxonomy of Viruses (ICTV). There are, however, various issues with the calculation of such measures that could potentially undermine the accuracy and consistency with which they can be applied to virus classification. Firstly, pairwise sequence identities computed based on multiple sequence alignments rather than on multiple independent pairwise alignments can lead to the deflation of identity scores with increasing dataset sizes. Also, when gap-characters need to be introduced during sequence alignments to account for insertions and deletions, methodological variations in the way that these characters are introduced and handled during pairwise genetic identity calculations can cause high degrees of inconsistency in the way that different methods classify the same sets of sequences. Here we present Sequence Demarcation Tool (SDT), a free user-friendly computer program that aims to provide a robust and highly reproducible means of objectively using pairwise genetic identity calculations to classify any set of nucleotide or amino acid sequences. SDT can produce publication quality pairwise identity plots and colour-coded distance matrices to further aid the classification of sequences according to ICTV approved taxonomic demarcation criteria. Besides a graphical interface version of the program for Windows computers, command-line versions of the program are available for a variety of different operating systems (including a parallel version for cluster computing platforms). PMID:25259891

  8. A Novel Alignment-Free Method for Comparing Transcription Factor Binding Site Motifs

    PubMed Central

    Xu, Minli; Su, Zhengchang

    2010-01-01

    Background Transcription factor binding site (TFBS) motifs can be accurately represented by position frequency matrices (PFM) or other equivalent forms. We often need to compare TFBS motifs using their PFMs in order to search for similar motifs in a motif database, or cluster motifs according to their binding preference. The majority of current methods for motif comparison involve a similarity metric for column-to-column comparison and a method to find the optimal position alignment between the two compared motifs. In some applications, alignment-free methods might be preferred; however, few such methods with high accuracy have been described. Methodology/Principal Findings Here we describe a novel alignment-free method for quantifying the similarity of motifs using their PFMs by converting PFMs into k-mer vectors. The motifs could then be compared by measuring the similarity among their corresponding k-mer vectors. Conclusions/Significance We demonstrate that our method in general achieves similar performance or outperforms the existing methods for clustering motifs according to their binding preference and identifying similar motifs of transcription factors of the same family. PMID:20098703

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

    NASA Astrophysics Data System (ADS)

    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.

  10. Intraocular lens alignment from an en face optical coherence tomography image Purkinje-like method

    NASA Astrophysics Data System (ADS)

    Sun, Mengchan; de Castro, Alberto; Ortiz, Sergio; Perez-Merino, Pablo; Birkenfeld, Judith; Marcos, Susana

    2014-06-01

    Measurement of intraocular lens (IOL) alignment implanted in patients in cataract surgery is important to understand their optical performance. We present a method to estimate tilt and decentration of IOLs based on optical coherence tomography (OCT) images. En face OCT images show Purkinje-like images that correspond to the specular reflections from the corneal and IOL surfaces. Unlike in standard Purkinje-imaging, the tomographic nature of OCT allows unequivocal association of the reflection with the corresponding surface. The locations of the Purkinje-like images are linear combinations of IOL tilt, IOL decentration, and eye rotation. The weighting coefficients depend on the individual anterior segment geometry, obtained from the same OCT datasets. The methodology was demonstrated on an artificial model eye with set amounts of lens tilt and decentration and five pseudophakic eyes. Measured tilt and decentration in the artificial eye differed by 3.7% and 0.9%, respectively, from nominal values. In patients, average IOL tilt and decentration from Purkinje were 3.30±4.68 deg and 0.16±0.16 mm, respectively, and differed on average by 0.5 deg and 0.09 mm, respectively, from direct measurements on distortion-corrected OCT images. Purkinje-based methodology from anterior segment en face OCT imaging provided, therefore, reliable measurements of IOL tilt and decentration.

  11. An Improved Alignment Method for the Strapdown Inertial Navigation System (SINS)

    PubMed Central

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

    2016-01-01

    In this paper, an innovative inertial navigation system (INS) mechanization and the associated Kalman filter (KF) are developed to implement a fine alignment for the strapdown INS (SINS) on stationary base. The improved mechanization is established in the pseudo-geographic frame, which is rebuilt based on the initial position. The new mechanization eliminates the effects of linear movement errors on the heading by decoupling. Compared with the traditional local-level mechanization, it has more advantages. The proposed algorithm requires lower coarse alignment accuracy in both the open-loop and closed-loop KFs and hence can improve the system reliability and decrease the total alignment time. Moreover, for the closed-loop KF, it can decrease oscillation caused by the system errors and improve the closed-loop system stability. In addition, the proposed algorithm can also be applied to polar alignment. The performance of the proposed algorithm is verified by both simulations and experiments and the results exhibit the superior performance of the proposed approach. PMID:27136565

  12. An Improved Alignment Method for the Strapdown Inertial Navigation System (SINS).

    PubMed

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

    2016-01-01

    In this paper, an innovative inertial navigation system (INS) mechanization and the associated Kalman filter (KF) are developed to implement a fine alignment for the strapdown INS (SINS) on stationary base. The improved mechanization is established in the pseudo-geographic frame, which is rebuilt based on the initial position. The new mechanization eliminates the effects of linear movement errors on the heading by decoupling. Compared with the traditional local-level mechanization, it has more advantages. The proposed algorithm requires lower coarse alignment accuracy in both the open-loop and closed-loop KFs and hence can improve the system reliability and decrease the total alignment time. Moreover, for the closed-loop KF, it can decrease oscillation caused by the system errors and improve the closed-loop system stability. In addition, the proposed algorithm can also be applied to polar alignment. The performance of the proposed algorithm is verified by both simulations and experiments and the results exhibit the superior performance of the proposed approach. PMID:27136565

  13. Phase Retrieval Using a Genetic Algorithm on the Systematic Image-Based Optical Alignment Testbed

    NASA Technical Reports Server (NTRS)

    Taylor, Jaime R.

    2003-01-01

    NASA s Marshall Space Flight Center s Systematic Image-Based Optical Alignment (SIBOA) Testbed was developed to test phase retrieval algorithms and hardware techniques. Individuals working with the facility developed the idea of implementing phase retrieval by breaking the determination of the tip/tilt of each mirror apart from the piston motion (or translation) of each mirror. Presented in this report is an algorithm that determines the optimal phase correction associated only with the piston motion of the mirrors. A description of the Phase Retrieval problem is first presented. The Systematic Image-Based Optical Alignment (SIBOA) Testbeb is then described. A Discrete Fourier Transform (DFT) is necessary to transfer the incoming wavefront (or estimate of phase error) into the spatial frequency domain to compare it with the image. A method for reducing the DFT to seven scalar/matrix multiplications is presented. A genetic algorithm is then used to search for the phase error. The results of this new algorithm on a test problem are presented.

  14. A three dimensional heart model based on anatomically aligned trusses.

    PubMed

    Witman, S; Gefen, A; Barnea, O

    2007-01-01

    A new approach for modeling and simulating the contraction of the heart is presented. The model is based on anatomical images and accounts for cardiac muscle fibers and their orientation. The heart is modeled as a structure built of trusses, each representing a group of myofibers with calculated deformations using matrix structural analysis. Three elements are represented; these are the contractile cardiac muscle, the elastic passive collagen, and intracardiac blood interacting with the heart's preload and afterload. Incompressibility of each element is preserved. The conduction system is simulated in the model by transferring the activating signal from one element to another or by Purkinje fibers activation. The method was demonstrated using a three-dimensional one-layer geometrical ventricle with orthogonal fibers and with anatomically oriented fibers. PMID:18002551

  15. A Fast and Scalable Kymograph Alignment Algorithm for Nanochannel-Based Optical DNA Mappings

    PubMed Central

    Noble, Charleston; Nilsson, Adam N.; Freitag, Camilla; Beech, Jason P.; Tegenfeldt, Jonas O.; Ambjörnsson, Tobias

    2015-01-01

    Optical mapping by direct visualization of individual DNA molecules, stretched in nanochannels with sequence-specific fluorescent labeling, represents a promising tool for disease diagnostics and genomics. An important challenge for this technique is thermal motion of the DNA as it undergoes imaging; this blurs fluorescent patterns along the DNA and results in information loss. Correcting for this effect (a process referred to as kymograph alignment) is a common preprocessing step in nanochannel-based optical mapping workflows, and we present here a highly efficient algorithm to accomplish this via pattern recognition. We compare our method with the one previous approach, and we find that our method is orders of magnitude faster while producing data of similar quality. We demonstrate proof of principle of our approach on experimental data consisting of melt mapped bacteriophage DNA. PMID:25875920

  16. Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs

    PubMed Central

    Paten, Benedict; Herrero, Javier; Beal, Kathryn; Fitzgerald, Stephen; Birney, Ewan

    2008-01-01

    Pairwise whole-genome alignment involves the creation of a homology map, capable of performing a near complete transformation of one genome into another. For multiple genomes this problem is generalized to finding a set of consistent homology maps for converting each genome in the set of aligned genomes into any of the others. The problem can be divided into two principal stages. First, the partitioning of the input genomes into a set of colinear segments, a process which essentially deals with the complex processes of rearrangement. Second, the generation of a base pair level alignment map for each colinear segment. We have developed a new genome-wide segmentation program, Enredo, which produces colinear segments from extant genomes handling rearrangements, including duplications. We have then applied the new alignment program Pecan, which makes the consistency alignment methodology practical at a large scale, to create a new set of genome-wide mammalian alignments. We test both Enredo and Pecan using novel and existing assessment analyses that incorporate both real biological data and simulations, and show that both independently and in combination they outperform existing programs. Alignments from our pipeline are publicly available within the Ensembl genome browser. PMID:18849524

  17. A three-dimensional vertically aligned functionalized multilayer graphene architecture: an approach for graphene-based thermal interfacial materials.

    PubMed

    Liang, Qizhen; Yao, Xuxia; Wang, Wei; Liu, Yan; Wong, Ching Ping

    2011-03-22

    Thermally conductive functionalized multilayer graphene sheets (fMGs) are efficiently aligned in large-scale by a vacuum filtration method at room temperature, as evidenced by SEM images and polarized Raman spectroscopy. A remarkably strong anisotropy in properties of aligned fMGs is observed. High electrical (∼386 S cm(-1)) and thermal conductivity (∼112 W m(-1) K(-1) at 25 °C) and ultralow coefficient of thermal expansion (∼-0.71 ppm K(-1)) in the in-plane direction of A-fMGs are obtained without any reduction process. Aligned fMGs are vertically assembled between contacted silicon/silicon surfaces with pure indium as a metallic medium. Thus-constructed three-dimensional vertically aligned fMG thermal interfacial material (VA-fMG TIM) architecture has significantly higher equivalent thermal conductivity (75.5 W m(-1) K(-1)) and lower contact thermal resistance (5.1 mm2 K W(-1)), compared with their counterpart from A-fMGs that are recumbent between silicon surfaces. This finding provides a throughout approach for a graphene-based TIM assembly as well as knowledge of vertically aligned graphene architectures, which may not only facilitate graphene's application in current demanding thermal management but also promote its widespread applications in electrodes of energy storage devices, conductive polymeric composites, etc. PMID:21384860

  18. Inverse image alignment method for image mosaicing and video stabilization in fundus indocyanine green angiography under confocal scanning laser ophthalmoscope.

    PubMed

    Zhou, Yongjin; Xue, Hui; Wan, Mingxi

    2003-01-01

    An efficient image registration algorithm, the Inverse Compositional image alignment method based on minimization of Sum of Squared Differences of images, is applied in fundus blood vessel angiography under confocal scanning laser ophthalmoscope, to build image mosaics which have larger field of view without loss of resolution to assist diagnosis. Furthermore, based on similar technique, the angiography video stabilization algorithm is implemented for fundus documenting. The actual underlying models of motion between images and corresponding convergence criteria are also discussed. The experiment results in fundus images demonstrate the effectiveness of the registration scheme. PMID:14575786

  19. Image alignment

    DOEpatents

    Dowell, Larry Jonathan

    2014-04-22

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

  20. STAR3D: a stack-based RNA 3D structural alignment tool

    PubMed Central

    Ge, Ping; Zhang, Shaojie

    2015-01-01

    The various roles of versatile non-coding RNAs typically require the attainment of complex high-order structures. Therefore, comparing the 3D structures of RNA molecules can yield in-depth understanding of their functional conservation and evolutionary history. Recently, many powerful tools have been developed to align RNA 3D structures. Although some methods rely on both backbone conformations and base pairing interactions, none of them consider the entire hierarchical formation of the RNA secondary structure. One of the major issues is that directly applying the algorithms of matching 2D structures to the 3D coordinates is particularly time-consuming. In this article, we propose a novel RNA 3D structural alignment tool, STAR3D, to take into full account the 2D relations between stacks without the complicated comparison of secondary structures. First, the 3D conserved stacks in the inputs are identified and then combined into a tree-like consensus. Afterward, the loop regions are compared one-to-one in accordance with their relative positions in the consensus tree. The experimental results show that the prediction of STAR3D is more accurate for both non-homologous and homologous RNAs than other state-of-the-art tools with shorter running time. PMID:26184875

  1. STAR3D: a stack-based RNA 3D structural alignment tool.

    PubMed

    Ge, Ping; Zhang, Shaojie

    2015-11-16

    The various roles of versatile non-coding RNAs typically require the attainment of complex high-order structures. Therefore, comparing the 3D structures of RNA molecules can yield in-depth understanding of their functional conservation and evolutionary history. Recently, many powerful tools have been developed to align RNA 3D structures. Although some methods rely on both backbone conformations and base pairing interactions, none of them consider the entire hierarchical formation of the RNA secondary structure. One of the major issues is that directly applying the algorithms of matching 2D structures to the 3D coordinates is particularly time-consuming. In this article, we propose a novel RNA 3D structural alignment tool, STAR3D, to take into full account the 2D relations between stacks without the complicated comparison of secondary structures. First, the 3D conserved stacks in the inputs are identified and then combined into a tree-like consensus. Afterward, the loop regions are compared one-to-one in accordance with their relative positions in the consensus tree. The experimental results show that the prediction of STAR3D is more accurate for both non-homologous and homologous RNAs than other state-of-the-art tools with shorter running time. PMID:26184875

  2. Multiple sequence alignment algorithm based on a dispersion graph and ant colony algorithm.

    PubMed

    Chen, Weiyang; Liao, Bo; Zhu, Wen; Xiang, Xuyu

    2009-10-01

    In this article, we describe a representation for the processes of multiple sequences alignment (MSA) and used it to solve the problem of MSA. By this representation, we took every possible aligning result into account by defining the representation of gap insertion, the value of heuristic information in every optional path and scoring rule. On the basis of the proposed multidimensional graph, we used the ant colony algorithm to find the better path that denotes a better aligning result. In our article, we proposed the instance of three-dimensional graph and four-dimensional graph and advanced a special ichnographic representation to analyze MSA. It is yet only an experimental software, and we gave an example for finding the best aligning result by three-dimensional graph and ant colony algorithm. Experimental results show that our method can improve the solution quality on MSA benchmarks. PMID:19130503

  3. Supervised descent method with low rank and sparsity constraints for robust face alignment

    NASA Astrophysics Data System (ADS)

    Sun, Yubao; Hu, Bin; Deng, Jiankang; Li, Xing

    2015-03-01

    Supervised Descent Method (SDM) learns the descent directions of nonlinear least square objective in a supervised manner, which has been efficiently used for face alignment. However, SDM still may fail in the cases of partial occlusions and serious pose variations. To deal with this issue, we present a new method for robust face alignment by utilizing the low rank prior of human face and enforcing sparse structure of the descent directions. Our approach consists of low rank face frontalization and sparse descent steps. Firstly, in terms of the low rank prior of face image, we recover such a low-rank face from its deformed image and the associated deformation despite significant distortion and corruption. Alignment of the recovered frontal face image is more simple and effective. Then, we propose a sparsity regularized supervised descent model by enforcing the sparse structure of the descent directions under the l1constraint, which makes the model more effective in computation and robust to partial occlusion. Extensive results on several benchmarks demonstrate that the proposed method is robust to facial occlusions and pose variations

  4. Links for Academic Learning (LAL): A Conceptual Model for Investigating Alignment of Alternate Assessments Based on Alternate Achievement Standards

    ERIC Educational Resources Information Center

    Flowers, Claudia; Wakeman, Shawnee; Browder, Diane M.; Karvonen, Meagan

    2009-01-01

    This article describes an alignment procedure, called Links for Academic Learning (LAL), for examining the degree of alignment of alternate assessments based on alternate achievement standards (AA-AAS) to grade-level content standards and instruction. Although some of the alignment criteria are similar to those used in general education…

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed Central

    2013-01-01

    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. PMID:24274897

  7. Melody Alignment and Similarity Metric for Content-Based Music Retrieval

    NASA Astrophysics Data System (ADS)

    Zhu, Yongwei; Kankanhalli, Mohan S.

    2003-01-01

    Music query-by-humming has attracted much research interest recently. It is a challenging problem since the hummed query inevitably contains much variation and inaccuracy. Furthermore, the similarity computation between the query tune and the reference melody is not easy due to the difficulty in ensuring proper alignment. This is because the query tune can be rendered at an unknown speed and it is usually an arbitrary subsequence of the target reference melody. Many of the previous methods, which adopt note segmentation and string matching, suffer drastically from the errors in the note segmentation, which affects retrieval accuracy and efficiency. Some methods solve the alignment issue by controlling the speed of the articulation of queries, which is inconvenient because it forces users to hum along a metronome. Some other techniques introduce arbitrary rescaling in time but this is computationally very inefficient. In this paper, we introduce a melody alignment technique, which addresses the robustness and efficiency issues. We also present a new melody similarity metric, which is performed directly on melody contours of the query data. This approach cleanly separates the alignment and similarity measurement in the search process. We show how to robustly and efficiently align the query melody with the reference melodies and how to measure the similarity subsequently. We have carried out extensive experiments. Our melody alignment method can reduce the matching candidate to 1.7% with 95% correct alignment rate. The overall retrieval system achieved 80% recall in the top 10 rank list. The results demonstrate the robustness and effectiveness the proposed methods.

  8. 1001 optimal PDB structure alignments: integer programming methods for finding the maximum contact map overlap.

    PubMed

    Caprara, Alberto; Carr, Robert; Istrail, Sorin; Lancia, Giuseppe; Walenz, Brian

    2004-01-01

    Protein structure comparison is a fundamental problem for structural genomics, with applications to drug design, fold prediction, protein clustering, and evolutionary studies. Despite its importance, there are very few rigorous methods and widely accepted similarity measures known for this problem. In this paper we describe the last few years of developments on the study of an emerging measure, the contact map overlap (CMO), for protein structure comparison. A contact map is a list of pairs of residues which lie in three-dimensional proximity in the protein's native fold. Although this measure is in principle computationally hard to optimize, we show how it can in fact be computed with great accuracy for related proteins by integer linear programming techniques. These methods have the advantage of providing certificates of near-optimality by means of upper bounds to the optimal alignment value. We also illustrate effective heuristics, such as local search and genetic algorithms. We were able to obtain for the first time optimal alignments for large similar proteins (about 1,000 residues and 2,000 contacts) and used the CMO measure to cluster proteins in families. The clusters obtained were compared to SCOP classification in order to validate the measure. Extensive computational experiments showed that alignments which are off by at most 10% from the optimal value can be computed in a short time. Further experiments showed how this measure reacts to the choice of the threshold defining a contact and how to choose this threshold in a sensible way. PMID:15072687

  9. Growth mechanism of vertically aligned fullerene micro tubes prepared by the liquid-liquid interfacial precipitation method

    NASA Astrophysics Data System (ADS)

    Toita, S.; Miyazawa, K.; Hotta, K.; Tachibana, M.

    2009-04-01

    C60-based materials such as FNWs and FNTs are new candidates for organic electronics and solar cells. Recently, a method to produce vertically-aligned fullerene microtube crystals (VFMTs) has been established. The VFMTs are exepected to be used as field emission devices, solar cells, fuel cells, and so forth. To realize such attractive applications, structures and arrangements of VFMTs should be controlled. In oder to know the growth mechanism of VFMTs, Scanning electron microscopy (SEM) observations were performed for several injection periods of VFMTs. In the initial stage of synthesis (IPA injection time of 60 min), vertically aligned thin non-tubular fullerene microwhiskers (VFMWs) formed on AAO substrates. The outer and inner diameter of VFMWs became increased with increasing the injected amount of IPA. And also the size of tube holes became larger. The tubular structures appeared at an injection time of around 90 min. At an injection time of 120 min, vertically aligned FMTs with hexagonal cross sections and holes were obtained and their diameter and structure did not change up to the final stage of injection time of 3 00 min.

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

    NASA Technical Reports Server (NTRS)

    Rakoczy, John; Steincamp, James; Taylor, Jaime

    2003-01-01

    A reduced surrogate, one point crossover genetic algorithm with random rank-based selection was used successfully to estimate the multiple phases of a segmented optical system modeled on the seven-mirror Systematic Image-Based Optical Alignment testbed located at NASA's Marshall Space Flight Center.

  11. Method for promoting specific alignment of short oligonucleotides on nucleic acids

    DOEpatents

    Studier, F. William; Kieleczawa, Jan; Dunn, John J.

    1996-01-01

    Disclosed is a method for promoting specific alignment of short oligonucleotides on a nucleic acid polymer. The nucleic acid polymer is incubated in a solution containing a single-stranded DNA-binding protein and a plurality of oligonucleotides which are perfectly complementary to distinct but adjacent regions of a predetermined contiguous nucleotide sequence in the nucleic acid polymer. The plurality of oligonucleotides anneal to the nucleic acid polymer to form a contiguous region of double stranded nucleic acid. Specific application of the methods disclosed include priming DNA synthesis and template-directed ligation.

  12. SVM-BALSA: Remote Homology Detection based on Bayesian Sequence Alignment

    SciTech Connect

    Webb-Robertson, Bobbie-Jo M.; Oehmen, Chris S.; Matzke, Melissa M.

    2005-11-10

    Using biopolymer sequence comparison methods to identify evolutionarily related proteins is one of the most common tasks in bioinformatics. Recently, support vector machines (SVMs) utilizing statistical learning theory have been employed in the problem of remote homology detection and shown to outperform iterative profile methods such as PSI-BLAST. In this study we demonstrate the utilization of a Bayesian alignment score, which accounts for the uncertainty of all possible alignments, in the SVM construction improves sensitivity compared to the traditional dynamic programming implementation.

  13. Overhead drilling: Comparing three bases for aligning a drilling jig to vertical

    PubMed Central

    Rempel, David; Star, Demetra; Barr, Alan; Janowitz, Ira

    2010-01-01

    Problem Drilling overhead into concrete or metal ceilings is a strenuous task done by construction workers to hang ductwork, piping, and electrical equipment. The task is associated with upper body pain and musculoskeletal disorders. Previously, we described a field usability evaluation of a foot lever and inverted drill press intervention devices that were compared to the usual method for overhead drilling. Both interventions were rated as inferior to the usual method based on poor setup time and mobility. Method Three new interventions, which differed on the design used for aligning the drilling column to vertical, were compared to the usual method for overhead drilling by commercial construction workers (n=16). Results The usual method was associated with the highest levels of regional body fatigue and the poorest usability ratings when compared to the three interventions. Conclusion Overall, the ‘Collar Base’ intervention design received the best usability ratings. Impact on Industry Intervention designs developed for overhead drilling may reduce shoulder fatigue and prevent subsequent musculoskeletal disorders. These designs may also be useful for other overhead work such as lifting and supporting materials (e.g., piping, ducts) that are installed near the ceiling. Workplace health and safety interventions may require multiple rounds of field-testing prior to achieving acceptable usability ratings by the end users. PMID:20630276

  14. Markov Random Field Based Automatic Image Alignment for ElectronTomography

    SciTech Connect

    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.

  15. Evidence of Statistical Inconsistency of Phylogenetic Methods in the Presence of Multiple Sequence Alignment Uncertainty

    PubMed Central

    Md Mukarram Hossain, A.S.; Blackburne, Benjamin P.; Shah, Abhijeet; Whelan, Simon

    2015-01-01

    Evolutionary studies usually use a two-step process to investigate sequence data. Step one estimates a multiple sequence alignment (MSA) and step two applies phylogenetic methods to ask evolutionary questions of that MSA. Modern phylogenetic methods infer evolutionary parameters using maximum likelihood or Bayesian inference, mediated by a probabilistic substitution model that describes sequence change over a tree. The statistical properties of these methods mean that more data directly translates to an increased confidence in downstream results, providing the substitution model is adequate and the MSA is correct. Many studies have investigated the robustness of phylogenetic methods in the presence of substitution model misspecification, but few have examined the statistical properties of those methods when the MSA is unknown. This simulation study examines the statistical properties of the complete two-step process when inferring sequence divergence and the phylogenetic tree topology. Both nucleotide and amino acid analyses are negatively affected by the alignment step, both through inaccurate guide tree estimates and through overfitting to that guide tree. For many alignment tools these effects become more pronounced when additional sequences are added to the analysis. Nucleotide sequences are particularly susceptible, with MSA errors leading to statistical support for long-branch attraction artifacts, which are usually associated with gross substitution model misspecification. Amino acid MSAs are more robust, but do tend to arbitrarily resolve multifurcations in favor of the guide tree. No inference strategies produce consistently accurate estimates of divergence between sequences, although amino acid MSAs are again more accurate than their nucleotide counterparts. We conclude with some practical suggestions about how to limit the effect of MSA uncertainty on evolutionary inference. PMID:26139831

  16. MET-XAlign: a metabolite cross-alignment tool for LC/MS-based comparative metabolomics.

    PubMed

    Zhang, Wenchao; Lei, Zhentian; Huhman, David; Sumner, Lloyd W; Zhao, Patrick X

    2015-09-15

    Liquid chromatography/mass spectrometry (LC/MS) metabolite profiling has been widely used in comparative metabolomics studies; however, LC/MS-based comparative metabolomics currently faces several critical challenges. One of the greatest challenges is how to effectively align metabolites across different LC/MS profiles; a single metabolite can give rise to multiple peak features, and the grouped peak features that can be used to construct a spectrum pattern of single metabolite can vary greatly between biochemical experiments and even between instrument runs. Another major challenge is that the observed retention time for a single metabolite can also be significantly affected by experimental conditions. To overcome these two key challenges, we present a novel metabolite-based alignment approach entitled MET-XAlign to align metabolites across LC/MS metabolomics profiles. MET-XAlign takes the deduced molecular mass and estimated compound retention time information that can be extracted by our previously published tool, MET-COFEA, and aligns metabolites based on this information. We demonstrate that MET-XAlign is able to cross-align metabolite compounds, either known or unknown, in LC/MS profiles not only across different samples but also across different biological experiments and different electrospray ionization modes. Therefore, our proposed metabolite-based cross-alignment approach is a great step forward and its implementation, MET-XAlign, is a very useful tool in LC/MS-based comparative metabolomics. MET-XAlign has been successfully implemented with core algorithm coding in C++, making it very efficient, and visualization interface coding in the Microsoft.NET Framework. The MET-XAlign software along with demonstrative data is freely available at http://bioinfo.noble.org/manuscript-support/met-xalign/ . PMID:26247233

  17. Markov random field based automatic alignment for low SNR imagesfor cryo electron tomography

    SciTech Connect

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

    2007-07-21

    We present a method for automatic full precision alignmentof the images in a tomographic tilt series. Full-precision automaticalignment of cryo electron microscopy images has remained a difficultchallenge to date, due to the limited electron dose and low imagecontrast. These facts lead to poor signal to noise ratio (SNR) in theimages, which causes automatic feature trackers to generate errors, evenwith high contrast gold particles as fiducial features. To enable fullyautomatic alignment for full-precision reconstructions, we frame theproblem probabilistically as finding the most likely particle tracksgiven a set of noisy images, using contextual information to make thesolution more robust to the noise in each image. To solve this maximumlikelihood problem, we use Markov Random Fields (MRF) to establish thecorrespondence of features in alignment and robust optimization forprojection model estimation. The resultingalgorithm, called RobustAlignment and Projection Estimation for Tomographic Reconstruction, orRAPTOR, has not needed any manual intervention for the difficult datasets we have tried, and has provided sub-pixel alignment that is as goodas the manual approach by an expert user. We are able to automaticallymap complete and partial marker trajectories and thus obtain highlyaccurate image alignment. Our method has been applied to challenging cryoelectron tomographic datasets with low SNR from intact bacterial cells,as well as several plastic section and x-ray datasets.

  18. Aligning Potency and Pharmacokinetic Properties for Pyridine-Based NCINIs.

    PubMed

    Fader, Lee D; Bailey, Murray; Beaulieu, Eric; Bilodeau, François; Bonneau, Pierre; Bousquet, Yves; Carson, Rebekah J; Chabot, Catherine; Coulombe, René; Duan, Jianmin; Fenwick, Craig; Garneau, Michel; Halmos, Ted; Jakalian, Araz; James, Clint; Kawai, Stephen H; Landry, Serge; LaPlante, Steven R; Mason, Stephen W; Morin, Sebastien; Rioux, Nathalie; Simoneau, Bruno; Surprenant, Simon; Thavonekham, Bounkham; Thibeault, Carl; Trinh, Thao; Tsantrizos, Youla; Tsoung, Jennifer; Yoakim, Christiane; Wernic, Dominik

    2016-08-11

    Optimization of pyridine-based noncatalytic site integrase inhibitors (NCINIs) based on compound 2 has led to the discovery of molecules capable of inhibiting virus harboring N124 variants of HIV integrase (IN) while maintaining minimal contribution of enterohepatic recirculation to clearance in rat. Structure-activity relationships at the C6 position established chemical space where the extent of enterohepatic recirculation in the rat is minimized. Desymmetrization of the C4 substituent allowed for potency optimization against virus having the N124 variant of integrase. Combination of these lessons led to the discovery of compound 20, having balanced serum-shifted antiviral potency and minimized excretion in to the biliary tract in rat, potentially representing a clinically viable starting point for a new treatment option for individuals infected with HIV. PMID:27563405

  19. PSAR: measuring multiple sequence alignment reliability by probabilistic sampling

    PubMed Central

    Kim, Jaebum; Ma, Jian

    2011-01-01

    Multiple sequence alignment, which is of fundamental importance for comparative genomics, is a difficult problem and error-prone. Therefore, it is essential to measure the reliability of the alignments and incorporate it into downstream analyses. We propose a new probabilistic sampling-based alignment reliability (PSAR) score. Instead of relying on heuristic assumptions, such as the correlation between alignment quality and guide tree uncertainty in progressive alignment methods, we directly generate suboptimal alignments from an input multiple sequence alignment by a probabilistic sampling method, and compute the agreement of the input alignment with the suboptimal alignments as the alignment reliability score. We construct the suboptimal alignments by an approximate method that is based on pairwise comparisons between each single sequence and the sub-alignment of the input alignment where the chosen sequence is left out. By using simulation-based benchmarks, we find that our approach is superior to existing ones, supporting that the suboptimal alignments are highly informative source for assessing alignment reliability. We apply the PSAR method to the alignments in the UCSC Genome Browser to measure the reliability of alignments in different types of regions, such as coding exons and conserved non-coding regions, and use it to guide cross-species conservation study. PMID:21576232

  20. Assessing Activity Pattern Similarity with Multidimensional Sequence Alignment based on a Multiobjective Optimization Evolutionary Algorithm

    PubMed Central

    Kwan, Mei-Po; Xiao, Ningchuan; Ding, Guoxiang

    2015-01-01

    Due to the complexity and multidimensional characteristics of human activities, assessing the similarity of human activity patterns and classifying individuals with similar patterns remains highly challenging. This paper presents a new and unique methodology for evaluating the similarity among individual activity patterns. It conceptualizes multidimensional sequence alignment (MDSA) as a multiobjective optimization problem, and solves this problem with an evolutionary algorithm. The study utilizes sequence alignment to code multiple facets of human activities into multidimensional sequences, and to treat similarity assessment as a multiobjective optimization problem that aims to minimize the alignment cost for all dimensions simultaneously. A multiobjective optimization evolutionary algorithm (MOEA) is used to generate a diverse set of optimal or near-optimal alignment solutions. Evolutionary operators are specifically designed for this problem, and a local search method also is incorporated to improve the search ability of the algorithm. We demonstrate the effectiveness of our method by comparing it with a popular existing method called ClustalG using a set of 50 sequences. The results indicate that our method outperforms the existing method for most of our selected cases. The multiobjective evolutionary algorithm presented in this paper provides an effective approach for assessing activity pattern similarity, and a foundation for identifying distinctive groups of individuals with similar activity patterns. PMID:26190858

  1. Fourier-based automatic alignment for improved Visual Cryptography schemes.

    PubMed

    Machizaud, Jacques; Chavel, Pierre; Fournel, Thierry

    2011-11-01

    In Visual Cryptography, several images, called "shadow images", that separately contain no information, are overlapped to reveal a shared secret message. We develop a method to digitally register one printed shadow image acquired by a camera with a purely digital shadow image, stored in memory. Using Fourier techniques derived from Fourier Optics concepts, the idea is to enhance and exploit the quasi periodicity of the shadow images, composed by a random distribution of black and white patterns on a periodic sampling grid. The advantage is to speed up the security control or the access time to the message, in particular in the cases of a small pixel size or of large numbers of pixels. Furthermore, the interest of visual cryptography can be increased by embedding the initial message in two shadow images that do not have identical mathematical supports, making manual registration impractical. Experimental results demonstrate the successful operation of the method, including the possibility to directly project the result onto the printed shadow image. PMID:22109152

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

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

    SciTech Connect

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

    2015-10-15

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

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

    PubMed

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

    2015-10-01

    This paper presents a rapid non-destructive method that provides information on the anisotropic internal structure of nanofibrous layers. A laser beam of a wavelength of 632.8 nm is directed at and passes through a nanofibrous layer prepared by electrostatic spinning. Information about the structural arrangement of nanofibers in the layer is directly visible in the form of a diffraction image formed on a projection screen or obtained from measured intensities of the laser beam passing through the sample which are determined by the dependency of the angle of the main direction of polarization of the laser beam on the axis of alignment of nanofibers in the sample. Both optical methods were verified on Polyvinyl alcohol (PVA) nanofibrous layers (fiber diameter of 470 nm) with random, single-axis aligned and crossed structures. The obtained results match the results of commonly used methods which apply the analysis of electron microscope images. The presented simple method not only allows samples to be analysed much more rapidly and without damaging them but it also makes possible the analysis of much larger areas, up to several square millimetres, at the same time. PMID:26521008

  5. A Method for Non-Rigid Face Alignment via Combining Local and Holistic Matching

    PubMed Central

    Yang, Yang; Chen, Zhuo

    2016-01-01

    We propose a method for non-rigid face alignment which only needs a single template, such as using a person’s smile face to match his surprise face. First, in order to be robust to outliers caused by complex geometric deformations, a new local feature matching method called K Patch Pairs (K-PP) is proposed. Specifically, inspired by the state-of-art similarity measure used in template matching, K-PP is to find the mutual K nearest neighbors between two images. A weight matrix is then presented to balance the similarity and the number of local matching. Second, we proposed a modified Lucas-Kanade algorithm combined with local matching constraint to solve the non-rigid face alignment, so that a holistic face representation and local features can be jointly modeled in the object function. Both the flexible ability of local matching and the robust ability of holistic fitting are included in our method. Furthermore, we show that the optimization problem can be efficiently solved by the inverse compositional algorithm. Comparison results with conventional methods demonstrate our superiority in terms of both accuracy and robustness. PMID:27494319

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

    PubMed Central

    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

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

    PubMed

    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]. PMID:26977430

  8. On-chip polarized light emitters based on (6,5) chirality-sorted carbon nanotube aligned arrays

    NASA Astrophysics Data System (ADS)

    Ma, Ze; Liang, Shuang; Liu, Yang; Wang, Fanglin; Wang, Sheng; Peng, Lian-Mao

    2016-02-01

    Electrically driven light-emitters based on carbon nanotubes are highly promising candidates for on-chip optical interconnection and nanophotonics. Here, we fabricated on-chip polarized light-emitters based on (6,5) chirality-sorted carbon nanotube aligned arrays obtained via an evaporation-induced self-assembly method. Electroluminescence results shows an impact excitation dominant mechanism originated from (6,5) defect-brightened dark exciton emission and trion emission. The degree of polarization of the carbon nanotube aligned arrays is characterized quantitatively and the average value is ˜76.8%. The importance of parallelism and orientation of nanotubes when integrated with on-chip waveguides is also discussed.

  9. Local Alignment Tool Based on Hadoop Framework and GPU Architecture

    PubMed Central

    Hung, Che-Lun; Hua, Guan-Jie

    2014-01-01

    With the rapid growth of next generation sequencing technologies, such as Slex, more and more data have been discovered and published. To analyze such huge data the computational performance is an important issue. Recently, many tools, such as SOAP, have been implemented on Hadoop and GPU parallel computing architectures. BLASTP is an important tool, implemented on GPU architectures, for biologists to compare protein sequences. To deal with the big biology data, it is hard to rely on single GPU. Therefore, we implement a distributed BLASTP by combining Hadoop and multi-GPUs. The experimental results present that the proposed method can improve the performance of BLASTP on single GPU, and also it can achieve high availability and fault tolerance. PMID:24955362

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

    PubMed

    Hung, Che-Lun; Hua, Guan-Jie

    2014-01-01

    With the rapid growth of next generation sequencing technologies, such as Slex, more and more data have been discovered and published. To analyze such huge data the computational performance is an important issue. Recently, many tools, such as SOAP, have been implemented on Hadoop and GPU parallel computing architectures. BLASTP is an important tool, implemented on GPU architectures, for biologists to compare protein sequences. To deal with the big biology data, it is hard to rely on single GPU. Therefore, we implement a distributed BLASTP by combining Hadoop and multi-GPUs. The experimental results present that the proposed method can improve the performance of BLASTP on single GPU, and also it can achieve high availability and fault tolerance. PMID:24955362

  11. WFST-based ground truth alignment for difficult historical documents with text modification and layout variations

    NASA Astrophysics Data System (ADS)

    Al Azawi, Mayce; Liwicki, Marcus; Breuel, Thomas M.

    2013-01-01

    This work proposes several approaches that can be used for generating correspondences between real scanned books and their transcriptions which might have different modifications and layout variations, also taking OCR errors into account. Our approaches for the alignment between the manuscript and the transcription are based on weighted finite state transducers (WFST). In particular, we propose adapted WFSTs to represent the transcription to be aligned with the OCR lattices. The character-level alignment has edit rules to allow edit operations (insertion, deletion, substitution). Those edit operations allow the transcription model to deal with OCR segmentation and recognition errors, and also with the task of aligning with different text editions. We implemented an alignment model with a hyphenation model, so it can adapt the non-hyphenated transcription. Our models also work with Fraktur ligatures, which are typically found in historical Fraktur documents. We evaluated our approach on Fraktur documents from Wanderungen durch die Mark Brandenburg" volumes (1862-1889) and observed the performance of those models under OCR errors. We compare the performance of our model for three different scenarios: having no information about the correspondence at the word (i), line (ii), sentence (iii) or page (iv) level.

  12. Alternative Assessment Practices of a Classroom Teacher: Alignment with Reform-Based Science Curriculum

    ERIC Educational Resources Information Center

    Serin, Gökhan

    2015-01-01

    The purpose of this study was to explore alignment between reform-based Turkish primary science curriculum and alternative assessment practices of a classroom teacher. Observational case study approach was utilized. A classroom teacher with 32 years of experience and his 31 students participated in the study. The data were collected during one…

  13. Efficient alignment scheme for zone-plates-based transmission soft X-ray microscope

    NASA Astrophysics Data System (ADS)

    Lim, Jun; Shin, Hyun-Joon; Hong, Chung Ki

    2010-12-01

    Alignment and operation of a zone-plate (ZP)-based transmission soft X-ray microscope (TXM) is difficult and time consuming, especially when the TXM has no dedicated X-ray source. We introduce here an efficient TXM alignment scheme. The TXM employed is a simple in-situ-experiment-capable setup. It includes ultrahigh-vacuum (UHV)-compatible conflat flanges and is mountable in tandem with any soft X-ray synchrotron radiation beamlines. Obtaining zeroth- and first-order diffracted (condenser-zone-plate [CZP]-focused) beams simultaneously by means of the objective zone plate (OZP) is the most essential step in the alignment scheme. We were able to acquire, in one hour at a radiation wavelength of 2.49 nm, an image of 50 nm spatial resolution.

  14. Method of alignment error control in free-form surface metrology with the tilted-wave-interferometer

    NASA Astrophysics Data System (ADS)

    Li, Jia; Shen, Hua; Zhu, Rihong

    2016-04-01

    Compared with conventional optical elements, free-form surface optical elements, as a kind of nonrotationally symmetrical shaped component, can provide more freedom in optical design, optimize the structure of the optical system, and improve its performance. However, the difficulties involved in the measurement of free-form elements restrict their manufacture and application. A tilted-wave-interferometer (TWI) can achieve high precision in free-form surface measurement, but it requires higher space attitude error control. We analyze the relation between the alignment error and the measurement error introduced by the misalignment in free-form surface metrology with TWI. The attitude control method in the rotation direction is proposed based on the moire fringe technique. Then, combining it with the five-dimensional space attitude control method of aspherical elements, we put forward an alignment error control process in measuring the free-form surface. An experiment of measuring a free-form surface using TWI shows the effectiveness of our method.

  15. Alignment nature of ZnO nanowires grown on polished and nanoscale etched lithium niobate surface through self-seeding thermal evaporation method

    SciTech Connect

    Mohanan, Ajay Achath; Parthiban, R.; Ramakrishnan, N.

    2015-08-15

    Highlights: • ZnO nanowires were grown directly on LiNbO{sub 3} surface for the first time by thermal evaporation. • Self-alignment of the nanowires due to step bunching of LiNbO{sub 3} surface is observed. • Increased roughness in surface defects promoted well-aligned growth of nanowires. • Well-aligned growth was then replicated in 50 nm deep trenches on the surface. • Study opens novel pathway for patterned growth of ZnO nanowires on LiNbO{sub 3} surface. - Abstract: High aspect ratio catalyst-free ZnO nanowires were directly synthesized on lithium niobate substrate for the first time through thermal evaporation method without the use of a buffer layer or the conventional pre-deposited ZnO seed layer. As-grown ZnO nanowires exhibited a crisscross aligned growth pattern due to step bunching of the polished lithium niobate surface during the nanowire growth process. On the contrary, scratches on the surface and edges of the substrate produced well-aligned ZnO nanowires in these defect regions due to high surface roughness. Thus, the crisscross aligned nature of high aspect ratio nanowire growth on the lithium niobate surface can be changed to well-aligned growth through controlled etching of the surface, which is further verified through reactive-ion etching of lithium niobate. The investigations and discussion in the present work will provide novel pathway for self-seeded patterned growth of well-aligned ZnO nanowires on lithium niobate based micro devices.

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

    PubMed Central

    Cárdenas-Peña, David; Collazos-Huertas, Diego; Castellanos-Dominguez, German

    2016-01-01

    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. PMID:27148392

  17. Physician-Hospital Alignment in Orthopedic Surgery.

    PubMed

    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. PMID:26375539

  18. Use of Monte Carlo Methods for Evaluating Probability of False Positives in Archaeoastronomy Alignments

    NASA Astrophysics Data System (ADS)

    Hull, Anthony B.; Ambruster, C.; Jewell, E.

    2012-01-01

    Simple Monte Carlo simulations can assist both the cultural astronomy researcher while the Research Design is developed and the eventual evaluators of research products. Following the method we describe allows assessment of the probability for there to be false positives associated with a site. Even seemingly evocative alignments may be meaningless, depending on the site characteristics and the number of degrees of freedom the researcher allows. In many cases, an observer may have to limit comments to "it is nice and it might be culturally meaningful, rather than saying "it is impressive so it must mean something". We describe a basic language with an associated set of attributes to be cataloged. These can be used to set up simple Monte Carlo simulations for a site. Without collaborating cultural evidence, or trends with similar attributes (for example a number of sites showing the same anticipatory date), the Monte Carlo simulation can be used as a filter to establish the likeliness that the observed alignment phenomena is the result of random factors. Such analysis may temper any eagerness to prematurely attribute cultural meaning to an observation. For the most complete description of an archaeological site, we urge researchers to capture the site attributes in a manner which permits statistical analysis. We also encourage cultural astronomers to record that which does not work, and that which may seem to align, but has no discernable meaning. Properly reporting situational information as tenets of the research design will reduce the subjective nature of archaeoastronomical interpretation. Examples from field work will be discussed.

  19. A rapid topographic mapping and eye alignment method using optical imaging in Macaque visual cortex

    PubMed Central

    HD, Lu; G, Chen; DY, Ts’o; AW, Roe

    2009-01-01

    In optical imaging experiments, it is often advantageous to map the field of view and to converge the eyes without electrophysiological recording. This occurs when limited space precludes placement of an electrode or in chronic optical chambers in which one may not want to introduce an electrode each session or for determining eye position in studies of ocular disparity response in visual cortex of anesthetized animals. For these purposes, we have developed a spot imaging method that can be conducted rapidly and repeatedly throughout an experiment. Using small 0.2° – 0.5° spots, the extent of the imaged field of view is mapped by imaging cortical response to single spots, placed at different positions (0.2° steps) in either the horizontal or vertical axes. By shifting the relative positions of two spots, one presented to each eye, eye convergence can be assessed to within 0.1° resolution. Once appropriate eye alignment is determined, stimuli for further optical imaging procedures (e.g. imaging random dot stimuli for study of disparity responses) can then be confidently placed. This procedure can be quickly repeated throughout the experiment to ensure maintained eye alignment. PMID:19013530

  20. Computerized tomography based “patient specific blocks” improve postoperative mechanical alignment in primary total knee arthroplasty

    PubMed Central

    Vaishya, Raju; Vijay, Vipul; Birla, Vikas P; Agarwal, Amit K

    2016-01-01

    AIM: To compare the postoperative mechanical alignment achieved after total knee arthroplasty (TKA) using computer tomography (CT) based patient specific blocks (PSB) to conventional instruments (CI). METHODS: Total 80 knees were included in the study, with 40 knees in both the groups operated using PSB and CI. All the knees were performed by a single surgeon using the same cruciate sacrificing implants. In our study we used CT based PSB to compare with CI. Postoperative mechanical femoro-tibial angle (MFT angle) was measured on long leg x-rays using picture archiving and communication system (PACS). We compared mechanical alignment achieved using PSB and CI in TKA using statistical analysis. RESULTS: The PSB group (group 1) included 17 females and seven males while in CI group (group 2) there were 15 females and eight males. The mean age of patients in group 1 was 60.5 years and in group 2 it was 60.2 years. The mean postoperative MFT angle measured on long-leg radiographs in group 1 was 178.23° (SD = 2.67°, range: 171.9° to 182.5°) while in group 2, the mean MFT angle was 175.73° (SD = 3.62°, range: 166.0° to 179.8°). There was significant improvement in postoperative mechanical alignment (P value = 0.001), in PSB group compared to CI. Number of outliers were also found to be less in group operated with PSB (7 Knee) compared to those operated with CI (17 Knee). CONCLUSION: PSB improve mechanical alignment after total knee arthroplasty, compared to CI. This may lead to lower rates of revision in the PSB based TKA as compared to the conventional instrumentation. PMID:27458553

  1. ATP Bioluminometers Analysis on the Surfaces of Removable Orthodontic Aligners after the Use of Different Cleaning Methods

    PubMed Central

    Levrini, Luca; Mangano, Alessandro; Margherini, Silvia; Tenconi, Camilla; Vigetti, Davide; Muollo, Raffaele; Marco Abbate, Gian

    2016-01-01

    Purpose. The aim was to quantify the bacteria concentration on the surface of orthodontic clear aligners using three different cleaning methods. Furthermore the objective was to validate the efficacy of the bioluminometer in assessing the bacteria concentration. Materials and Methods. Twenty subjects (six males and fourteen females) undergoing orthodontic therapy with clear aligners (Invisalign® Align Technology, Santa Clara, California) were enrolled in this study. The observation time was of six weeks. The patients were instructed to use different cleaning methods (water, brushing with toothpaste, and brushing with toothpaste and use of sodium carbonate and sulphate tablet). At the end of each phase a microbiological analysis was performed using the bioluminometer. Results. The highest bacteria concentration was found on aligners cleaned using only water (583 relative light units); a value of 189 relative light units was found on aligners cleaned with brushing and toothpaste. The lowest bacteria concentration was recorded on aligners cleaned with brushing and toothpaste and the use of sodium carbonate and sulfate tablet. Conclusions. The mechanical removal of the bacterial biofilm proved to be effective with brushing and toothpaste. The best results in terms of bacteria concentration were achieved adding the use of sodium carbonate and sulfate tablet. PMID:27242901

  2. Semiautomated improvement of RNA alignments

    PubMed Central

    Andersen, Ebbe S.; Lind-Thomsen, Allan; Knudsen, Bjarne; Kristensen, Susie E.; Havgaard, Jakob H.; Torarinsson, Elfar; Larsen, Niels; Zwieb, Christian; Sestoft, Peter; Kjems, Jørgen; Gorodkin, Jan

    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: the mir-399 RNA, vertebrate telomase RNA (vert-TR), bacterial transfer-messenger RNA (tmRNA), and the signal recognition particle (SRP) RNA. The general use of the method is illustrated by the ability to accommodate pseudoknots and handle even large and divergent RNA families. The open architecture of the SARSE editor makes it a flexible tool to improve all RNA alignments with relatively little human intervention. Online documentation and software are available at http://sarse.ku.dk. PMID:17804647

  3. An Alignment Method for the Integration of Underwater 3D Data Captured by a Stereovision System and an Acoustic Camera

    PubMed Central

    Lagudi, Antonio; Bianco, Gianfranco; Muzzupappa, Maurizio; Bruno, Fabio

    2016-01-01

    The integration of underwater 3D data captured by acoustic and optical systems is a promising technique in various applications such as mapping or vehicle navigation. It allows for compensating the drawbacks of the low resolution of acoustic sensors and the limitations of optical sensors in bad visibility conditions. Aligning these data is a challenging problem, as it is hard to make a point-to-point correspondence. This paper presents a multi-sensor registration for the automatic integration of 3D data acquired from a stereovision system and a 3D acoustic camera in close-range acquisition. An appropriate rig has been used in the laboratory tests to determine the relative position between the two sensor frames. The experimental results show that our alignment approach, based on the acquisition of a rig in several poses, can be adopted to estimate the rigid transformation between the two heterogeneous sensors. A first estimation of the unknown geometric transformation is obtained by a registration of the two 3D point clouds, but it ends up to be strongly affected by noise and data dispersion. A robust and optimal estimation is obtained by a statistical processing of the transformations computed for each pose. The effectiveness of the method has been demonstrated in this first experimentation of the proposed 3D opto-acoustic camera. PMID:27089344

  4. An Alignment Method for the Integration of Underwater 3D Data Captured by a Stereovision System and an Acoustic Camera.

    PubMed

    Lagudi, Antonio; Bianco, Gianfranco; Muzzupappa, Maurizio; Bruno, Fabio

    2016-01-01

    The integration of underwater 3D data captured by acoustic and optical systems is a promising technique in various applications such as mapping or vehicle navigation. It allows for compensating the drawbacks of the low resolution of acoustic sensors and the limitations of optical sensors in bad visibility conditions. Aligning these data is a challenging problem, as it is hard to make a point-to-point correspondence. This paper presents a multi-sensor registration for the automatic integration of 3D data acquired from a stereovision system and a 3D acoustic camera in close-range acquisition. An appropriate rig has been used in the laboratory tests to determine the relative position between the two sensor frames. The experimental results show that our alignment approach, based on the acquisition of a rig in several poses, can be adopted to estimate the rigid transformation between the two heterogeneous sensors. A first estimation of the unknown geometric transformation is obtained by a registration of the two 3D point clouds, but it ends up to be strongly affected by noise and data dispersion. A robust and optimal estimation is obtained by a statistical processing of the transformations computed for each pose. The effectiveness of the method has been demonstrated in this first experimentation of the proposed 3D opto-acoustic camera. PMID:27089344

  5. Longitudinal graph-based segmentation of macular OCT using fundus alignment

    NASA Astrophysics Data System (ADS)

    Lang, Andrew; Carass, Aaron; Al-Louzi, Omar; Bhargava, Pavan; Ying, Howard S.; Calabresi, Peter A.; Prince, Jerry L.

    2015-03-01

    Segmentation of retinal layers in optical coherence tomography (OCT) has become an important diagnostic tool for a variety of ocular and neurological diseases. Currently all OCT segmentation algorithms analyze data independently, ignoring previous scans, which can lead to spurious measurements due to algorithm variability and failure to identify subtle changes in retinal layers. In this paper, we present a graph-based segmentation framework to provide consistent longitudinal segmentation results. Regularization over time is accomplished by adding weighted edges between corresponding voxels at each visit. We align the scans to a common subject space before connecting the graphs by registering the data using both the retinal vasculature and retinal thickness generated from a low resolution segmentation. This initial segmentation also allows the higher dimensional temporal problem to be solved more efficiently by reducing the graph size. Validation is performed on longitudinal data from 24 subjects, where we explore the variability between our longitudinal graph method and a cross-sectional graph approach. Our results demonstrate that the longitudinal component improves segmentation consistency, particularly in areas where the boundaries are difficult to visualize due to poor scan quality.

  6. Radial liquid crystal alignment based on circular rubbing of a substrate coated with poly(N-vinyl carbazole) film

    NASA Astrophysics Data System (ADS)

    Chen, Yuan-Di; Ying-Guey Fuh, Andy; Liu, Cheng-Kai; Cheng, Ko-Ting

    2011-06-01

    This paper presents a simple method to produce radial liquid crystal (LC) alignment layers using circular rubbing of poly(N-vinyl carbazole) (PVK) films. The produced layer can be used for fabricating axially symmetric homogeneous-radial, homeotropic-radial and radial-radial LC alignment devices by combining a rubbed PVK-coated substrate with another one with a desired LC alignment layer. The transmittance-voltage curves of the fabricated LC devices at various positions are measured to examine the uniformity of the alignment effect. Additionally, the PVK film does not absorb visible light, and can be operated at high temperatures.

  7. System and method for aligning heliostats of a solar power tower

    DOEpatents

    Convery, Mark R.

    2013-01-01

    Disclosed is a solar power tower heliostat alignment system and method that includes a solar power tower with a focal area, a plurality of heliostats that each reflect sunlight towards the focal area of the solar power tower, an off-focal area location substantially close to the focal area of the solar power tower, a communication link between the off-focal area location and a misaligned heliostat, and a processor that interprets the communication between the off-focal area location and the misaligned heliostat to identify the misaligned heliostat from the plurality of heliostats and that determines a correction for the identified misaligned heliostat to realign the misaligned heliostat to reflect sunlight towards the focal area of the solar power tower.

  8. Injection method of barrier bucket supported by off-aligned electron cooling for CRing of HIAF

    NASA Astrophysics Data System (ADS)

    Shen, Guo-Dong; Yang, Jian-Cheng; Xia, Jia-Wen; Mao, Li-Jun; Yin, Da-Yu; Chai, Wei-Ping; Shi, Jian; Sheng, Li-Na; Smirnov, A.; Wu, Bo; Zhao, He

    2016-08-01

    A new accelerator complex, HIAF (the High Intensity Heavy Ion Accelerator Facility), has been approved in China. It is designed to provide intense primary and radioactive ion beams for research in high energy density physics, nuclear physics, atomic physics as well as other applications. In order to achieve a high intensity of up to 5×1011 ppp 238U34+, the Compression Ring (CRing) needs to stack more than 5 bunches transferred from the Booster Ring (BRing). However, the normal bucket to bucket injection scheme can only achieve an intensity gain of 2, so an injection method, fixed barrier bucket (BB) supported by electron cooling, is proposed. To suppress the severe space charge effect during the stacking process, off-alignment is adopted in the cooler to control the transverse emittance. In this paper, simulation and optimization with the BETACOOL program are presented. Supported by New Interdisciplinary and Advanced Pilot Fund of Chinese Academy of Sciences

  9. Transducer-actuator systems and methods for performing on-machine measurements and automatic part alignment

    DOEpatents

    Barkman, William E.; Dow, Thomas A.; Garrard, Kenneth P.; Marston, Zachary

    2016-07-12

    Systems and methods for performing on-machine measurements and automatic part alignment, including: a measurement component operable for determining the position of a part on a machine; and an actuation component operable for adjusting the position of the part by contacting the part with a predetermined force responsive to the determined position of the part. The measurement component consists of a transducer. The actuation component consists of a linear actuator. Optionally, the measurement component and the actuation component consist of a single linear actuator operable for contacting the part with a first lighter force for determining the position of the part and with a second harder force for adjusting the position of the part. The actuation component is utilized in a substantially horizontal configuration and the effects of gravitational drop of the part are accounted for in the force applied and the timing of the contact.

  10. A Novel Synthesis Method for Aligned Carbon Nanotubes in Organic Liquids

    NASA Astrophysics Data System (ADS)

    Zhang, Yafei; Nishitani-Gamo, Mikka; Xiao, Changyong; Ando, Toshihiro

    2002-04-01

    Aligned carbon nanotube arrays have been grown on Si substrates in methanol by using a hot-substrate method. Samples were grown in a glass chamber equipped with a function in which methanol and ethanol vapors were condensed by means of water-cooling. Si substrates with a thin Fe film were electrically heated to 930°C in liquid methanol. Hollow mutiwalled carbon nanotubes standing well on the Si substrates were obtained with external diameters ranging from 13 to 26 nm and lengths up to 20 μm, with the ratio of tube radius to the thickness of tube shells ranging from 1.7 to 2.1. The top ends of the nanotubes were closed with nearly seamless caps. The mechanism of nanotube growth is a catalytic process at the substrate surface under thermal non-equilibrium.

  11. Energy-based RNA consensus secondary structure prediction in multiple sequence alignments.

    PubMed

    Washietl, Stefan; Bernhart, Stephan H; Kellis, Manolis

    2014-01-01

    Many biologically important RNA structures are conserved in evolution leading to characteristic mutational patterns. RNAalifold is a widely used program to predict consensus secondary structures in multiple alignments by combining evolutionary information with traditional energy-based RNA folding algorithms. Here we describe the theory and applications of the RNAalifold algorithm. Consensus secondary structure prediction not only leads to significantly more accurate structure models, but it also allows to study structural conservation of functional RNAs. PMID:24639158

  12. Aligning brains and minds

    PubMed Central

    Tong, Frank

    2012-01-01

    In this issue of Neuron, Haxby and colleagues describe a new method for aligning functional brain activity patterns across participants. Their study demonstrates that objects are similarly represented across different brains, allowing for reliable classification of one person’s brain activity based on another’s. PMID:22017984

  13. Multiscale peak alignment for chromatographic datasets.

    PubMed

    Zhang, Zhi-Min; Liang, Yi-Zeng; Lu, Hong-Mei; Tan, Bin-Bin; Xu, Xiao-Na; Ferro, Miguel

    2012-02-01

    Chromatography has been extensively applied in many fields, such as metabolomics and quality control of herbal medicines. Preprocessing, especially peak alignment, is a time-consuming task prior to the extraction of useful information from the datasets by chemometrics and statistics. To accurately and rapidly align shift peaks among one-dimensional chromatograms, multiscale peak alignment (MSPA) is presented in this research. Peaks of each chromatogram were detected based on continuous wavelet transform (CWT) and aligned against a reference chromatogram from large to small scale gradually, and the aligning procedure is accelerated by fast Fourier transform cross correlation. The presented method was compared with two widely used alignment methods on chromatographic dataset, which demonstrates that MSPA can preserve the shapes of peaks and has an excellent speed during alignment. Furthermore, MSPA method is robust and not sensitive to noise and baseline. MSPA was implemented and is available at http://code.google.com/p/mspa. PMID:22222564

  14. Method and apparatus for ion mobility spectrometry with alignment of dipole direction (IMS-ADD)

    DOEpatents

    Shvartsburg, Alexandre A.; Tang, Keqi; Smith, Richard D.

    2007-01-30

    Techniques and instrumentation are described for analyses of substances, including complex samples/mixtures that require separation prior to characterization of individual components. A method is disclosed for separation of ion mixtures and identification of ions, including protein and other macromolecular ions and their different structural isomers. Analyte ions are not free to rotate during the separation, but are substantially oriented with respect to the drift direction. Alignment is achieved by applying, at a particular angle to the drift field, a much stronger alternating electric field that "locks" the ion dipoles with moments exceeding a certain value. That value depends on the buffer gas composition, pressure, and temperature, but may be as low as .about.3 Debye under certain conditions. The presently disclosed method measures the direction-specific cross-sections that provide the structural information complementing that obtained from known methods, and, when coupled to those methods, increases the total peak capacity and specificity of gas-phase separations. Simultaneous 2-D separations by direction-specific cross sections along and orthogonally to the ion dipole direction are also possible.

  15. Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method

    PubMed Central

    Burger, Lukas; van Nimwegen, Erik

    2008-01-01

    Accurate and large-scale prediction of protein–protein interactions directly from amino-acid sequences is one of the great challenges in computational biology. Here we present a new Bayesian network method that predicts interaction partners using only multiple alignments of amino-acid sequences of interacting protein domains, without tunable parameters, and without the need for any training examples. We first apply the method to bacterial two-component systems and comprehensively reconstruct two-component signaling networks across all sequenced bacteria. Comparisons of our predictions with known interactions show that our method infers interaction partners genome-wide with high accuracy. To demonstrate the general applicability of our method we show that it also accurately predicts interaction partners in a recent dataset of polyketide synthases. Analysis of the predicted genome-wide two-component signaling networks shows that cognates (interacting kinase/regulator pairs, which lie adjacent on the genome) and orphans (which lie isolated) form two relatively independent components of the signaling network in each genome. In addition, while most genes are predicted to have only a small number of interaction partners, we find that 10% of orphans form a separate class of ‘hub' nodes that distribute and integrate signals to and from up to tens of different interaction partners. PMID:18277381

  16. Alignment and integration of large optical systems based on advanced metrology.

    NASA Astrophysics Data System (ADS)

    Aliverti, M.; Riva, M.; Moschetti, M.; Pariani, G.; Genoni, M.; Zerbi, F. M.

    Optical alignment is a key activity in opto-mechanical system Integration. Traditional techniques require adjustable mounting, driven by optical references that allows the tuning of the optics position along all 6 Degree of Freedom. Nevertheless, the required flexibility imposes reduced stiffness and consequently less stability of the system. The Observatory of Brera (OAB) started few years ago a research activity focused onto the overcoming of this limits exploiting the high metrology performances of Coordinate Measuring Machines (CMM) with the main objectives of relax the manufacturing tolerances and maximize mounting stiffness. Through the T-REX grants, OAB acquired all the instrumentation needed for that activity furthermore considering the ESPRESSO project training and testing also oriented to large scale instrumentation like the E-ELT one. We will present in this paper the definition of the VLTs convergence point and the feasibility study of large mirrors alignment done by mechanical measurements methods. skip=8pt

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

    PubMed

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

    2016-01-01

    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. PMID:27420977

  18. A Semi-Automatic Alignment Method for Math Educational Standards Using the MP (Materialization Pattern) Model

    ERIC Educational Resources Information Center

    Choi, Namyoun

    2010-01-01

    Educational standards alignment, which matches similar or equivalent concepts of educational standards, is a necessary task for educational resource discovery and retrieval. Automated or semi-automated alignment systems for educational standards have been recently available. However, existing systems frequently result in inconsistency in…

  19. Numerical Analysis of Tip Cavitation on Marine Propeller with Wake Alignment Using a Simple Surface Panel Method “SQCM”

    NASA Astrophysics Data System (ADS)

    Kanemaru, T.; Ando, J.

    2015-12-01

    This paper presents the calculation method of tip cavitation with wake alignment. Tip cavitation consists of tip vortex cavitation and tip super cavitation which means the undeveloped and local super cavitation around blade tip. The feature of this study is that the method applies the wake alignment model in order to express the realistic phenomena of tip cavitation and predict the pressure fluctuation more accurately. In the present method, the wake sheet is deformed according to the induced velocity vector on the vortex lines. The singularity of the potential vortex can be removed by using the Rankine Vortex model. This paper shows the calculated results regarding cavitation pattern, pressure fluctuation etc. comparing with published experimental data and calculated results without wake alignment.

  20. Method to determine and adjust the alignment of the transmitter and receiver fields of view of a LIDAR system

    DOEpatents

    Schmitt, Randal L.; Henson, Tammy D.; Krumel, Leslie J.; Hargis, Jr., Philip J.

    2006-06-20

    A method to determine the alignment of the transmitter and receiver fields of view of a light detection and ranging (LIDAR) system. This method can be employed to determine the far-field intensity distribution of the transmitter beam, as well as the variations in transmitted laser beam pointing as a function of time, temperature, or other environmental variables that may affect the co-alignment of the LIDAR system components. In order to achieve proper alignment of the transmitter and receiver optical systems when a LIDAR system is being used in the field, this method employs a laser-beam-position-sensing detector as an integral part of the receiver optics of the LIDAR system.

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

    PubMed

    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. PMID:23929504

  2. Wet etch methods for InAs nanowire patterning and self-aligned electrical contacts

    NASA Astrophysics Data System (ADS)

    Fülöp, G.; d’Hollosy, S.; Hofstetter, L.; Baumgartner, A.; Nygård, J.; Schönenberger, C.; Csonka, S.

    2016-05-01

    Advanced synthesis of semiconductor nanowires (NWs) enables their application in diverse fields, notably in chemical and electrical sensing, photovoltaics, or quantum electronic devices. In particular, indium arsenide (InAs) NWs are an ideal platform for quantum devices, e.g. they may host topological Majorana states. While the synthesis has been continously perfected, only a few techniques have been developed to tailor individual NWs after growth. Here we present three wet chemical etch methods for the post-growth morphological engineering of InAs NWs on the sub-100 nm scale. The first two methods allow the formation of self-aligned electrical contacts to etched NWs, while the third method results in conical shaped NW profiles ideal for creating smooth electrical potential gradients and shallow barriers. Low temperature experiments show that NWs with etched segments have stable transport characteristics and can serve as building blocks of quantum electronic devices. As an example we report the formation of a single electrically stable quantum dot between two etched NW segments.

  3. Wet etch methods for InAs nanowire patterning and self-aligned electrical contacts.

    PubMed

    Fülöp, G; d'Hollosy, S; Hofstetter, L; Baumgartner, A; Nygård, J; Schönenberger, C; Csonka, S

    2016-05-13

    Advanced synthesis of semiconductor nanowires (NWs) enables their application in diverse fields, notably in chemical and electrical sensing, photovoltaics, or quantum electronic devices. In particular, indium arsenide (InAs) NWs are an ideal platform for quantum devices, e.g. they may host topological Majorana states. While the synthesis has been continously perfected, only a few techniques have been developed to tailor individual NWs after growth. Here we present three wet chemical etch methods for the post-growth morphological engineering of InAs NWs on the sub-100 nm scale. The first two methods allow the formation of self-aligned electrical contacts to etched NWs, while the third method results in conical shaped NW profiles ideal for creating smooth electrical potential gradients and shallow barriers. Low temperature experiments show that NWs with etched segments have stable transport characteristics and can serve as building blocks of quantum electronic devices. As an example we report the formation of a single electrically stable quantum dot between two etched NW segments. PMID:27040175

  4. Alignment fixture

    DOEpatents

    Bell, Grover C.; Gibson, O. Theodore

    1980-01-01

    A part alignment fixture is provided which may be used for precise variable lateral and tilt alignment relative to the fixture base of various shaped parts. The fixture may be used as a part holder for machining or inspection of parts or alignment of parts during assembly and the like. The fixture includes a precisely machined diameter disc-shaped hub adapted to receive the part to be aligned. The hub is nested in a guide plate which is adapted to carry two oppositely disposed pairs of positioning wedges so that the wedges may be reciprocatively positioned by means of respective micrometer screws. The sloping faces of the wedges contact the hub at respective quadrants of the hub periphery. The lateral position of the hub relative to the guide plate is adjusted by positioning the wedges with the associated micrometer screws. The tilt of the part is adjusted relative to a base plate, to which the guide plate is pivotally connected by means of a holding plate. Two pairs of oppositely disposed wedges are mounted for reciprocative lateral positioning by means of separate micrometer screws between flanges of the guide plate and the base plate. Once the wedges are positioned to achieve the proper tilt of the part or hub on which the part is mounted relative to the base plate, the fixture may be bolted to a machining, inspection, or assembly device.

  5. Beam-based alignment technique for the SLC (Stanford Linear Collider) linac

    SciTech Connect

    Adolphsen, C.E.; Lavine, T.L.; Atwood, W.B.; Himel, T.M.; Lee, M.J.; Mattison, T.S.; Pitthan, R.; Seeman, J.T.; Williams, S.H.; Trilling, G.H.

    1989-03-01

    Misalignment of quadrupole magnets and beam position monitors (BPMs) in the linac of the SLAC Linear Collider (SLC) cause the electron and positron beams to be steered off-center in the disk-loaded waveguide accelerator structures. Off-center beams produce wakefields which limit the SLC performance at high beam intensities by causing emittance growth. Here, we present a general method for simultaneously determining quadrupole magnet and BPM offsets using beam trajectory measurements. Results from the application of the method to the SLC linac are described. The alignment precision achieved is approximately 100 ..mu..m, which is significantly better than that obtained using optical surveying techniques. 2 refs., 4 figs.

  6. Metallic filament formation by aligned oxygen vacancies in ZnO-based resistive switches

    SciTech Connect

    Gu, Tingkun

    2014-05-28

    The electronic structure of ZnO with defects of oxygen vacancies were investigated by using first-principles methods. Some structure models were constructed in order to investigate the effects of the distribution of oxygen vacancies on the electronic properties of ZnO. By analyzing the calculated results, we found that only the aligned oxygen vacancies can form the conducting channel in ZnO, and the transformation of the oxygen vacancy from charged state to neutral state is consistent with the energetics rule of the forming aligned oxygen vacancies. As for the heterojunction of Pt/ZnO/Pt, the oxygen vacancies near the interface of Pt/ZnO depress the local Schottky barrier effectively, and the aligned oxygen vacancies in ZnO form a conducting filament connecting two Pt electrodes. The metallic filament formation in Pt/ZnO/Pt resistive switching cells should be closely related to the carrier injection from Pt electrode into ZnO and the arrangement of oxygen vacancies in ZnO slab.

  7. Metallic filament formation by aligned oxygen vacancies in ZnO-based resistive switches

    NASA Astrophysics Data System (ADS)

    Gu, Tingkun

    2014-05-01

    The electronic structure of ZnO with defects of oxygen vacancies were investigated by using first-principles methods. Some structure models were constructed in order to investigate the effects of the distribution of oxygen vacancies on the electronic properties of ZnO. By analyzing the calculated results, we found that only the aligned oxygen vacancies can form the conducting channel in ZnO, and the transformation of the oxygen vacancy from charged state to neutral state is consistent with the energetics rule of the forming aligned oxygen vacancies. As for the heterojunction of Pt/ZnO/Pt, the oxygen vacancies near the interface of Pt/ZnO depress the local Schottky barrier effectively, and the aligned oxygen vacancies in ZnO form a conducting filament connecting two Pt electrodes. The metallic filament formation in Pt/ZnO/Pt resistive switching cells should be closely related to the carrier injection from Pt electrode into ZnO and the arrangement of oxygen vacancies in ZnO slab.

  8. Imaging geological contact utilizing 2D resistivity method for light rail transit (LRT) track alignment

    NASA Astrophysics Data System (ADS)

    Ali, Nisa'; Saad, Rosli; Muztaza, Nordiana M.; Ismail, Noer E. H.

    2013-05-01

    The purpose of this study was to locate the geological contact using 2D resistivity method for Light Rail Transit (LRT) track alignment. The resistivity method was conducted on eight survey lines with the length of line 1 was 600m. The length of line 2, 3, 4, 5, 6, and 7 were 200m each while line 8 is 115m. All the survey used minimum electrode spacing of 5m and using Pole-dipole array with minimum current is 2mA and maximum was 20mA. The result obtained from the pseudosection showed that the area generally divided into three main zones, fill materials/residual soil with a resistivity value of <500 Ωm, saturated zone with a resistivity value of 30-100 Ωm and bedrock with a resistivity value of >2000 Ωm. Three fractured zones were detected along line L1 and a lot of boulders were detected at L1, L3, L4, L5 and L6. The geological contact was between the residual soil and granite bedrock.

  9. Single-mode array optoelectronic packaging based on actively aligned planar optical waveguides

    NASA Astrophysics Data System (ADS)

    Kalman, Robert F.; Silva, Edward R.; Knapp, Daniel F.

    1996-03-01

    Packaging of integrated optoelectronic devices (e.g., laser diode arrays and OEICs) is motivated by potential cost savings and the increased functionality of more highly integrated devices. To date, attempts to package integrated optoelectronic devices with arrays of single- mode fibers have tended to exhibit high optical losses. We have developed a single-mode array packaging process based on the use of an intermediate silica-on-silicon planar optical waveguides (POWs) assembly to which optical fibers are attached using V-grooves. By lensing the POWs, we have achieved coupling efficiencies of greater than 50%. The photolithographic registration of the POWs allows a large (greater than or equal to 8) array of POWs with attached fibers to be aligned to an array of optoelectronic devices in a single active alignment procedure. This single active alignment step is well-suited to automation, and our approach is thus well-suited to achieving low cost in a manufacturing environment. We also discuss our positioning and mounting techniques, which provide high-stability coupling in adverse temperature and vibration environments and are compatible with hermetic packaging.

  10. Computerized "drag-and-drop" alignment of GPC-based optical micromanipulation system.

    PubMed

    Dam, Jeppe Seidelin; Rodrigo, Peter John; Perch-Nielsen, Ivan R; Alonzo, Carlo Amadeo; Glückstad, Jesper

    2007-02-19

    In the past, aligning the counterpropagating beams in our 3D real-time generalized phase contrast (GPC) trapping system has been a task requiring moderate skills and prior experience with optical instrumentation. A ray transfer matrix analysis and computer-controlled actuation of mirrors, objective, and sample stage has made this process user friendly. The alignment procedure can now be done in a very short time with just a few drag-and-drop tasks in the user-interface. The future inclusion of an image recognition algorithm will allow the alignment process to be executed completely without any user interaction. An automated sample loading tray with a loading precision of a few microns has also been added to simplify the switching of samples under study. These enhancements have significantly reduced the level of skill and experience required to operate the system, thus making the GPC-based micromanipulation system more accessible to people with little or no technical expertise in optics. PMID:19532431

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

    SciTech Connect

    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.

  12. Detection and Alignment of 3D Domain Swapping Proteins Using Angle-Distance Image-Based Secondary Structural Matching Techniques

    PubMed Central

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

    2010-01-01

    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

  13. Method for making alignment-enhancing feed-through conductors for stackable silicon-on-sapphire

    NASA Technical Reports Server (NTRS)

    Anthony, Thomas R. (Inventor)

    1985-01-01

    Alignment-enhancing electrically conductive feed-through paths are provided for the high-speed low-loss transfer of electrical signals between integrated circuits of a plurality of silicon-on-sapphire bodies arrayed in a stack. The alignment-enhancing feed-throughs are made by a process of this invention involving the drilling of holes through the body, double-sided sputtering, electroplating, and the filling of the holes with solder by capillary action. The alignment-enhancing feed-throughs are activated by forming a stack of wafers and remelting the solder whereupon the wafers, and the feed-through paths, are pulled into alignment by surface tension forces.

  14. Composite Materials with Magnetically Aligned Carbon Nanoparticles Having Enhanced Electrical Properties and Methods of Preparation

    NASA Technical Reports Server (NTRS)

    Hong, Haiping (Inventor); Peterson, G.P. (Bud) (Inventor); Salem, David R. (Inventor)

    2016-01-01

    Magnetically aligned carbon nanoparticle composites have enhanced electrical properties. The composites comprise carbon nanoparticles, a host material, magnetically sensitive nanoparticles and a surfactant. In addition to enhanced electrical properties, the composites can have enhanced mechanical and thermal properties.

  15. Shape-based alignment of genomic landscapes in multi-scale resolution

    PubMed Central

    Ashida, Hiroki; Asai, Kiyoshi; Hamada, Michiaki

    2012-01-01

    Due to dramatic advances in DNA technology, quantitative measures of annotation data can now be obtained in continuous coordinates across the entire genome, allowing various heterogeneous ‘genomic landscapes’ to emerge. Although much effort has been devoted to comparing DNA sequences, not much attention has been given to comparing these large quantities of data comprehensively. In this article, we introduce a method for rapidly detecting local regions that show high correlations between genomic landscapes. We overcame the size problem for genome-wide data by converting the data into series of symbols and then carrying out sequence alignment. We also decomposed the oscillation of the landscape data into different frequency bands before analysis, since the real genomic landscape is a mixture of embedded and confounded biological processes working at different scales in the cell nucleus. To verify the usefulness and generality of our method, we applied our approach to well investigated landscapes from the human genome, including several histone modifications. Furthermore, by applying our method to over 20 genomic landscapes in human and 12 in mouse, we found that DNA replication timing and the density of Alu insertions are highly correlated genome-wide in both species, even though the Alu elements have amplified independently in the two genomes. To our knowledge, this is the first method to align genomic landscapes at multiple scales according to their shape. PMID:22561376

  16. Nearest Alignment Space Termination

    2006-07-13

    Near Alignment Space Termination (NAST) is the Greengenes algorithm that matches up submitted sequences with the Greengenes database to look for similarities and align the submitted sequences based on those similarities.

  17. Beam-Based Alignment of Magnetic Field in the Fermilab Electron Cooler Cooling Section

    SciTech Connect

    Seletskiy, S. M.; Tupikov, V.

    2006-03-20

    The Fermilab Electron Cooling Project requires low effective anglular spread of electrons in the cooling section. One of the main components of the effective electron angles is an angle of electron beam centroid with respect to antiproton beam. This angle is caused by the poor quality of magnetic field in the 20 m long cooling section solenoid and by the mismatch of the beam centroid to the entrance of the cooling section. This paper focuses on the beam-based procedure of the alignment of the cooling section field and beam centroid matching. The discussed procedure allows to suppress the beam centroid angles below the critical value of 0.1 mrad.

  18. Octree-Based SIMD Strategy for Icp Registration and Alignment of 3d Point Clouds

    NASA Astrophysics Data System (ADS)

    Eggert, D.; Dalyot, S.

    2012-07-01

    Matching and fusion of 3D point clouds, such as close range laser scans, is important for creating an integrated 3D model data infrastructure. The Iterative Closest Point algorithm for alignment of point clouds is one of the most commonly used algorithms for matching of rigid bodies. Evidently, scans are acquired from different positions and might present different data characterization and accuracies, forcing complex data-handling issues. The growing demand for near real-time applications also introduces new computational requirements and constraints into such processes. This research proposes a methodology to solving the computational and processing complexities in the ICP algorithm by introducing specific performance enhancements to enable more efficient analysis and processing. An Octree data structure together with the caching of localized Delaunay triangulation-based surface meshes is implemented to increase computation efficiency and handling of data. Parallelization of the ICP process is carried out by using the Single Instruction, Multiple Data processing scheme - based on the Divide and Conquer multi-branched paradigm - enabling multiple processing elements to be performed on the same operation on multiple data independently and simultaneously. When compared to the traditional non-parallel list processing the Octree-based SIMD strategy showed a sharp increase in computation performance and efficiency, together with a reliable and accurate alignment of large 3D point clouds, contributing to a qualitative and efficient application.

  19. Studies on structure-based sequence alignment and phylogenies of beta-lactamases.

    PubMed

    Salahuddin, Parveen; Khan, Asad U

    2014-01-01

    The β-lactamases enzymes cleave the amide bond in β-lactam ring, rendering β-lactam antibiotics harmless to bacteria. In this communication we have studied structure-function relationship and phylogenies of class A, B and D beta-lactamases using structure-based sequence alignment and phylip programs respectively. The data of structure-based sequence alignment suggests that in different isolates of TEM-1, mutations did not occur at or near sequence motifs. Since deletions are reported to be lethal to structure and function of enzyme. Therefore, in these variants antibiotic hydrolysis profile and specificity will be affected. The alignment data of class A enzyme SHV-1, CTX-M-15, class D enzyme, OXA-10, and class B enzyme VIM-2 and SIM-1 show sequence motifs along with other part of polypeptide are essentially conserved. These results imply that conformations of betalactamases are close to native state and possess normal hydrolytic activities towards beta-lactam antibiotics. However, class B enzyme such as IMP-1 and NDM-1 are less conserved than other class A and D studied here because mutation and deletions occurred at critically important region such as active site. Therefore, the structure of these beta-lactamases will be altered and antibiotic hydrolysis profile will be affected. Phylogenetic studies suggest that class A and D beta-lactamases including TOHO-1 and OXA-10 respectively evolved by horizontal gene transfer (HGT) whereas other member of class A such as TEM-1 evolved by gene duplication mechanism. Taken together, these studies justify structure-function relationship of beta-lactamases and phylogenetic studies suggest these enzymes evolved by different mechanisms. PMID:24966539

  20. Studies on structure-based sequence alignment and phylogenies of beta-lactamases

    PubMed Central

    Salahuddin, Parveen; Khan, Asad U

    2014-01-01

    The β-lactamases enzymes cleave the amide bond in β-lactam ring, rendering β-lactam antibiotics harmless to bacteria. In this communication we have studied structure-function relationship and phylogenies of class A, B and D beta-lactamases using structure-based sequence alignment and phylip programs respectively. The data of structure-based sequence alignment suggests that in different isolates of TEM-1, mutations did not occur at or near sequence motifs. Since deletions are reported to be lethal to structure and function of enzyme. Therefore, in these variants antibiotic hydrolysis profile and specificity will be affected. The alignment data of class A enzyme SHV-1, CTX-M-15, class D enzyme, OXA-10, and class B enzyme VIM-2 and SIM-1 show sequence motifs along with other part of polypeptide are essentially conserved. These results imply that conformations of betalactamases are close to native state and possess normal hydrolytic activities towards beta-lactam antibiotics. However, class B enzyme such as IMP-1 and NDM-1 are less conserved than other class A and D studied here because mutation and deletions occurred at critically important region such as active site. Therefore, the structure of these beta-lactamases will be altered and antibiotic hydrolysis profile will be affected. Phylogenetic studies suggest that class A and D beta-lactamases including TOHO-1 and OXA-10 respectively evolved by horizontal gene transfer (HGT) whereas other member of class A such as TEM-1 evolved by gene duplication mechanism. Taken together, these studies justify structure-function relationship of beta-lactamases and phylogenetic studies suggest these enzymes evolved by different mechanisms. PMID:24966539

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

    PubMed

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

    2015-08-01

    Here we present the MSA-PAD application, a DNA multiple sequence alignment framework that uses PFAM protein domain information to align DNA sequences encoding either single or multiple protein domains. MSA-PAD has two alignment options: gene and genome mode. PMID:25819080

  2. Temporal Effects of Alignment in Text-Based, Task-Oriented Discourse

    ERIC Educational Resources Information Center

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

    2015-01-01

    Communicative alignment refers to adaptation to one's communication partner. Temporal aspects of such alignment have been little explored. This article examines temporal aspects of lexical and syntactic alignment (i.e., tendencies to use the interlocutor's lexical items and syntactic structures) in task-oriented discourse. In particular, we…

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

    NASA Astrophysics Data System (ADS)

    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.

  4. A comparative in-vivo evaluation of the alignment efficiency of 5 ligation methods: A prospective randomized clinical trial

    PubMed Central

    Reddy, Vijaya Bhaskara; Kumar, Talapaneni Ashok; Prasad, Mandava; Nuvvula, Sivakumar; Patil, Rajedra Goud; Reddy, Praveen Kumar

    2014-01-01

    Objectives: To conduct a prospective randomized study comparing the efficiency of 5 different ligation systems (ELL; elastomeric ligature, SSL; stainless steel ligature, LL; leone slide ligature, PSL; passive self-ligation and ASL; active self-ligation) over the duration of mandibular crowding alleviation. Materials and Methods: Fifty consecutive patients (54.2% male, 45.8% female; mean age: 16.69 years) satisfying the inclusion criteria were randomly allocated to 5 ligation groups with an equal sample size of 10 per group. The 5 groups received treatment with 0.022-inch MBT pre-adjusted edge-wise technique (ELL: Gemini 3M Unitek, SSL: Gemini 3M Unitek, LL: Gemini 3M Unitek, PSL: SmartClip 3M Unitek and ASL: In-Ovation R Euro GAC International). The models and cephalograms were evaluated for anterior arch alignment, extraction space closure, and lower incisal inclinations at pre-treatment T1 and at the end of initial alignment T2. Analysis of variance (ANOVA) and Post-hoc tests were used for data analysis. Results: Forty-eight participants completed the study, and SL systems showed a significant difference over CL groups in time to alignment, passive space closure, and incisal inclination. Multiple regression showed a reduction of 5.28 days in time to alignment by changing the ligation group in the order of ELL to ASL group and 1 mm increase in initial irregularity index increases time to alignment by 11.68 days. Conclusion: Self-ligation brackets were more efficient than conventional ligation brackets during initial leveling and alignment. PMID:24966742

  5. Optical Alignment of the Chromospheric Lyman-Alpha SpectroPolarimeter using Sophisticated Methods to Minimize Activities under Vacuum

    NASA Technical Reports Server (NTRS)

    Giono, G.; Katsukawa, Y.; Ishikawa, R.; Narukage, N.; Kano, R.; Kubo, M.; Ishikawa, S.; Bando, T.; Hara, H.; Suematsu, Y.; Winebarger, A.; Kobayashi, K.

    2016-01-01

    The Chromospheric Lyman-Alpha Spectro-Polarimeter (CLASP) is a sounding-rocket instrument developed at the National Astronomical Observatory of Japan (NAOJ) as a part of an international collaboration. The in- strument main scientific goal is to achieve polarization measurement of the Lyman-alpha line at 121.56 nm emitted from the solar upper-chromosphere and transition region with an unprecedented 0.1% accuracy. For this purpose, the optics are composed of a Cassegrain telescope coated with a "cold mirror" coating optimized for UV reflection and a dual-channel spectrograph allowing for simultaneous observation of the two orthogonal states of polarization. Although the polarization sensitivity is the most important aspect of the instrument, the spatial and spectral resolutions of the instrument are also crucial to observe the chromospheric features and resolve the Ly- pro les. A precise alignment of the optics is required to ensure the resolutions, but experiments under vacuum conditions are needed since Ly-alpha is absorbed by air, making the alignment experiments difficult. To bypass this issue, we developed methods to align the telescope and the spectrograph separately in visible light. We will explain these methods and present the results for the optical alignment of the CLASP telescope and spectrograph. We will then discuss the combined performances of both parts to derive the expected resolutions of the instrument, and compare them with the flight observations performed on September 3rd 2015.

  6. NOTE: A method for determining the alignment accuracy of the treatment table axis at an isocentric irradiation facility

    NASA Astrophysics Data System (ADS)

    Karger, Christian P.; Hartmann, Günther H.; Heeg, Peter; Jäkel, Oliver

    2001-01-01

    At an isocentric irradiation facility, the rotation axis of the treatment table has to be accurately aligned in vertical orientation to the isocentre, which is usually marked by three perpendicular laser planes. In particular, high precision radiotherapy techniques, such as radiosurgery or intensity modulated radiotherapy, require a higher alignment accuracy of the table axis than routinely specified by the manufacturers. A simple and efficient method is presented to measure the direction and the size of the displacement of the table axis from the isocentre as marked by the lasers. In addition, the inclination of the table axis against the vertical direction can be determined. The measured displacement and inclination provide the required data to correct for possible misalignments of the treatment table axis and to maintain its alignment. Measurements were performed over a period of two years for a treatment table located at the German heavy ion therapy facility. The mean radial distance between the table axis and the isocentre was found to be 0.25±0.25 mm. The mean inclination of the table axis in the XZ- and YZ-planes was measured to be -0.03±0.02° and -0.04±0.01°, respectively. The measurements demonstrate the good alignment of the treatment table over the analysed time period. The described method can be applied to any isocentric irradiation facility, especially including isocentric linear accelerators used for radiosurgery or other high precision irradiation techniques.

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

    PubMed

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

    2015-01-01

    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

  8. Array of aligned and dispersed carbon nanotubes and method of producing the array

    DOEpatents

    Ivanov, Ilia N; Simpson, John T; Hendricks, Troy R

    2013-06-11

    An array of aligned and dispersed carbon nanotubes includes an elongate drawn body including a plurality of channels extending therethrough from a first end to a second end of the body, where the channels have a number density of at least about 100,000 channels/mm.sup.2 over a transverse cross-section of the body. A plurality of carbon nanotubes are disposed in each channel, and the carbon nanotubes are sufficiently dispersed and aligned along a length of the channels for the array to comprise an average resistivity per channel of about 9700 .OMEGA.m or less.

  9. Array of aligned and dispersed carbon nanotubes and method of producing the array

    DOEpatents

    Ivanov, Ilia N.; Simpson, John T.; Hendricks, Troy R.

    2012-06-19

    An array of aligned and dispersed carbon nanotubes includes an elongate drawn body including a plurality of channels extending therethrough from a first end to a second end of the body, where the channels have a number density of at least about 100,000 channels/mm.sup.2 over a transverse cross-section of the body. A plurality of carbon nanotubes are disposed in each channel, and the carbon nanotubes are sufficiently dispersed and aligned along a length of the channels for the array to comprise an average resistivity per channel of about 9700 .OMEGA.m or less.

  10. Ultrahigh sensitivity in liquid-crystal-based immunodetection by surface modification of the alignment layer

    NASA Astrophysics Data System (ADS)

    Lee, Mon-Juan; Su, Hui-Wen; Sun, Shih-Hung; Lee, Wei

    2014-10-01

    Liquid crystals (LCs) can be employed in biological sensing and applied to label-free immunodetection owing to their unique birefringent, anchoring, alignment and collective properties. Like all different kinds of immunoassays, both sensitivity and specificity are universally the most important key points of concern. In this study, we developed various approaches toward ultrahigh sensitivity in LC-based immunoassays for potential clinical applications. The LC-based immunodetection technique was demonstrated with the cancer biomarker CA125, which is a mucin-like glycoprotein commonly present in the serum of patients with ovarian and other types of cancer. By using LCs with larger birefringence, such as HDN, the sensitivity of immunodetection was drastically enhanced compared to 5CB, which has a relatively lower birefringence and is commonly used in LC biosensing studies. In addition, UV modification of the monolayer of dimethyloctadecyl[3-(trimethoxysilyl)propyl]ammonium chloride (DMOAP), which functions as the alignment layer for LCs, is suggested to increase functional groups suitable for covalent binding of biomolecules, stabilizing the immobilized anti-CA125 antibody and the immunocomplex thus formed, and contributing to the lowered detection limit. Finally, we show that it is possible to directly identify the formation of CA125 immunocomplex with HDN in a mixture of antigen and antibody without the need to eliminate unbound or unreacted biomolecules through washing, thereby creating a simplified procedure for faster LC-based immunoassay. It is evident from our results that label-free immunodetection based on birefringent LCs represents a novel biosensing technique with potentials to detect a wide range of biomolecules, providing an alternative to conventional label-based immunoassays.

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

    PubMed

    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. PMID:25927488

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

    PubMed

    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. PMID:21891837

  13. Early elementary curricular alignment and teacher perspectives on standards-based reform.

    PubMed

    Cawthon, Stephanie W

    The author investigated the alignment of reading instruction to Wisconsin Model Academic Standards for Reading, grades 1-4 (Wisconsin Department of Public Instruction, 1998a). Teachers in 18 hearing-only, 10 mixed (hearing and deaf students), and 8 deaf-only classrooms were study participants. Teacher groups demonstrated equal alignment to the standards. The study also measured teachers' views on standards. Teachers in hearing-only and deaf-only classrooms scored higher on a scale measuring receptivity toward standards than teachers in mixed classrooms. Teachers in hearing-only classrooms considered the standards good guidelines though perhaps too prescriptive. Teachers in deaf-only and mixed classrooms viewed standards as tools to ensure equity for students but also focused on challenges like the emphasis on phonetics and their need to include sign in deaf students' instruction. Limitations include the challenge of generalizing standards-based analysis, the small number of participants, and use of self-report measures of classroom instruction. PMID:15727062

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

    NASA Astrophysics Data System (ADS)

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

    2011-09-01

    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.

  15. Spartans: Single-Sample Periocular-Based Alignment-Robust Recognition Technique Applied to Non-Frontal Scenarios.

    PubMed

    Juefei-Xu, Felix; Luu, Khoa; Savvides, Marios

    2015-12-01

    In this paper, we investigate a single-sample periocular-based alignment-robust face recognition technique that is pose-tolerant under unconstrained face matching scenarios. Our Spartans framework starts by utilizing one single sample per subject class, and generate new face images under a wide range of 3D rotations using the 3D generic elastic model which is both accurate and computationally economic. Then, we focus on the periocular region where the most stable and discriminant features on human faces are retained, and marginalize out the regions beyond the periocular region since they are more susceptible to expression variations and occlusions. A novel facial descriptor, high-dimensional Walsh local binary patterns, is uniformly sampled on facial images with robustness toward alignment. During the learning stage, subject-dependent advanced correlation filters are learned for pose-tolerant non-linear subspace modeling in kernel feature space followed by a coupled max-pooling mechanism which further improve the performance. Given any unconstrained unseen face image, the Spartans can produce a highly discriminative matching score, thus achieving high verification rate. We have evaluated our method on the challenging Labeled Faces in the Wild database and solidly outperformed the state-of-the-art algorithms under four evaluation protocols with a high accuracy of 89.69%, a top score among image-restricted and unsupervised protocols. The advancement of Spartans is also proven in the Face Recognition Grand Challenge and Multi-PIE databases. In addition, our learning method based on advanced correlation filters is much more effective, in terms of learning subject-dependent pose-tolerant subspaces, compared with many well-established subspace methods in both linear and non-linear cases. PMID:26285149

  16. An Accurate Timing Alignment Method with Time-to-Digital Converter Linearity Calibration for High-Resolution TOF PET

    PubMed Central

    Li, Hongdi; Wang, Chao; An, Shaohui; Lu, Xingyu; Dong, Yun; Liu, Shitao; Baghaei, Hossain; Zhang, Yuxuan; Ramirez, Rocio; Wong, Wai-Hoi

    2015-01-01

    Accurate PET system timing alignment minimizes the coincidence time window and therefore reduces random events and improves image quality. It is also critical for time-of-flight (TOF) image reconstruction. Here, we use a thin annular cylinder (shell) phantom filled with a radioactive source and located axially and centrally in a PET camera for the timing alignment of a TOF PET system. This timing alignment method involves measuring the time differences between the selected coincidence detector pairs, calibrating the differential and integral nonlinearity of the time-to-digital converter (TDC) with the same raw data and deriving the intrinsic time biases for each detector using an iterative algorithm. The raw time bias for each detector is downloaded to the front-end electronics and the residual fine time bias can be applied during the TOF list-mode reconstruction. Our results showed that a timing alignment accuracy of better than ±25 ps can be achieved, and a preliminary timing resolution of 473 ps (full width at half maximum) was measured in our prototype TOF PET/CT system. PMID:26543243

  17. A method for aligning trans-tibial residual limb shapes so as to identify regions of shape change.

    PubMed

    Zachariah, Santosh G; Sorenson, Elizabeth; Sanders, Joan E

    2005-12-01

    Quantification of the change in shape of a residual limb over time is relevant to the fitting of an external prosthesis. Three algorithms were developed and evaluated to align residual limb shapes: iterative closest points (ICP), mean absolute difference, and weighted surface normals/mean absolute difference. Evaluations were conducted by aligning residual limb shapes with known deformations and transformations with their original shapes. Results showed that ICP did not perform well in that it tended to favor a global distribution of local shape difference rather than localization of the error. The mean absolute difference algorithm performed well as long as the shape difference was localized to one region. Weighted mean surface normals/absolute difference provided the best alignment results, performing well both if shape changes were localized and if they were globally distributed. Mean alignment errors for this method were less than 0.285 mm for each of the three translation directions and less than 0.357 degrees for each of the three rotation directions. This algorithm could be helpful to patients, prosthetists, and researchers developing treatments to overcome the detrimental fitting effects of residual limb shape change. PMID:16425837

  18. Phylogenetic Inference From Conserved sites Alignments

    SciTech Connect

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

    1999-08-15

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

  19. Assessment of tonotopically organised subdivisions in human auditory cortex using volumetric and surface-based cortical alignments.

    PubMed

    Langers, Dave R M

    2014-04-01

    Although orderly representations of sound frequency in the brain play a guiding role in the investigation of auditory processing, a rigorous statistical evaluation of cortical tonotopic maps has so far hardly been attempted. In this report, the group-level significance of local tonotopic gradients was assessed using mass-multivariate statistics. The existence of multiple fields on the superior surface of the temporal lobe in both hemispheres was shown. These fields were distinguishable on the basis of tonotopic gradient direction and may likely be identified with the human homologues of the core areas AI and R in primates. Moreover, an objective comparison was made between the usage of volumetric and surface-based registration methods. Although the surface-based method resulted in a better registration across subjects of the grey matter segment as a whole, the alignment of functional subdivisions within the cortical sheet did not appear to improve over volumetric methods. This suggests that the variable relationship between the structural and the functional characteristics of auditory cortex is a limiting factor that cannot be overcome by morphology-based registration techniques alone. Finally, to illustrate how the proposed approach may be used in clinical practice, the method was used to test for focal differences regarding the tonotopic arrangements in healthy controls and tinnitus patients. No significant differences were observed, suggesting that tinnitus does not necessarily require tonotopic reorganisation to occur. PMID:23633425

  20. A new sensor alignment method for an 8k x 4k-pixel ultrahigh definition camera with four imagers

    NASA Astrophysics Data System (ADS)

    Yamashita, Takayuki; Mitani, Kohji; Shimamoto, Hiroshi; Shirakawa, Miho; Okano, Fumio

    2004-06-01

    We describe a precise alignment method of attaching imagers to a prism to produce an ultra-high definition color camera system. We have already developed a prototype camera with 4-k scanning lines using this alignment method. To increase its spatial resolution, this camera has four 8-megapixel imagers (GGBR), which are attached to a prism with a half-pixel pitch offset so that their pixel arrangement is equivalent to that of a single-chip color-imaging sensor with a Bayer-pattern color filter. The precision of their positioning influences the resolution of the reproduced images. The small pixels in the latest imager make it more difficult to maintain precise imager positions. A precise alignment method for attaching imagers to prism is therefore essential for developing a camera system with high resolution. We propose a method with high detectivity using a sinusoidal pattern chart that easily reproduced by one imager, and a signal process. Images from this camera can attain a limiting resolution of more than 3200 TV lines.

  1. A novel alignment repulsion algorithm for flocking of multi-agent systems based on the number of neighbours per agent

    NASA Astrophysics Data System (ADS)

    Kahani, R.; Sedigh, A. K.; Mahjani, M. Gh.

    2015-12-01

    In this paper, an energy-based control methodology is proposed to satisfy the Reynolds three rules in a flock of multiple agents. First, a control law is provided that is directly derived from the passivity theorem. In the next step, the Number of Neighbours Alignment/Repulsion algorithm is introduced for a flock of agents which loses the cohesion ability and uniformly joint connectivity condition. With this method, each agent tries to follow the agents which escape its neighbourhood by considering the velocity of escape time and number of neighbours. It is mathematically proved that the motion of multiple agents converges to a rigid and uncrowded flock if the group is jointly connected just for an instant. Moreover, the conditions for collision avoidance are guaranteed during the entire process. Finally, simulation results are presented to show the effectiveness of the proposed methodology.

  2. Large-area graphene-based nanofiltration membranes by shear alignment of discotic nematic liquid crystals of graphene oxide

    NASA Astrophysics Data System (ADS)

    Akbari, Abozar; Sheath, Phillip; Martin, Samuel T.; Shinde, Dhanraj B.; Shaibani, Mahdokht; Banerjee, Parama Chakraborty; Tkacz, Rachel; Bhattacharyya, Dibakar; Majumder, Mainak

    2016-03-01

    Graphene-based membranes demonstrating ultrafast water transport, precise molecular sieving of gas and solvated molecules shows great promise as novel separation platforms; however, scale-up of these membranes to large-areas remains an unresolved problem. Here we demonstrate that the discotic nematic phase of graphene oxide (GO) can be shear aligned to form highly ordered, continuous, thin films of multi-layered GO on a support membrane by an industrially adaptable method to produce large-area membranes (13 × 14 cm2) in <5 s. Pressure driven transport data demonstrate high retention (>90%) for charged and uncharged organic probe molecules with a hydrated radius above 5 Å as well as modest (30-40%) retention of monovalent and divalent salts. The highly ordered graphene sheets in the plane of the membrane make organized channels and enhance the permeability (71+/-5 l m-2 hr-1 bar-1 for 150+/-15 nm thick membranes).

  3. Large-area graphene-based nanofiltration membranes by shear alignment of discotic nematic liquid crystals of graphene oxide.

    PubMed

    Akbari, Abozar; Sheath, Phillip; Martin, Samuel T; Shinde, Dhanraj B; Shaibani, Mahdokht; Banerjee, Parama Chakraborty; Tkacz, Rachel; Bhattacharyya, Dibakar; Majumder, Mainak

    2016-01-01

    Graphene-based membranes demonstrating ultrafast water transport, precise molecular sieving of gas and solvated molecules shows great promise as novel separation platforms; however, scale-up of these membranes to large-areas remains an unresolved problem. Here we demonstrate that the discotic nematic phase of graphene oxide (GO) can be shear aligned to form highly ordered, continuous, thin films of multi-layered GO on a support membrane by an industrially adaptable method to produce large-area membranes (13 × 14 cm(2)) in <5 s. Pressure driven transport data demonstrate high retention (>90%) for charged and uncharged organic probe molecules with a hydrated radius above 5 Å as well as modest (30-40%) retention of monovalent and divalent salts. The highly ordered graphene sheets in the plane of the membrane make organized channels and enhance the permeability (71 ± 5 l m(-2) hr(-1) bar(-1) for 150 ± 15 nm thick membranes). PMID:26947916

  4. Effect of Catalyst Concentration on the Growth of Palm oil Based Vertically Aligned Carbon Nanotubes

    NASA Astrophysics Data System (ADS)

    Suriani, A. B.; Mohamad, F.; Azira, A. A.; Hajar, Nadya; Mamat, M. H.; Sarah, M. S. P.; Musa, M. Z.; Nor, Roslan Md; Rusop, M.

    2010-07-01

    The effects of catalyst concentration on the synthesis of vertically aligned carbon nanotubes (VACNTs) using ferrocene as catalyst and palm oil as bio-hydrocarbon source in thermal chemical vapor deposition (CVD) method were studied. The CVD reaction took 30 minutes followed by 10 minutes annealing process at various ferrocene concentration; 0.66, 1.33, 2.66, 3.99, 5.33, 6.66 and 7.99 wt% at fixed synthesis temperature 750 °C. The VACNTs were characterized by field emission scanning electron microscopy (FESEM) and Raman spectroscopy. The growth rate, the diameters, and the degree of crystalinity of the VACNTs were found to be dependent on the catalyst concentration.

  5. Sparse alignment for robust tensor learning.

    PubMed

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

    2014-10-01

    Multilinear/tensor extensions of manifold learning based algorithms have been widely used in computer vision and pattern recognition. This paper first provides a systematic analysis of the multilinear extensions for the most popular methods by using alignment techniques, thereby obtaining a general tensor alignment framework. From this framework, it is easy to show that the manifold learning based tensor learning methods are intrinsically different from the alignment techniques. Based on the alignment framework, a robust tensor learning method called sparse tensor alignment (STA) is then proposed for unsupervised tensor feature extraction. Different from the existing tensor learning methods, L1- and L2-norms are introduced to enhance the robustness in the alignment step of the STA. The advantage of the proposed technique is that the difficulty in selecting the size of the local neighborhood can be avoided in the manifold learning based tensor feature extraction algorithms. Although STA is an unsupervised learning method, the sparsity encodes the discriminative information in the alignment step and provides the robustness of STA. Extensive experiments on the well-known image databases as well as action and hand gesture databases by encoding object images as tensors demonstrate that the proposed STA algorithm gives the most competitive performance when compared with the tensor-based unsupervised learning methods. PMID:25291733

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

    NASA Astrophysics Data System (ADS)

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    Maier, Sebastian; Gold, Peter; Forchel, Alfred; Gregersen, Niels; Mørk, Jesper; Höfling, Sven; Schneider, Christian; Kamp, Martin

    2014-04-01

    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 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 avenue for efficient (up to 42% demonstrated) and pure (g(2)(0) value of 0.023) single-photon emission. PMID:24718190

  9. Improved spatiotemporal-multiplexing super-multiview display based on planar aligned OLED microdisplays.

    PubMed

    Teng, Dongdong; Pang, Zhiyong; Zhang, Yueli; Wu, Dong; Wang, Jiahui; Liu, Lilin; Wang, Biao

    2015-08-24

    Through gating spectrum plane of multiple planar aligned OLED microdisplays by a timely sequential manner, a super-multiview (SMV) three-dimensional (3D) display based on spatiotemporal-multiplexing was developed in our previous paper. But an upper limit of the allowable sub-viewing-zones (SVZs) for an OLED microdisplay did exist in the previous system, even if microdisplays with very high frame rates could be commercially available. In this manuscript, an improved spatiotemporal-multiplexing SMV displays system is developed, which removes the above limitation through controllable fusing of light beams from adjacent OLED microdisplays. The employment of a liquid-crystal panel as the gating-aperture array allows the improved system to accommodate multiple rows of OLED microdisplays for denser SVZs. Experimentally, a prototype system is demonstrated by 24 OLED microdisplays, resulting in 120 SVZs with an interval small to 1.07mm. PMID:26368135

  10. Fabrication and characterization of groove-gate MOSFETs based on a self-aligned CMOS process

    NASA Astrophysics Data System (ADS)

    Ma, Xiao-Hua; Hao, Yue; Sun, Bao-Gang; Gao, Hai-Xia; Ren, Hong-Xia; Zhang, Jin-Cheng; Zhang, Jin-Feng; Zhang, Xiao-Ju; Zhang, Wei-Dong

    2006-01-01

    N and P-channel groove-gate MOSFETs based on a self-aligned CMOS process have been fabricated and characterized. For the devices with channel length of 140nm, the measured drain induced barrier lowering (DIBL) was 66mV/V for n-MOSFETs and 82mV/V for p-MOSFETs. The substrate current of a groove-gate n-MOSFET was 150 times less than that of a conventional planar n-MOSFET. These results demonstrate that groove-gate MOSFETs have excellent capabilities in suppressing short-channel effects. It is worth emphasizing that our groove-gate MOSFET devices are fabricated by using a simple process flow, with the potential of fabricating devices in the sub-100nm range.

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

    NASA Technical Reports Server (NTRS)

    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.

  12. A simple method of producing aligned carbon nanotubes from an unconventional precursor Camphor

    NASA Astrophysics Data System (ADS)

    Kumar, Mukul; Ando, Yoshinori

    2003-06-01

    Vertically aligned multi-wall carbon nanotubes of diameter 20-40 nm and length ˜200 μm were grown on quartz substrate by pyrolyzing camphor with ferrocene catalyst at 900 °C in argon atmosphere at ambient pressure. Catalyst requirement with camphor was found to be low by a factor of 10 as compared to available reports of aligned nanotubes from conventional precursors. Because of the low catalyst requirement with camphor, as-grown nanotubes are least contaminated with metal particles, whereas the oxygen atom present in camphor helps in oxidizing amorphous carbon in-situ, eliminating the need of post-deposition purification. Good graphitization of the tube layers was observed by TEM, whereas high purity was confirmed by EDX analysis. The estimated yield of as-grown nanotubes is ˜90%.

  13. Virtual tissue alignment and cutting plane definition – a new method to obtain optimal longitudinal histological sections

    PubMed Central

    Danz, J C; Habegger, M; Bosshardt, D D; Katsaros, C; Stavropoulos, A

    2014-01-01

    Histomorphometric evaluation of the buccal aspects of periodontal tissues in rodents requires reproducible alignment of maxillae and highly precise sections containing central sections of buccal roots; this is a cumbersome and technically sensitive process due to the small specimen size. The aim of the present report is to describe and analyze a method to transfer virtual sections of micro-computer tomographic (CT)-generated image stacks to the microtome for undecalcified histological processing and to describe the anatomy of the periodontium in rat molars. A total of 84 undecalcified sections of all buccal roots of seven untreated rats was analyzed. The accuracy of section coordinate transfer from virtual micro-CT slice to the histological slice, right–left side differences and the measurement error for linear and angular measurements on micro-CT and on histological micrographs were calculated using the Bland–Altman method, interclass correlation coefficient and the method of moments estimator. Also, manual alignment of the micro-CT-scanned rat maxilla was compared with multiplanar computer-reconstructed alignment. The supra alveolar rat anatomy is rather similar to human anatomy, whereas the alveolar bone is of compact type and the keratinized gingival epithelium bends apical to join the junctional epithelium. The high methodological standardization presented herein ensures retrieval of histological slices with excellent display of anatomical microstructures, in a reproducible manner, minimizes random errors, and thereby may contribute to the reduction of number of animals needed. PMID:24266502

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

    ERIC Educational Resources Information Center

    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…

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

    PubMed

    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. PMID:25738306

  16. Alignment issues, correlation techniques and their assessment for a visible light imaging-based 3D printer quality control system

    NASA Astrophysics Data System (ADS)

    Straub, Jeremy

    2016-05-01

    Quality control is critical to manufacturing. Frequently, techniques are used to define object conformity bounds, based on historical quality data. This paper considers techniques for bespoke and small batch jobs that are not statistical model based. These techniques also serve jobs where 100% validation is needed due to the mission or safety critical nature of particular parts. One issue with this type of system is alignment discrepancies between the generated model and the physical part. This paper discusses and evaluates techniques for characterizing and correcting alignment issues between the projected and perceived data sets to prevent errors attributable to misalignment.

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

    ERIC Educational Resources Information Center

    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.…

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

    PubMed Central

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

    2015-01-01

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

  19. A patient alignment solution for lung SBRT setups based on a deformable registration technique

    SciTech Connect

    Lu Bo; Mittauer, Kathryn; Li, Jonathan; Samant, Sanjiv; Dagan, Roi; Okunieff, Paul; Kahler, Darren; Liu, Chihray

    2012-12-15

    Purpose: In this work, the authors propose a novel registration strategy for translation-only correction scenarios of lung stereotactic body radiation therapy setups, which can achieve optimal dose coverage for tumors as well as preserve the consistency of registrations with minimal human interference. Methods: The proposed solution (centroid-to-centroidor CTC solution) uses the average four-dimensional CT (A4DCT) as the reference CT. The cone-beam CT (CBCT) is deformed to acquire a new centroid for the internal target volume (ITV) on the CBCT. The registration is then accomplished by simply aligning the centroids of the ITVs between the A4DCT and the CBCT. Sixty-seven cases using 64 patients (each case is associated with separate isocenters) have been investigated with the CTC method and compared with the conventional gray-value (G) mode and bone (B) mode registration methods. Dosimetric effects among the tree methods were demonstrated by 18 selected cases. The uncertainty of the CTC method has also been studied. Results: The registration results demonstrate the superiority of the CTC method over the other two methods. The differences in the D99 and D95 ITV dose coverage between the CTC method and the original plan is small (within 5%) for all of the selected cases except for one for which the tumor presented significant growth during the period between the CT scan and the treatment. Meanwhile, the dose coverage differences between the original plan and the registration results using either the B or G method are significant, as tumor positions varied dramatically, relative to the rib cage, from their positions on the original CT. The largest differences between the D99 and D95 dose coverage of the ITV using the B or G method versus the original plan are as high as 50%. The D20 differences between any of the methods versus the original plan are all less than 2%. Conclusions: The CTC method can generate optimal dose coverage to tumors with much better consistency

  20. Alignment of multiple proteins with an ensemble of Hidden Markov Models

    PubMed Central

    Song, Yinglei; Qu, Junfeng; Hura, Gurdeep S.

    2011-01-01

    In this paper, we developed a new method that progressively construct and update a set of alignments by adding sequences in certain order to each of the existing alignments. Each of the existing alignments is modelled with a profile Hidden Markov Model (HMM) and an added sequence is aligned to each of these profile HMMs. We introduced an integer parameter for the number of profile HMMs. The profile HMMs are then updated based on the alignments with leading scores. Our experiments on BaliBASE showed that our approach could efficiently explore the alignment space and significantly improve the alignment accuracy. PMID:20376922

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

    PubMed Central

    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

  2. A Modified Method of Proximal Segment Alignment After Sagittal Split Ramus Osteotomy for Patients With Mandibular Asymmetry

    PubMed Central

    Xia, James J.; Wang, Xudong

    2015-01-01

    Purpose The purpose of this study was to evaluate a modified method of aligning the proximal segment after bilateral sagittal split ramus osteotomy (BSSO) in the treatment of patients with facial asymmetry. Patients and Methods Eleven patients with mandibular excess and facial asymmetries were enrolled in this prospective study. The surgery was planned according to a computer-aided surgical simulation protocol. In addition, the proximal segment on the hypoplastic side was intentionally flared out after the distal segment was rotationally set back. If the gap between the proximal and distal segments was too wide, then bone grafts were used. The surgery was completed according to the computerized plan. The proximal segment on the hypoplastic side was fixed with bicortical lag screws, and the proximal segment on the hyperplastic side was fixed with a 4-hole titanium miniplate. Postoperative evaluation was performed 6 months after surgery. Statistical analyses were performed. Results All surgeries were completed uneventfully. Of the 11 patients, 4 also underwent genioplasty and 3 underwent bone grafting to fill in the gap and smooth the anterior step. The physicians and patients were satisfied with the surgical outcomes. Only 1 patient underwent a secondary revision using an onlay hydroxyapatite implant. Results of statistical analyses showed that the computerized surgical plan could be accurately transferred to the patients at the time of surgery and the surgical outcomes achieved with this modified method were better than with the routine method of aligning the proximal and distal segments in maximal contact. Conclusion The present modified method of aligning the proximal segment for BSSO can effectively correct mandibular asymmetry and obviate a secondary revision surgery. PMID:26026710

  3. Aligned silver nanowire-based transparent electrodes for engineering polarisation-selective optoelectronics.

    PubMed

    Park, Byoungchoo; Bae, In-Gon; Huh, Yoon Ho

    2016-01-01

    We herein report on a remarkably simple, fast, and economic way of fabricating homogeneous and well oriented silver nanowires (AgNWs) that exhibit strong in-plane electrical and optical anisotropies. Using a small quantity of AgNW suspension, the horizontal-dip (H-dip) coating method was applied, in which highly oriented AgNWs were deposited unidirectionally along the direction of coating over centimetre-scale lengths very rapidly. In applying the H-dip-coating method, we adjusted the shear strain rate of the capillary flow in the Landau-Levich meniscus of the AgNW suspension, which induced a high degree of uniaxial orientational ordering (0.37-0.43) of the AgNWs, comparable with the ordering seen in archetypal nematic liquid crystal (LC) materials. These AgNWs could be used to fabricate not only transparent electrodes, but also LC-alignment electrodes for LC devices and/or polarising electrodes for organic photovoltaic devices, having the potential to revolutionise the architectures of a number of polarisation-selective opto-electronic devices for use in printed/organic electronics. PMID:26778621

  4. Aligned silver nanowire-based transparent electrodes for engineering polarisation-selective optoelectronics

    NASA Astrophysics Data System (ADS)

    Park, Byoungchoo; Bae, In-Gon; Huh, Yoon Ho

    2016-01-01

    We herein report on a remarkably simple, fast, and economic way of fabricating homogeneous and well oriented silver nanowires (AgNWs) that exhibit strong in-plane electrical and optical anisotropies. Using a small quantity of AgNW suspension, the horizontal-dip (H-dip) coating method was applied, in which highly oriented AgNWs were deposited unidirectionally along the direction of coating over centimetre-scale lengths very rapidly. In applying the H-dip-coating method, we adjusted the shear strain rate of the capillary flow in the Landau-Levich meniscus of the AgNW suspension, which induced a high degree of uniaxial orientational ordering (0.37-0.43) of the AgNWs, comparable with the ordering seen in archetypal nematic liquid crystal (LC) materials. These AgNWs could be used to fabricate not only transparent electrodes, but also LC-alignment electrodes for LC devices and/or polarising electrodes for organic photovoltaic devices, having the potential to revolutionise the architectures of a number of polarisation-selective opto-electronic devices for use in printed/organic electronics.

  5. Aligned silver nanowire-based transparent electrodes for engineering polarisation-selective optoelectronics

    PubMed Central

    Park, Byoungchoo; Bae, In-Gon; Huh, Yoon Ho

    2016-01-01

    We herein report on a remarkably simple, fast, and economic way of fabricating homogeneous and well oriented silver nanowires (AgNWs) that exhibit strong in-plane electrical and optical anisotropies. Using a small quantity of AgNW suspension, the horizontal-dip (H-dip) coating method was applied, in which highly oriented AgNWs were deposited unidirectionally along the direction of coating over centimetre-scale lengths very rapidly. In applying the H-dip-coating method, we adjusted the shear strain rate of the capillary flow in the Landau-Levich meniscus of the AgNW suspension, which induced a high degree of uniaxial orientational ordering (0.37–0.43) of the AgNWs, comparable with the ordering seen in archetypal nematic liquid crystal (LC) materials. These AgNWs could be used to fabricate not only transparent electrodes, but also LC-alignment electrodes for LC devices and/or polarising electrodes for organic photovoltaic devices, having the potential to revolutionise the architectures of a number of polarisation-selective opto-electronic devices for use in printed/organic electronics. PMID:26778621

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

    PubMed Central

    2015-01-01

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

  7. Automated method and system for the alignment and correlation of images from two different modalities

    DOEpatents

    Giger, Maryellen L.; Chen, Chin-Tu; Armato, Samuel; Doi, Kunio

    1999-10-26

    A method and system for the computerized registration of radionuclide images with radiographic images, including generating image data from radiographic and radionuclide images of the thorax. Techniques include contouring the lung regions in each type of chest image, scaling and registration of the contours based on location of lung apices, and superimposition after appropriate shifting of the images. Specific applications are given for the automated registration of radionuclide lungs scans with chest radiographs. The method in the example given yields a system that spatially registers and correlates digitized chest radiographs with V/Q scans in order to correlate V/Q functional information with the greater structural detail of chest radiographs. Final output could be the computer-determined contours from each type of image superimposed on any of the original images, or superimposition of the radionuclide image data, which contains high activity, onto the radiographic chest image.

  8. Efficient and Accurate OTU Clustering with GPU-Based Sequence Alignment and Dynamic Dendrogram Cutting.

    PubMed

    Nguyen, Thuy-Diem; Schmidt, Bertil; Zheng, Zejun; Kwoh, Chee-Keong

    2015-01-01

    De novo clustering is a popular technique to perform taxonomic profiling of a microbial community by grouping 16S rRNA amplicon reads into operational taxonomic units (OTUs). In this work, we introduce a new dendrogram-based OTU clustering pipeline called CRiSPy. The key idea used in CRiSPy to improve clustering accuracy is the application of an anomaly detection technique to obtain a dynamic distance cutoff instead of using the de facto value of 97 percent sequence similarity as in most existing OTU clustering pipelines. This technique works by detecting an abrupt change in the merging heights of a dendrogram. To produce the output dendrograms, CRiSPy employs the OTU hierarchical clustering approach that is computed on a genetic distance matrix derived from an all-against-all read comparison by pairwise sequence alignment. However, most existing dendrogram-based tools have difficulty processing datasets larger than 10,000 unique reads due to high computational complexity. We address this difficulty by developing two efficient algorithms for CRiSPy: a compute-efficient GPU-accelerated parallel algorithm for pairwise distance matrix computation and a memory-efficient hierarchical clustering algorithm. Our experiments on various datasets with distinct attributes show that CRiSPy is able to produce more accurate OTU groupings than most OTU clustering applications. PMID:26451819

  9. Higher-power supercapacitor electrodes based on mesoporous manganese oxide coating on vertically aligned carbon nanofibers.

    PubMed

    Klankowski, Steven A; Pandey, Gaind P; Malek, Gary; Thomas, Conor R; Bernasek, Steven L; Wu, Judy; Li, Jun

    2015-05-14

    A study on the development of high-power supercapacitor materials based on formation of thick mesoporous MnO2 shells on a highly conductive 3D template using vertically aligned carbon nanofibers (VACNFs). Coaxial manganese shells of 100 to 600 nm nominal thicknesses are sputter-coated on VACNFs and then electrochemically oxidized into rose-petal-like mesoporous MnO2 structure. Such a 3D MnO2/VACNF hybrid architecture provides enhanced ion diffusion throughout the whole MnO2 shell and yields excellent current collection capability through the VACNF electrode. These two effects collectively enable faster electrochemical reactions during charge-discharge of MnO2 in 1 M Na2SO4. Thick MnO2 shells (up to 200 nm in radial thickness) can be employed, giving a specific capacitance up to 437 F g(-1). More importantly, supercapacitors employing such a 3D MnO2/VACNF hybrid electrode illustrate more than one order of magnitude higher specific power than the state-of-the-art ones based on other MnO2 structures, reaching ∼240 kW kg(-1), while maintaining a comparable specific energy in the range of 1 to 10 Wh kg(-1). This hybrid approach demonstrates the potential of 3D core-shell architectures for high-power energy storage devices. PMID:25894255

  10. Girder Alignment Plan

    SciTech Connect

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

    2010-11-18

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

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

    SciTech Connect

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

    2008-05-01

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

  12. A convenient alignment approach for x-ray imaging experiments based on laser positioning devices

    SciTech Connect

    Zhang Da; Donovan, Molly; Wu Xizeng; Liu Hong

    2008-11-15

    This study presents a two-laser alignment approach for facilitating the precise alignment of various imaging and measuring components with respect to the x-ray beam. The first laser constantly pointed to the output window of the source, in a direction parallel to the path along which the components are placed. The second laser beam, originating from the opposite direction, was calibrated to coincide with the first laser beam. Thus, a visible indicator of the direction of the incident x-ray beam was established, and the various components could then be aligned conveniently and accurately with its help.

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

    NASA Technical Reports Server (NTRS)

    Coulter, Phillip; Ohl, Raymond G.; Blake, Peter N.; Bos, Brent J.; Casto, Gordon V.; Eichhorn, William L.; Gum, Jeffrey S.; Hadjimichael, Theodore J.; Hagopian, John G.; Hayden, Joseph E.; Hicks, Samantha L.; Kubalak, Dave; Mclean, Kyle F.; McMann, Joseph; Redman, Kevin; Wenzel, Greg; Young, Jerrod

    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.

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

    NASA Technical Reports Server (NTRS)

    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.

  15. Simulation of water impregnation through vertically aligned CNT forests using a molecular dynamics method.

    PubMed

    Tajiri, Tomohiro; Matsuzaki, Ryosuke; Shimamura, Yoshinobu

    2016-01-01

    The flow rate of water through carbon nanotube (CNT) membranes is considerably large. Hence, CNT membranes can be used in nanofluidic applications. In this work, we performed a molecular dynamics (MD) simulation of the introduction of water into CNTs in the CNT membranes, especially in vertically aligned CNT forests. The results showed that the Knudsen number (Kn) increased with an increasing volume fraction of CNT (VC) and was greater than 10(-3) for each VC. Beyond this value, the flow became a slip flow. Further, the permeability increased as VC increased in the actual state calculated by the MD simulation, whereas the permeability in the no-slip state predicted by the Hagen-Poiseuille relationship decreased. Thus, a clear divergence in the permeability trend existed between the states. Finally, the flow enhancement ranged from 0.1 to 23,800, and the results show that water easily permeates as VC increases. PMID:27562112

  16. Simulation of water impregnation through vertically aligned CNT forests using a molecular dynamics method

    PubMed Central

    Tajiri, Tomohiro; Matsuzaki, Ryosuke; Shimamura, Yoshinobu

    2016-01-01

    The flow rate of water through carbon nanotube (CNT) membranes is considerably large. Hence, CNT membranes can be used in nanofluidic applications. In this work, we performed a molecular dynamics (MD) simulation of the introduction of water into CNTs in the CNT membranes, especially in vertically aligned CNT forests. The results showed that the Knudsen number (Kn) increased with an increasing volume fraction of CNT (VC) and was greater than 10−3 for each VC. Beyond this value, the flow became a slip flow. Further, the permeability increased as VC increased in the actual state calculated by the MD simulation, whereas the permeability in the no-slip state predicted by the Hagen–Poiseuille relationship decreased. Thus, a clear divergence in the permeability trend existed between the states. Finally, the flow enhancement ranged from 0.1 to 23,800, and the results show that water easily permeates as VC increases. PMID:27562112

  17. Image Quality of the Evryscope: Method for On-Site Optical Alignment

    NASA Astrophysics Data System (ADS)

    Wulfken, Philip J.; Law, Nicholas M.; Ratzloff, Jeffrey; Fors, Octavi

    2015-01-01

    Previous wide field surveys have been conducted by taking many images each night to cover thousands of square degrees. The Evryscope is a new type of system designed to search for transiting exoplanets around nearby bright stars, M-dwarfs, white dwarfs, and other transients. The Evryscope is an array of 70 mm telescopes that will continuously image 10200 square degrees of the night sky at once. One of the image quality requirements is for the PSFs to be well-sampled at two pixels across and it was found that tilt caused by slight misalignment between the optics and the CCD increased the size of the FWHM towards the edges and corners of the image. Here we describe the image quality of the Evryscope cameras and the alignment procedure to achieve the required 2 pixel FWHM.

  18. Pixel-to-pixel correspondence alignment method of a 2CCD camera by using absolute phase map

    NASA Astrophysics Data System (ADS)

    Huang, Shujun; Liu, Yue; Bai, Xuefei; Wang, Zhangying; Zhang, Zonghua

    2015-06-01

    An alignment method of a 2CCD camera to build pixel-to-pixel correspondence between the infrared (IR) CCD sensor and the visible CCD sensor by using the absolute phase data is presented. Vertical and horizontal sinusoidal fringe patterns are generated by software and displayed on a liquid crystal display screen. The displayed fringe patterns are captured simultaneously by the IR sensor and the visible sensor of the 2CCD camera. The absolute phase values of each pixel at IR and visible channels are calculated from the captured fringe pattern images by using Fourier transform and the optimum three-fringe number selection method. The accurate pixel corresponding relationship between the two sensors can be determined along the vertical and the horizontal directions by comparing the obtained absolute phase data in IR and visible channels. Experimental results show the high accuracy, effectiveness, and validity of the proposed 2CCD alignment method. By using the continuous absolute phase information, this method can determine the pixel-to-pixel correspondence with high resolution.

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

    SciTech Connect

    Zwaska, R.; Bishai, M.; Childress, S.; Drake, G.; Escobar, C.; Gouffon, P.; Harris, D.A.; Hylen, J.; Indurthy, D.; Koizumi, G.; Kopp, S.; /Argonne /Brookhaven /Frascati /Sao Paulo U. /Campinas State U. /Texas U.

    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.

  20. Implementation of a parallel protein structure alignment service on cloud.

    PubMed

    Hung, Che-Lun; Lin, Yaw-Ling

    2013-01-01

    Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform. PMID:23671842

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

    PubMed Central

    Hung, Che-Lun; Lin, Yaw-Ling

    2013-01-01

    Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform. PMID:23671842

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

    NASA Astrophysics Data System (ADS)

    Mueller, M.; Voegtle, T.

    2016-06-01

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

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

    NASA Astrophysics Data System (ADS)

    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.

  4. CMOS compatible on-chip decoupling capacitor based on vertically aligned carbon nanofibers

    NASA Astrophysics Data System (ADS)

    Saleem, A. M.; Göransson, G.; Desmaris, V.; Enoksson, P.

    2015-05-01

    On-chip decoupling capacitor of specific capacitance 55 pF/μm2 (footprint area) which is 10 times higher than the commercially available discrete and on-chip (65 nm technology node) decoupling capacitors is presented. The electrodes of the capacitor are based on vertically aligned carbon nanofibers (CNFs) capable of being integrated directly on CMOS chips. The carbon nanofibers employed in this study were grown on CMOS chips using direct current plasma enhanced chemical vapor deposition (DC-PECVD) technique at CMOS compatible temperature. The carbon nanofibers were grown at temperature from 390 °C to 550 °C. The capacitance of the carbon nanofibers was measured by cyclic voltammetry and thus compared. Futhermore the capacitance of decoupling capacitor was measured using different voltage scan rate to show their high charge storage capability and finally the cyclic voltammetry is run for 1000 cycles to assess their suitability as electrode material for decoupling capacitor. Our results show the high specific capacitance and long-term reliability of performance of the on-chip decoupling capacitors. Moreover, the specific capacitance shown is larger for carbon nanofibers grown at higher temperature.

  5. Phonon processes in vertically aligned silicon nanowire arrays produced by low-cost all-solution galvanic displacement method

    NASA Astrophysics Data System (ADS)

    Banerjee, Debika; Trudeau, Charles; Gerlein, Luis Felipe; Cloutier, Sylvain G.

    2016-03-01

    The nanoscale engineering of silicon can significantly change its bulk optoelectronic properties to make it more favorable for device integration. Phonon process engineering is one way to enhance inter-band transitions in silicon's indirect band structure alignment. This paper demonstrates phonon localization at the tip of silicon nanowires fabricated by galvanic displacement using wet electroless chemical etching of a bulk silicon wafer. High-resolution Raman micro-spectroscopy reveals that such arrayed structures of silicon nanowires display phonon localization behaviors, which could help their integration into the future generations of nano-engineered silicon nanowire-based devices such as photodetectors and solar cells.

  6. A template and catalyst-free metal-etching-oxidation method to synthesize aligned oxide nanowire arrays: NiO as an example.

    PubMed

    Wei, Zhi Peng; Arredondo, Miryam; Peng, Hai Yang; Zhang, Zhou; Guo, Dong Lai; Xing, Guo Zhong; Li, Yong Feng; Wong, Lai Mun; Wang, Shi Jie; Valanoor, Nagarajan; Wu, Tom

    2010-08-24

    Although NiO is one of the canonical functional binary oxides, there has been no report so far on the effective fabrication of aligned single crystalline NiO nanowire arrays. Here we report a novel vapor-based metal-etching-oxidation method to synthesize high-quality NiO nanowire arrays with good vertical alignment and morphology control. In this method, Ni foils are used as both the substrates and the nickel source; NiCl(2) powder serves as the additional Ni source and provides Cl(2) to initiate mild etching. No template is deliberately employed; instead a nanograined NiO scale formed on the NiO foil guides the vapor infiltration and assists the self-assembled growth of NiO nanowires via a novel process comprising simultaneous Cl(2) etching and gentle oxidation. Furthermore, using CoO nanowires and Co-doped NiO as examples, we show that this general method can be employed to produce nanowires of other oxides as well as the doped counterparts. PMID:20614899

  7. Refinement by shifting secondary structure elements improves sequence alignments.

    PubMed

    Tong, Jing; Pei, Jimin; Otwinowski, Zbyszek; Grishin, Nick V

    2015-03-01

    Constructing a model of a query protein based on its alignment to a homolog with experimentally determined spatial structure (the template) is still the most reliable approach to structure prediction. Alignment errors are the main bottleneck for homology modeling when the query is distantly related to the template. Alignment methods often misalign secondary structural elements by a few residues. Therefore, better alignment solutions can be found within a limited set of local shifts of secondary structures. We present a refinement method to improve pairwise sequence alignments by evaluating alignment variants generated by local shifts of template-defined secondary structures. Our method SFESA is based on a novel scoring function that combines the profile-based sequence score and the structure score derived from residue contacts in a template. Such a combined score frequently selects a better alignment variant among a set of candidate alignments generated by local shifts and leads to overall increase in alignment accuracy. Evaluation of several benchmarks shows that our refinement method significantly improves alignments made by automatic methods such as PROMALS, HHpred and CNFpred. The web server is available at http://prodata.swmed.edu/sfesa. PMID:25546158

  8. Refinement by shifting secondary structure elements improves sequence alignments

    PubMed Central

    Tong, Jing; Pei, Jimin; Otwinowski, Zbyszek; Grishin, Nick V.

    2015-01-01

    Constructing a model of a query protein based on its alignment to a homolog with experimentally determined spatial structure (the template) is still the most reliable approach to structure prediction. Alignment errors are the main bottleneck for homology modeling when the query is distantly related to the template. Alignment methods often misalign secondary structural elements by a few residues. Therefore, better alignment solutions can be found within a limited set of local shifts of secondary structures. We present a refinement method to improve pairwise sequence alignments by evaluating alignment variants generated by local shifts of template-defined secondary structures. Our method SFESA is based on a novel scoring function that combines the profile-based sequence score and the structure score derived from residue contacts in a template. Such a combined score frequently selects a better alignment variant among a set of candidate alignments generated by local shifts and leads to overall increase in alignment accuracy. Evaluation of several benchmarks shows that our refinement method significantly improves alignments made by automatic methods such as PROMALS, HHpred and CNFpred. The web server is available at http://prodata.swmed.edu/sfesa. PMID:25546158

  9. Algorithms, applications, and challenges of protein structure alignment.

    PubMed

    Ma, Jianzhu; Wang, Sheng

    2014-01-01

    As a fundamental problem in computational structure biology, protein structure alignment has attracted the focus of the community for more than 20 years. While the pairwise structure alignment could be applied to measure the similarity between two proteins, which is a first step for homology search and fold space construction, the multiple structure alignment could be used to understand evolutionary conservation and divergence from a family of protein structures. Structure alignment is an NP-hard problem, which is only computationally tractable by using heuristics. Three levels of heuristics for pairwise structure alignment have been proposed, from the representations of protein structure, the perspectives of viewing protein as a rigid-body or flexible, to the scoring functions as well as the search algorithms for the alignment. For multiple structure alignment, the fourth level of heuristics is applied on how to merge all input structures to a multiple structure alignment. In this review, we first present a small survey of current methods for protein pairwise and multiple alignment, focusing on those that are publicly available as web servers. In more detail, we also discuss the advancements on the development of the new approaches to increase the pairwise alignment accuracy, to efficiently and reliably merge input structures to the multiple structure alignment. Finally, besides broadening the spectrum of the applications of structure alignment for protein template-based prediction, we also list several open problems that need to be solved in the future, such as the large complex alignment and the fast database search. PMID:24629187

  10. Higher-power supercapacitor electrodes based on mesoporous manganese oxide coating on vertically aligned carbon nanofibers

    NASA Astrophysics Data System (ADS)

    Klankowski, Steven A.; Pandey, Gaind P.; Malek, Gary; Thomas, Conor R.; Bernasek, Steven L.; Wu, Judy; Li, Jun

    2015-04-01

    A study on the development of high-power supercapacitor materials based on formation of thick mesoporous MnO2 shells on a highly conductive 3D template using vertically aligned carbon nanofibers (VACNFs). Coaxial manganese shells of 100 to 600 nm nominal thicknesses are sputter-coated on VACNFs and then electrochemically oxidized into rose-petal-like mesoporous MnO2 structure. Such a 3D MnO2/VACNF hybrid architecture provides enhanced ion diffusion throughout the whole MnO2 shell and yields excellent current collection capability through the VACNF electrode. These two effects collectively enable faster electrochemical reactions during charge-discharge of MnO2 in 1 M Na2SO4. Thick MnO2 shells (up to 200 nm in radial thickness) can be employed, giving a specific capacitance up to 437 F g-1. More importantly, supercapacitors employing such a 3D MnO2/VACNF hybrid electrode illustrate more than one order of magnitude higher specific power than the state-of-the-art ones based on other MnO2 structures, reaching ~240 kW kg-1, while maintaining a comparable specific energy in the range of 1 to 10 Wh kg-1. This hybrid approach demonstrates the potential of 3D core-shell architectures for high-power energy storage devices.A study on the development of high-power supercapacitor materials based on formation of thick mesoporous MnO2 shells on a highly conductive 3D template using vertically aligned carbon nanofibers (VACNFs). Coaxial manganese shells of 100 to 600 nm nominal thicknesses are sputter-coated on VACNFs and then electrochemically oxidized into rose-petal-like mesoporous MnO2 structure. Such a 3D MnO2/VACNF hybrid architecture provides enhanced ion diffusion throughout the whole MnO2 shell and yields excellent current collection capability through the VACNF electrode. These two effects collectively enable faster electrochemical reactions during charge-discharge of MnO2 in 1 M Na2SO4. Thick MnO2 shells (up to 200 nm in radial thickness) can be employed, giving a

  11. On comparing two structured RNA multiple alignments.

    PubMed

    Patel, Vandanaben; Wang, Jason T L; Setia, Shefali; Verma, Anurag; Warden, Charles D; Zhang, Kaizhong

    2010-12-01

    We present a method, called BlockMatch, for aligning two blocks, where a block is an RNA multiple sequence alignment with the consensus secondary structure of the alignment in Stockholm format. The method employs a quadratic-time dynamic programming algorithm for aligning columns and column pairs of the multiple alignments in the blocks. Unlike many other tools that can perform pairwise alignment of either single sequences or structures only, BlockMatch takes into account the characteristics of all the sequences in the blocks along with their consensus structures during the alignment process, thus being able to achieve a high-quality alignment result. We apply BlockMatch to phylogeny reconstruction on a set of 5S rRNA sequences taken from fifteen bacteria species. Experimental results showed that the phylogenetic tree generated by our method is more accurate than the tree constructed based on the widely used ClustalW tool. The BlockMatch algorithm is implemented into a web server, accessible at http://bioinformatics.njit.edu/blockmatch. A jar file of the program is also available for download from the web server. PMID:21121021

  12. Evaluation of the Quantitative Accuracy of 3D Reconstruction of Edentulous Jaw Models with Jaw Relation Based on Reference Point System Alignment

    PubMed Central

    Li, Weiwei; Yuan, Fusong; Lv, Peijun; Wang, Yong; Sun, Yuchun

    2015-01-01

    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. PMID:25659133

  13. Method of making self-aligned lightly-doped-drain structure for MOS transistors

    DOEpatents

    Weiner, Kurt H.; Carey, Paul G.

    2001-01-01

    A process for fabricating lightly-doped-drains (LDD) for short-channel metal oxide semiconductor (MOS) transistors. The process utilizes a pulsed laser process to incorporate the dopants, thus eliminating the prior oxide deposition and etching steps. During the process, the silicon in the source/drain region is melted by the laser energy. Impurities from the gas phase diffuse into the molten silicon to appropriately dope the source/drain regions. By controlling the energy of the laser, a lightly-doped-drain can be formed in one processing step. This is accomplished by first using a single high energy laser pulse to melt the silicon to a significant depth and thus the amount of dopants incorporated into the silicon is small. Furthermore, the dopants incorporated during this step diffuse to the edge of the MOS transistor gate structure. Next, many low energy laser pulses are used to heavily dope the source/drain silicon only in a very shallow region. Because of two-dimensional heat transfer at the MOS transistor gate edge, the low energy pulses are inset from the region initially doped by the high energy pulse. By computer control of the laser energy, the single high energy laser pulse and the subsequent low energy laser pulses are carried out in a single operational step to produce a self-aligned lightly-doped-drain-structure.

  14. Design and performance of an automated video-based laser beam alignment system

    SciTech Connect

    Rundle, W.J. ); Kartz, M.W. ); Bliss, E.S.; English, R.E. Jr.; Peterson, R.L.; Thompson, G.R.; Uhlich, D.M. )

    1992-07-14

    This paper describes the design and performance of an automated, closed-loop, laser beam alignment system. Its function is to sense a beam alignment error in a laser beam transport system and automatically steer mirrors preceding the sensor location as required to maintain beam alignment. The laser beam is sampled by an optomechanical package which uses video cameras to sense pointing and centering errors. The camera outputs are fed to an image processing module, which includes video digitizers and uses image storage and software to sense the centroid of the image. Signals are sent through a VMEbus to an optical device controller'' (ODC), which drives stepper-motor actuators on mirror mounts preceding the beam-sampling location to return the beam alignment to the prescribed condition. Photodiodes are also used to extend the control bandwidth beyond that which is achievable with video cameras. This system has been operated at LLNL in the Atomic Vapor Laser Isotope Separation (AVLIS) program to maintain the alignment of copper and dye laser beams, the latter to within [plus minus]2 [mu]r in pointing and less than 1 mm in centering. The optomechanical design of the instrumented package, which includes lens, mirror, and video mounts in a rigid housing, the automated control system architecture, and the performance of this equipment is described.

  15. Design and performance of an automated video-based laser beam alignment system

    SciTech Connect

    Rundle, W.J.; Kartz, M.W.; Bliss, E.S.; English, R.E. Jr.; Peterson, R.L.; Thompson, G.R.; Uhlich, D.M.

    1992-07-14

    This paper describes the design and performance of an automated, closed-loop, laser beam alignment system. Its function is to sense a beam alignment error in a laser beam transport system and automatically steer mirrors preceding the sensor location as required to maintain beam alignment. The laser beam is sampled by an optomechanical package which uses video cameras to sense pointing and centering errors. The camera outputs are fed to an image processing module, which includes video digitizers and uses image storage and software to sense the centroid of the image. Signals are sent through a VMEbus to an ``optical device controller`` (ODC), which drives stepper-motor actuators on mirror mounts preceding the beam-sampling location to return the beam alignment to the prescribed condition. Photodiodes are also used to extend the control bandwidth beyond that which is achievable with video cameras. This system has been operated at LLNL in the Atomic Vapor Laser Isotope Separation (AVLIS) program to maintain the alignment of copper and dye laser beams, the latter to within {plus_minus}2 {mu}r in pointing and less than 1 mm in centering. The optomechanical design of the instrumented package, which includes lens, mirror, and video mounts in a rigid housing, the automated control system architecture, and the performance of this equipment is described.

  16. Teaching Evidence-Based Psychiatry: Integrating and Aligning the Formal and Hidden Curricula

    ERIC Educational Resources Information Center

    Agrawal, Sacha; Szatmari, Peter; Hanson, Mark

    2008-01-01

    Objective: The authors argue that adopting evidence-based psychiatry will require a paradigm shift in the training of psychiatry residents, and offer some suggestions for how this transformation might be achieved. Methods: The authors review the growing literature that addresses how best to teach evidence-based medicine and highlight several…

  17. [100] or [110] aligned, semiconductor-based, large-area, flexible, electronic devices

    SciTech Connect

    Goyal, Amit

    2015-03-24

    Novel articles and methods to fabricate the same resulting in flexible, large-area, [100] or [110] textured, semiconductor-based, electronic devices are disclosed. Potential applications of resulting articles are in areas of photovoltaic devices, flat-panel displays, thermophotovoltaic devices, ferroelectric devices, light emitting diode devices, computer hard disc drive devices, magnetoresistance based devices, photoluminescence based devices, non-volatile memory devices, dielectric devices, thermoelectric devices and quantum dot laser devices.

  18. XUV ionization of aligned molecules

    SciTech Connect

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

    2011-11-15

    New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO{sub 2} molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

  19. Synthesis of Vertically Aligned ZnO Nanorods on Ni-Based Buffer Layers Using a Thermal Evaporation Process

    NASA Astrophysics Data System (ADS)

    Kuo, Dong-Hau; He, Jheng-Yu; Huang, Ying-Sheng

    2012-03-01

    Uniform, vertically aligned ZnO nanorods have been grown mainly on Au-coated and ZnO-coated sapphire substrates, ZnO- and GaN-coated substrates, or self-catalyzing substrates. Conventionally, Ni-coated substrates have resulted in thick rods with diameter more than 250 nm, rods with nonuniform distribution in diameter, or rods with an alignment problem. In the best result in this paper, slender, uniform, vertically aligned, solely UV-emitting ZnO nanorods with diameter of 110 ± 25 nm and length of 30 ± 10 μm have been successfully grown at 700°C for 2 h on sapphire substrates covered with Ni-based buffer layers by using metallic zinc and oxygen as reactants. Scanning electron microscopy and room-temperature photoluminescence have been used to investigate the effects of process conditions on the slenderness and vertical alignment of the ZnO rods. To develop the desired ZnO nanorods, etched sapphire substrates, a second metallic Sn buffer layer on top of a spin-coated nickel oxide layer, polyvinyl alcohol binder at 10% concentration in solution of iron nitrate, and pyrolysis and reduction reactions were involved. Defect photoemission for thick ZnO rods is attributed to insufficient oxygen supply during the growth process with fixed oxygen flow rate.

  20. Systems and Methods for Fabricating Carbon Nanotube-Based Vacuum Electronic Devices

    NASA Technical Reports Server (NTRS)

    Manohara, Harish (Inventor); Toda, Risaku (Inventor); Del Castillo, Linda Y. (Inventor); Murthy, Rakesh (Inventor)

    2015-01-01

    Systems and methods in accordance with embodiments of the invention proficiently produce carbon nanotube-based vacuum electronic devices. In one embodiment a method of fabricating a carbon nanotube-based vacuum electronic device includes: growing carbon nanotubes onto a substrate to form a cathode; assembling a stack that includes the cathode, an anode, and a first layer that includes an alignment slot; disposing a microsphere partially into the alignment slot during the assembling of the stack such that the microsphere protrudes from the alignment slot and can thereby separate the first layer from an adjacent layer; and encasing the stack in a vacuum sealed container.

  1. Direct synthesis of vertically aligned ZnO nanowires on FTO substrates using a CVD method and the improvement of photovoltaic performance

    PubMed Central

    2012-01-01

    In this work, we report a direct synthesis of vertically aligned ZnO nanowires on fluorine-doped tin oxide-coated substrates using the chemical vapor deposition (CVD) method. ZnO nanowires with a length of more than 30 μm were synthesized, and dye-sensitized solar cells (DSSCs) based on the as-grown nanowires were fabricated, which showed improvement of the device performance compared to those fabricated using transferred ZnO nanowires. Dependence of the cell performance on nanowire length and annealing temperature was also examined. This synthesis method provided a straightforward, one-step CVD process to grow relatively long ZnO nanowires and avoided subsequent nanowire transfer process, which simplified DSSC fabrication and improved cell performance. PMID:22673046

  2. Aligning Experimental and Theoretical Anisotropic B-Factors: Water Models, Normal-Mode Analysis Methods, and Metrics

    PubMed Central

    2014-01-01

    The strength of X-ray crystallography in providing the information for protein dynamics has been under appreciated. The anisotropic B-factors (ADPs) from high-resolution structures are invaluable in studying the relationship among structure, dynamics, and function. Here, starting from an in-depth evaluation of the metrics used for comparing the overlap between two ellipsoids, we applied normal-mode analysis (NMA) to predict the theoretical ADPs and then align them with experimental results. Adding an extra layer of explicitly treated water on protein surface significantly improved the energy minimization results and better reproduced the anisotropy of experimental ADPs. In comparing experimental and theoretical ADPs, we focused on the overlap in shape, the alignment of dominant directions, and the similarity in magnitude. The choices of water molecules, NMA methods, and the metrics for evaluating the overlap of ADPs determined final results. This study provides useful information for exploring the physical basis and the application potential of experimental ADPs. PMID:24673391

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

    PubMed Central

    Vihstadt, Corrie; Evans, Roni

    2015-01-01

    Background: 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. Methods: 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. Results: 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. Conclusion: 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. PMID:26421233

  4. Large-area graphene-based nanofiltration membranes by shear alignment of discotic nematic liquid crystals of graphene oxide

    PubMed Central

    Akbari, Abozar; Sheath, Phillip; Martin, Samuel T.; Shinde, Dhanraj B.; Shaibani, Mahdokht; Banerjee, Parama Chakraborty; Tkacz, Rachel; Bhattacharyya, Dibakar; Majumder, Mainak

    2016-01-01

    Graphene-based membranes demonstrating ultrafast water transport, precise molecular sieving of gas and solvated molecules shows great promise as novel separation platforms; however, scale-up of these membranes to large-areas remains an unresolved problem. Here we demonstrate that the discotic nematic phase of graphene oxide (GO) can be shear aligned to form highly ordered, continuous, thin films of multi-layered GO on a support membrane by an industrially adaptable method to produce large-area membranes (13 × 14 cm2) in <5 s. Pressure driven transport data demonstrate high retention (>90%) for charged and uncharged organic probe molecules with a hydrated radius above 5 Å as well as modest (30–40%) retention of monovalent and divalent salts. The highly ordered graphene sheets in the plane of the membrane make organized channels and enhance the permeability (71±5 l m−2 hr−1 bar−1 for 150±15 nm thick membranes). PMID:26947916

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

    PubMed Central

    Shahrudin, Shahriza

    2015-01-01

    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. PMID:25802839

  6. Critical Alignment in Inquiry-Based Practice in Developing Mathematics Teaching

    ERIC Educational Resources Information Center

    Goodchild, Simon; Fuglestad, Anne Berit; Jaworski, Barbara

    2013-01-01

    This paper reports a case study from a mathematics teaching developmental research project. The theoretical foundation for the research comprises "communities of inquiry" and "critical alignment," with which the developmental methodology has a particular synergy. This synergy is the main focus of the paper. The paper elaborates…

  7. Tidal alignment of galaxies

    NASA Astrophysics Data System (ADS)

    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.

  8. A simple method for fabrication of electrospun fibers with controlled degree of alignment having potential for nerve regeneration applications.

    PubMed

    Vimal, Sunil Kumar; Ahamad, Nadim; Katti, Dhirendra S

    2016-06-01

    In peripheral nerve injuries where direct suturing of nerve endings is not feasible, nerve regeneration has been facilitated through the use of artificially aligned fibrous scaffolds that provide directional growth of neurons to bridge the gap. The degree of fiber alignment is crucial and can impact the directionality of cells in a fibrous scaffold. While there have been multiple approaches that have been used for controlling fiber alignment, however, they have been associated with a compromised control on other properties, such as diameter, morphology, curvature, and topology of fibers. Therefore, the present study demonstrates a modified electrospinning set-up, that enabled fabrication of electrospun fibers with controlled degree of alignment from non-aligned (NA), moderately aligned (MA, 75%) to highly aligned (HA, 95%) sub-micron fibers while keeping other physical properties unchanged. The results demonstrate that the aligned fibers (MA and HA) facilitated directional growth of human astrocytoma cells (U373), wherein the aspect ratio of cells was found to increase with an increase in degree of fibers alignment. In contrast to NA and MA fibers, the HA fibers showed improved contact guidance to U373 cells that was demonstrated by a significantly higher cell aspect ratio and nuclear aspect ratio. In conclusion, the present study demonstrated a modified electrospinning setup to fabricate differentially aligned fibrous scaffolds with the HA fibers showing potential for use in neural tissue engineering. PMID:27040257

  9. Alignability of Optical Interconnects

    NASA Astrophysics Data System (ADS)

    Beech, Russell Scott

    With the continuing drive towards higher speed, density, and functionality in electronics, electrical interconnects become inadequate. Due to optics' high speed and bandwidth, freedom from capacitive loading effects, and freedom from crosstalk, optical interconnects can meet more stringent interconnect requirements. But, an optical interconnect requires additional components, such as an optical source and detector, lenses, holographic elements, etc. Fabrication and assembly of an optical interconnect requires precise alignment of these components. The successful development and deployment of optical interconnects depend on how easily the interconnect components can be aligned and/or how tolerant the interconnect is to misalignments. In this thesis, a method of quantitatively specifying the relative difficulty of properly aligning an optical interconnect is described. Ways of using this theory of alignment to obtain design and packaging guidelines for optical interconnects are examined. The measure of the ease with which an optical interconnect can be aligned, called the alignability, uses the efficiency of power transfer as a measure of alignment quality. The alignability is related to interconnect package design through the overall cost measure, which depends upon various physical parameters of the interconnect, such as the cost of the components and the time required for fabrication and alignment. Through a mutual dependence on detector size, the relationship between an interconnect's alignability and its bandwidth, signal-to-noise ratio, and bit-error -rate is examined. The results indicate that a range of device sizes exists for which given performance threshold values are satisfied. Next, the alignability of integrated planar-optic backplanes is analyzed in detail. The resulting data show that the alignability can be optimized by varying the substrate thickness or the angle of reflection. By including the effects of crosstalk, in a multi-channel backplane, the

  10. FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions

    PubMed Central

    Gatto, Alberto; Torroja-Fungairiño, Carlos; Mazzarotto, Francesco; Cook, Stuart A.; Barton, Paul J. R.; Sánchez-Cabo, Fátima; Lara-Pezzi, Enrique

    2014-01-01

    Alternative splicing is the main mechanism governing protein diversity. The recent developments in RNA-Seq technology have enabled the study of the global impact and regulation of this biological process. However, the lack of standardized protocols constitutes a major bottleneck in the analysis of alternative splicing. This is particularly important for the identification of exon–exon junctions, which is a critical step in any analysis workflow. Here we performed a systematic benchmarking of alignment tools to dissect the impact of design and method on the mapping, detection and quantification of splice junctions from multi-exon reads. Accordingly, we devised a novel pipeline based on TopHat2 combined with a splice junction detection algorithm, which we have named FineSplice. FineSplice allows effective elimination of spurious junction hits arising from artefactual alignments, achieving up to 99% precision in both real and simulated data sets and yielding superior F1 scores under most tested conditions. The proposed strategy conjugates an efficient mapping solution with a semi-supervised anomaly detection scheme to filter out false positives and allows reliable estimation of expressed junctions from the alignment output. Ultimately this provides more accurate information to identify meaningful splicing patterns. FineSplice is freely available at https://sourceforge.net/p/finesplice/. PMID:24574529

  11. FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions.

    PubMed

    Gatto, Alberto; Torroja-Fungairiño, Carlos; Mazzarotto, Francesco; Cook, Stuart A; Barton, Paul J R; Sánchez-Cabo, Fátima; Lara-Pezzi, Enrique

    2014-04-01

    Alternative splicing is the main mechanism governing protein diversity. The recent developments in RNA-Seq technology have enabled the study of the global impact and regulation of this biological process. However, the lack of standardized protocols constitutes a major bottleneck in the analysis of alternative splicing. This is particularly important for the identification of exon-exon junctions, which is a critical step in any analysis workflow. Here we performed a systematic benchmarking of alignment tools to dissect the impact of design and method on the mapping, detection and quantification of splice junctions from multi-exon reads. Accordingly, we devised a novel pipeline based on TopHat2 combined with a splice junction detection algorithm, which we have named FineSplice. FineSplice allows effective elimination of spurious junction hits arising from artefactual alignments, achieving up to 99% precision in both real and simulated data sets and yielding superior F1 scores under most tested conditions. The proposed strategy conjugates an efficient mapping solution with a semi-supervised anomaly detection scheme to filter out false positives and allows reliable estimation of expressed junctions from the alignment output. Ultimately this provides more accurate information to identify meaningful splicing patterns. FineSplice is freely available at https://sourceforge.net/p/finesplice/. PMID:24574529

  12. A Case Study of the Alignment between Curriculum and Assessment in the New York State Earth Science Standards-Based System

    ERIC Educational Resources Information Center

    Contino, Julie

    2013-01-01

    In a standards-based system, it is important for all components of the system to align in order to achieve the intended goals. No Child Left Behind law mandates that assessments be fully aligned with state standards, be valid, reliable and fair, be reported to all stakeholders, and provide evidence that all students in the state are meeting the…

  13. Exploring the alignment of writing self-efficacy with writing achievement using rasch measurement theory and qualitative methods.

    PubMed

    Engelhard, George; Behizadeh, Nadia

    2012-01-01

    Alignment of writing self-efficacy and writing achievement is defined as the congruence between student confidence regarding writing skills (writing self-efficacy) and the actual performance on these writing skills as reflected in teacher grades (achievement). One purpose of this study is to examine the relationship between these two variables. A second purpose is to demonstrate a mixed-methods approach to investigating relationships between affective variables using Rasch measurement and interviews. Participants were eighth grade students (N = 94) from an ethnically and socioeconomically diverse school in the southeastern United States. Our results suggest that students who struggle with the mechanics of writing yet appreciate the expressive capacity of writing, may have higher senses of writing self-efficacy that are not predictive of performance. PMID:22805358

  14. Chip electrochromatographic systems: Novel vertically aligned carbon nanotube and silica monoliths based separations

    NASA Astrophysics Data System (ADS)

    Goswami, Shubhodeep

    2009-12-01

    Miniaturized chemical analysis systems, also know as 'lab-on-a-chip' devices have been rapidly developing over the last decade. Capillary electrochromatography (CEC), a multidimensional separation technique combining capillary electrophoresis (CE) and liquid chromatography (LC) has been of great interest for chip based applications. Preliminary work has been undertaken to develop vertically aligned carbon nanotubes and photopolymerizable silica solgel as novel stationary phase materials for 'chip CEC' separations. Patterned growth of CNTs in a specific location of the channel has been carried out using a solid phase Fe-Al catalyst as well as a vapor deposited ferrocene catalyst. Characterization of the CNT "forests" was achieved using optical microscopy, secondary electron microscopy, high resolution tunneling electron microscopy and Raman spectroscopy. Proof-of-concept applications were demonstrated using reversed phase CEC separations as well as solid phase extraction of a glycosylated protein using concanavilin A immobilized onto the CNT bed. Photopolymerizable silica solgel materials were developed as stationary phase for microfluidic electrochromatographic separations in disposable polydimethylsiloxane (PDMS) chip devices. Effect on morphology and pore size of gels were studied as function of UV and solgel polymerization conditions, porogen, salt additives, geometry and hydrolyzable methoxy-ies. Structural morphologies were studied with Secondary Electron Microscopy (SEM). Pore size and pore volumes were characterized by thermal porometry, nitrogen BET adsorptions and differential scanning calorimetry. Computational fluid dynamics and confocal microscopy tools were employed to study the transport of fluids and model analytes. These investigations were directed towards evolving improved strategies for rinsing of uncrosslinked monomers to form porous monoliths as well as to effect a desired separation under a set of electrochromatograhic conditions

  15. School-Based Assessment of ADHD: Purpose, Alignment with Best Practice Guidelines, and Training

    ERIC Educational Resources Information Center

    Ogg, Julia; Fefer, Sarah; Sundman-Wheat, Ashley; McMahan, Melanie; Stewart, Tiffany; Chappel, Ashley; Bateman, Lisa

    2013-01-01

    Youth exhibiting symptoms of attention deficit hyperactivity disorder are frequently referred to school psychologists because of academic, social, and behavioral difficulties that they face. To address these difficulties, evidence-based assessment methods have been outlined for multiple purposes of assessment. The goals of this study were to…

  16. Alignment-Free Sequence Comparison Based on Next-Generation Sequencing Reads

    PubMed Central

    Song, Kai; Ren, Jie; Zhai, Zhiyuan; Liu, Xuemei

    2013-01-01

    Abstract Next-generation sequencing (NGS) technologies have generated enormous amounts of shotgun read data, and assembly of the reads can be challenging, especially for organisms without template sequences. We study the power of genome comparison based on shotgun read data without assembly using three alignment-free sequence comparison statistics, D2, \\documentclass{aastex}\\usepackage{amsbsy}\\usepackage{amsfonts}\\usepackage{amssymb}\\usepackage{bm}\\usepackage{mathrsfs}\\usepackage{pifont}\\usepackage{stmaryrd}\\usepackage{textcomp}\\usepackage{portland, xspace}\\usepackage{amsmath, amsxtra}\\pagestyle{empty}\\DeclareMathSizes{10}{9}{7}{6}\\begin{document} $$\\textbf{\\textit{D}}_{\\bf 2}^{\\bf *}$$ \\end{document}, and \\documentclass{aastex}\\usepackage{amsbsy}\\usepackage{amsfonts}\\usepackage{amssymb}\\usepackage{bm}\\usepackage{mathrsfs}\\usepackage{pifont}\\usepackage{stmaryrd}\\usepackage{textcomp}\\usepackage{portland, xspace}\\usepackage{amsmath, amsxtra}\\pagestyle{empty}\\DeclareMathSizes{10}{9}{7}{6}\\begin{document} $$\\textbf{\\textit{D}}_{\\bf 2}^S$$ \\end{document}, both theoretically and by simulations. Theoretical formulas for the power of detecting the relationship between two sequences related through a common motif model are derived. It is shown that both \\documentclass{aastex}\\usepackage{amsbsy}\\usepackage{amsfonts}\\usepackage{amssymb}\\usepackage{bm}\\usepackage{mathrsfs}\\usepackage{pifont}\\usepackage{stmaryrd}\\usepackage{textcomp}\\usepackage{portland, xspace}\\usepackage{amsmath, amsxtra}\\pagestyle{empty}\\DeclareMathSizes{10}{9}{7}{6}\\begin{document} $$\\textbf{\\textit{D}}_{\\bf 2}^{\\bf *}$$ \\end{document} and \\documentclass{aastex}\\usepackage{amsbsy}\\usepackage{amsfonts}\\usepackage{amssymb}\\usepackage{bm}\\usepackage{mathrsfs}\\usepackage{pifont}\\usepackage{stmaryrd}\\usepackage{textcomp}\\usepackage{portland, xspace}\\usepackage{amsmath, amsxtra}\\pagestyle{empty}\\DeclareMathSizes{10}{9}{7}{6}\\begin

  17. KMAD: knowledge-based multiple sequence alignment for intrinsically disordered proteins

    PubMed Central

    Lange, Joanna; Wyrwicz, Lucjan S.; Vriend, Gert

    2016-01-01

    Summary: Intrinsically disordered proteins (IDPs) lack tertiary structure and thus differ from globular proteins in terms of their sequence–structure–function relations. IDPs have lower sequence conservation, different types of active sites and a different distribution of functionally important regions, which altogether make their multiple sequence alignment (MSA) difficult. The KMAD MSA software has been written specifically for the alignment and annotation of IDPs. It augments the substitution matrix with knowledge about post-translational modifications, functional domains and short linear motifs. Results: MSAs produced with KMAD describe well-conserved features among IDPs, tend to agree well with biological intuition, and are a good basis for designing new experiments to shed light on this large, understudied class of proteins. Availability and implementation: KMAD web server is accessible at http://www.cmbi.ru.nl/kmad/. A standalone version is freely available. Contact: vriend@cmbi.ru.nl PMID:26568635

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

    NASA Astrophysics Data System (ADS)

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

  20. Aligning Person-Centred Methods and Young People's Conceptualizations of Diversity

    ERIC Educational Resources Information Center

    Waite, Sue; Boyask, Ruth; Lawson, Hazel

    2010-01-01

    Many existing studies of diversity are concerned with social groups identified by externally determined factors, for example, ethnicity, gender, or educational attainment, and examine, either quantitatively or qualitatively, issues delineated by these. In evaluating methods used in previous research, we consider ways in which the adoption of…

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

    PubMed

    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. PMID:27237223

  2. Scanning electron microscopy analysis of the growth of dental plaque on the surfaces of removable orthodontic aligners after the use of different cleaning methods

    PubMed Central

    Levrini, Luca; Novara, Francesca; Margherini, Silvia; Tenconi, Camilla; Raspanti, Mario

    2015-01-01

    Background Advances in orthodontics are leading to the use of minimally invasive technologies, such as transparent removable aligners, and are able to meet high demands in terms of performance and esthetics. However, the most correct method of cleaning these appliances, in order to minimize the effects of microbial colonization, remains to be determined. Purpose The aim of the present study was to identify the most effective method of cleaning removable orthodontic aligners, analyzing the growth of dental plaque as observed under scanning electron microscopy. Methods Twelve subjects were selected for the study. All were free from caries and periodontal disease and were candidates for orthodontic therapy with invisible orthodontic aligners. The trial had a duration of 6 weeks, divided into three 2-week stages, during which three sets of aligners were used. In each stage, the subjects were asked to use a different method of cleaning their aligners: 1) running water (control condition); 2) effervescent tablets containing sodium carbonate and sulfate crystals followed by brushing with a toothbrush; and 3) brushing alone (with a toothbrush and toothpaste). At the end of each 2-week stage, the surfaces of the aligners were analyzed under scanning electron microscopy. Results The best results were obtained with brushing combined with the use of sodium carbonate and sulfate crystals; brushing alone gave slightly inferior results. Conclusion On the basis of previous literature results relating to devices in resin, studies evaluating the reliability of domestic ultrasonic baths for domestic use should be encouraged. At present, pending the availability of experimental evidence, it can be suggested that dental hygienists should strongly advise patients wearing orthodontic aligners to clean them using a combination of brushing and commercially available tablets for cleaning oral appliances. PMID:26719726

  3. Embedded arrays of vertically aligned carbon nanotube carpets and methods for making them

    DOEpatents

    Kim, Myung Jong; Nicholas, Nolan Walker; Kittrell, W. Carter; Schmidt, Howard K.

    2015-06-30

    According to some embodiments, the present invention provides a system and method for supporting a carbon nanotube array that involve an entangled carbon nanotube mat integral with the array, where the mat is embedded in an embedding material. The embedding material may be depositable on a carbon nanotube. A depositable material may be metallic or nonmetallic. The embedding material may be an adhesive material. The adhesive material may optionally be mixed with a metal powder. The embedding material may be supported by a substrate or self-supportive. The embedding material may be conductive or nonconductive. The system and method provide superior mechanical and, when applicable, electrical, contact between the carbon nanotubes in the array and the embedding material. The optional use of a conductive material for the embedding material provides a mechanism useful for integration of carbon nanotube arrays into electronic devices.

  4. Method for photolithographic definition of recessed features on a semiconductor wafer utilizing auto-focusing alignment

    DOEpatents

    Farino, A.J.; Montague, S.; Sniegowski, J.J.; Smith, J.H.; McWhorter, P.J.

    1998-07-21

    A method is disclosed for photolithographically defining device features up to the resolution limit of an auto-focusing projection stepper when the device features are to be formed in a wafer cavity at a depth exceeding the depth of focus of the stepper. The method uses a focusing cavity located in a die field at the position of a focusing light beam from the auto-focusing projection stepper, with the focusing cavity being of the same depth as one or more adjacent cavities wherein a semiconductor device is to be formed. The focusing cavity provides a bottom surface for referencing the focusing light beam and focusing the stepper at a predetermined depth below the surface of the wafer, whereat the device features are to be defined. As material layers are deposited in each device cavity to build up a semiconductor structure such as a microelectromechanical system (MEMS) device, the same material layers are deposited in the focusing cavity, raising the bottom surface and re-focusing the stepper for accurately defining additional device features in each succeeding material layer. The method is especially applicable for forming MEMS devices within a cavity or trench and integrating the MEMS devices with electronic circuitry fabricated on the wafer surface. 15 figs.

  5. Method for photolithographic definition of recessed features on a semiconductor wafer utilizing auto-focusing alignment

    DOEpatents

    Farino, Anthony J.; Montague, Stephen; Sniegowski, Jeffry J.; Smith, James H.; McWhorter, Paul J.

    1998-01-01

    A method is disclosed for photolithographically defining device features up to the resolution limit of an auto-focusing projection stepper when the device features are to be formed in a wafer cavity at a depth exceeding the depth of focus of the stepper. The method uses a focusing cavity located in a die field at the position of a focusing light beam from the auto-focusing projection stepper, with the focusing cavity being of the same depth as one or more adjacent cavities wherein a semiconductor device is to be formed. The focusing cavity provides a bottom surface for referencing the focusing light beam and focusing the stepper at a predetermined depth below the surface of the wafer, whereat the device features are to be defined. As material layers are deposited in each device cavity to build up a semiconductor structure such as a microelectromechanical system (MEMS) device, the same material layers are deposited in the focusing cavity, raising the bottom surface and re-focusing the stepper for accurately defining additional device features in each succeeding material layer. The method is especially applicable for forming MEMS devices within a cavity or trench and integrating the MEMS devices with electronic circuitry fabricated on the wafer surface.

  6. Exploration of Tunnel Alignment using Geophysical Methods to Increase Safety for Planning and Minimizing Risk

    NASA Astrophysics Data System (ADS)

    Lehmann, Bodo; Orlowsky, Dirk; Misiek, Rüdiger

    2010-02-01

    Engineering geophysics provides valuable and continuous information for the planning and execution of tunnel construction projects. For geotechnical purposes special high-resolution geophysical methods have been developed during the last decades. The importance of applying geophysical methods in addition to usually used geological and geotechnical exploration techniques is increasing. The main goal is to achieve an accurate and continuous model of the subsurface in a relative short period of operation time. The routine application of engineering geophysical methods will increase in the coming years. Due to the high acceptance of engineering geophysics at construction sites, much wider application of geophysical investigations is expected. The combination of different methods—geophysics, geology, and geotechnics as well as the so-called joint interpretation techniques—will be of essential importance. Engineering geophysics will play an important role during the three phases: geological investigation, tunnel planning, and execution of tunnel construction. If hazards are well known in advance of a tunnel project the safety of workers will essentially be increased and geological risks will be minimized by means of successful and interdisciplinary cooperation.

  7. A fast alignment method for breast MRI follow-up studies using automated breast segmentation and current-prior registration

    NASA Astrophysics Data System (ADS)

    Wang, Lei; Strehlow, Jan; Rühaak, Jan; Weiler, Florian; Diez, Yago; Gubern-Merida, Albert; Diekmann, Susanne; Laue, Hendrik; Hahn, Horst K.

    2015-03-01

    In breast cancer screening for high-risk women, follow-up magnetic resonance images (MRI) are acquired with a time interval ranging from several months up to a few years. Prior MRI studies may provide additional clinical value when examining the current one and thus have the potential to increase sensitivity and specificity of screening. To build a spatial correlation between suspicious findings in both current and prior studies, a reliable alignment method between follow-up studies is desirable. However, long time interval, different scanners and imaging protocols, and varying breast compression can result in a large deformation, which challenges the registration process. In this work, we present a fast and robust spatial alignment framework, which combines automated breast segmentation and current-prior registration techniques in a multi-level fashion. First, fully automatic breast segmentation is applied to extract the breast masks that are used to obtain an initial affine transform. Then, a non-rigid registration algorithm using normalized gradient fields as similarity measure together with curvature regularization is applied. A total of 29 subjects and 58 breast MR images were collected for performance assessment. To evaluate the global registration accuracy, the volume overlap and boundary surface distance metrics are calculated, resulting in an average Dice Similarity Coefficient (DSC) of 0.96 and root mean square distance (RMSD) of 1.64 mm. In addition, to measure local registration accuracy, for each subject a radiologist annotated 10 pairs of markers in the current and prior studies representing corresponding anatomical locations. The average distance error of marker pairs dropped from 67.37 mm to 10.86 mm after applying registration.

  8. Self-aligned BCB planarization method for high-frequency signal injection in a VCSEL with an integrated modulator

    NASA Astrophysics Data System (ADS)

    Marigo-Lombart, Ludovic; Doucet, Jean-Baptiste; Lecestre, Aurélie; Reig, Benjamin; Rousset, Bernard; Thienpont, Hugo; Panajotov, Krassimir; Almuneau, Guilhem

    2016-04-01

    The huge increase of datacom capacities requires lasers sources with more and more bandwidth performances. Vertical-Cavity Surface-Emitting Lasers (VCSEL) in direct modulation is a good candidate, already widely used for short communication links such as in datacenters. Recently several different approaches have been proposed to further extend the direct modulation bandwidth of these devices, by improving the VCSEL structure, or by combining the VCSEL with another high speed element such as lateral slow light modulator or transistor/laser based structure (TVCSEL). We propose to increase the modulation bandwidth by vertically integrating a continuous-wave VCSEL with a high-speed electro-modulator. This vertical structure implies multiple electrodes with sufficiently good electrical separation between the different input electrical signals. This high frequency modulation requires both good electrical insulation between metal electrodes and an optimized design of the coplanar lines. BenzoCyclobutene (BCB) thanks to its low dielectric constant, low losses, low moisture absorption and good thermal stability, is often used as insulating layer. Also, BCB planarization offers the advantages of simpler and more reliable technological process flow in such integrated VCSEL/modulator structures with important reliefs. As described by Burdeaux et al. a degree of planarization (DOP) of about 95% can be achieved by simple spin coating whatever the device thickness. In most of the cases, the BCB planarization process requires an additional photolithography step in order to open an access to the mesa surface, thus involving a tight mask alignment and resulting in a degraded planarization. In this paper, we propose a self-aligned process with improved BCB planarization by combining a hot isostatic pressing derived from nanoimprint techniques with a dry plasma etching step.

  9. Alignment validation

    SciTech Connect

    ALICE; ATLAS; CMS; LHCb; Golling, Tobias

    2008-09-06

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

  10. Photo-aligned ferroelectric liquid crystals in microchannels.

    PubMed

    Budaszewski, Daniel; Srivastava, Abhishek K; Tam, Alwin M W; Wolinski, Tomasz R; Chigrinov, Vladimir G; Kwok, Hoi-Sing

    2014-08-15

    In this Letter we disclose a method to realize a good alignment of ferroelectric liquid crystals (FLCs) in microchannels, based on photo-alignment. The sulfonic azo dye used in our research offers variable anchoring energy depending on the irradiation energy and thus provides good control on the FLC alignment in microchannels. The good FLC alignment has been observed only when anchoring energy normalized to the capillary diameter is less than the elastic energy of the FLC helix. The same approach can also be used for the different microstructures viz. photonic crystal fibers, microwaveguides, etc. which gives an opportunity for designing a photonic devices based on FLC. PMID:25121847

  11. Aligned crystalline semiconducting film on a glass substrate and method of making

    DOEpatents

    Findikoglu, Alp T.

    2010-08-24

    A semiconducting structure having a glass substrate. In one embodiment, the glass substrate has a softening temperature of at least about 750.degree. C. The structure includes a nucleation layer formed on a surface of the substrate, a template layer deposited on the nucleation layer by one of ion assisted beam deposition and reactive ion beam deposition, at least on biaxially oriented buffer layer epitaxially deposited on the template layer, and a biaxially oriented semiconducting layer epitaxially deposited on the buffer layer. A method of making the semiconducting structure is also described.

  12. Automated target segmentation and real space fast alignment methods for high-throughput classification and averaging of crowded cryo-electron subtomograms

    PubMed Central

    Xu, Min; Alber, Frank

    2013-01-01

    Motivation: Cryo-electron tomography allows the imaging of macromolecular complexes in near living conditions. To enhance the nominal resolution of a structure it is necessary to align and average individual subtomograms each containing identical complexes. However, if the sample of complexes is heterogeneous, it is necessary to first classify subtomograms into groups of identical complexes. This task becomes challenging when tomograms contain mixtures of unknown complexes extracted from a crowded environment. Two main challenges must be overcomed: First, classification of subtomograms must be performed without knowledge of template structures. However, most alignment methods are too slow to perform reference-free classification of a large number of (e.g. tens of thousands) of subtomograms. Second, subtomograms extracted from crowded cellular environments, contain often fragments of other structures besides the target complex. However, alignment methods generally assume that each subtomogram only contains one complex. Automatic methods are needed to identify the target complexes in a subtomogram even when its shape is unknown. Results: In this article, we propose an automatic and systematic method for the isolation and masking of target complexes in subtomograms extracted from crowded environments. Moreover, we also propose a fast alignment method using fast rotational matching in real space. Our experiments show that, compared with our previously proposed fast alignment method in reciprocal space, our new method significantly improves the alignment accuracy for highly distorted and especially crowded subtomograms. Such improvements are important for achieving successful and unbiased high-throughput reference-free structural classification of complexes inside whole-cell tomograms. Contact: alber@usc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23812994

  13. Alignment as a Teacher Variable

    ERIC Educational Resources Information Center

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

    2007-01-01

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

  14. Surface modification of alignment layer by ultraviolet irradiation to dramatically improve the detection limit of liquid-crystal-based immunoassay for the cancer biomarker CA125.

    PubMed

    Su, Hui-Wen; Lee, Mon-Juan; Lee, Wei

    2015-05-01

    Liquid crystal (LC)-based biosensing has attracted much attention in recent years. We focus on improving the detection limit of LC-based immunoassay techniques by surface modification of the surfactant alignment layer consisting of dimethyloctadecyl[3-(trimethoxysilyl)propyl]ammonium chloride (DMOAP). The cancer biomarker CA125 was detected with an array of anti-CA125 antibodies immobilized on the ultraviolet (UV)-modified DMOAP monolayer. Compared with a pristine counterpart, UV irradiation enhanced the binding affinity of the CA125 antibody and reproducibility of immunodetection in which a detection limit of 0.01 ng∕ml for the cancer biomarker CA125 was achieved. Additionally, the optical texture observed under a crossed polarized microscope was correlated with the analyte concentration. In a proof-of-concept experiment using CA125-spiked human serum as the analyte, specific binding between the CA125 antigen and the anti-CA125 antibody resulted in a distinct and concentration-dependent optical response despite the high background caused by nonspecific binding of other biomolecules in the human serum. Results from this study indicate that UVmodification of the alignment layer, as well as detection with LCs of large birefringence, contributes to the enhanced performance of the label-free LC-based immunodetection, which may be considered a promising alternative to conventional label-based methods. PMID:26000796

  15. Surface modification of alignment layer by ultraviolet irradiation to dramatically improve the detection limit of liquid-crystal-based immunoassay for the cancer biomarker CA125

    NASA Astrophysics Data System (ADS)

    Su, Hui-Wen; Lee, Mon-Juan; Lee, Wei

    2015-05-01

    Liquid crystal (LC)-based biosensing has attracted much attention in recent years. We focus on improving the detection limit of LC-based immunoassay techniques by surface modification of the surfactant alignment layer consisting of dimethyloctadecyl[3-(trimethoxysilyl)propyl]ammonium chloride (DMOAP). The cancer biomarker CA125 was detected with an array of anti-CA125 antibodies immobilized on the ultraviolet (UV)-modified DMOAP monolayer. Compared with a pristine counterpart, UV irradiation enhanced the binding affinity of the CA125 antibody and reproducibility of immunodetection in which a detection limit of 0.01 ng/ml for the cancer biomarker CA125 was achieved. Additionally, the optical texture observed under a crossed polarized microscope was correlated with the analyte concentration. In a proof-of-concept experiment using CA125-spiked human serum as the analyte, specific binding between the CA125 antigen and the anti-CA125 antibody resulted in a distinct and concentration-dependent optical response despite the high background caused by nonspecific binding of other biomolecules in the human serum. Results from this study indicate that UV modification of the alignment layer, as well as detection with LCs of large birefringence, contributes to the enhanced performance of the label-free LC-based immunodetection, which may be considered a promising alternative to conventional label-based methods.

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

    PubMed Central

    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. PMID:27313898

  17. Experimental study of laser-detected magnetic resonance based on atomic alignment

    SciTech Connect

    Di Domenico, Gianni; Bison, Georg; Groeger, Stephan; Knowles, Paul; Pazgalev, Anatoly S.; Rebetez, Martin; Saudan, Herve; Weis, Antoine

    2006-12-15

    We present an experimental study of the spectra produced by optical-radio-frequency double resonance in which resonant linearly polarized laser light is used in the optical pumping and detection processes. We show that the experimental spectra obtained for cesium are in excellent agreement with a very general theoretical model developed in our group [Weis, Bison, and Pazgalev, Phys. Rev. A 74, 033401 (2006)] and we investigate the limitations of this model. Finally, the results are discussed in view of their use in the study of relaxation processes in aligned alkali-metal vapors.

  18. Testing and alignment of freeform-based multi-mirror telescopes

    NASA Astrophysics Data System (ADS)

    Zhang, Xue-jun; Hu, Hai-xiang; Xue, Dong-lin; Li, Ming

    2015-09-01

    Three Mirror Anastigmat (TMA) systems including both on-axis and off-axis configurations have been widely used in space applications. In some designs, to correct for high order aberrations and realize large FOV, freeform surfaces are used to provide more design freedoms. This trend brings challenges to optical manufacturing and testing community. Since testing is critical to make high accurate aspheres and freeform surfaces, the paper addressed Computer Generated Hologram (CGH) design and implement to measure large freeform mirrors. In particular, CGH assisted alignment procedure for TMA telescopes were discussed in detail.

  19. Identification of Anoectochilus based on rDNA ITS sequences alignment and SELDI-TOF-MS.

    PubMed

    Gao, Chuan; Zhang, Fusheng; Zhang, Jun; Guo, Shunxing; Shao, Hongbo

    2009-01-01

    The internal transcribed spacer (ITS) sequences alignment and proteomic difference of Anoectochilus interspecies have been studied by means of ITS molecular identification and surface enhanced laser desorption ionization time of flight mass spectrography. Results showed that variety certification on Anoectochilus by ITS sequences can not determine species, and there is proteomic difference among Anoectochilus interspecies. Moreover, proteomic finger printings of five Anoectochilus species have been established for identifying species, and genetic relationships of five species within Anoectochilus have been deduced according to proteomic differences among five species. PMID:20016748

  20. Identification of Anoectochilus based on rDNA ITS sequences alignment and SELDI-TOF-MS

    PubMed Central

    Gao, Chuan; Zhang, Fusheng; Zhang, Jun; Guo, Shunxing; Shao, Hongbo

    2009-01-01

    The internal transcribed spacer (ITS) sequences alignment and proteomic difference of Anoectochilus interspecies have been studied by means of ITS molecular identification and surface enhanced laser desorption ionization time of flight mass spectrography. Results showed that variety certification on Anoectochilus by ITS sequences can not determine species, and there is proteomic difference among Anoectochilus interspecies. Moreover, proteomic finger printings of five Anoectochilus species have been established for identifying species, and genetic relationships of five species within Anoectochilus have been deduced according to proteomic differences among five species. PMID:20016748

  1. GUTSS: An Alignment-Free Sequence Comparison Method for Use in Human Intestinal Microbiome and Fecal Microbiota Transplantation Analysis

    PubMed Central

    Heltshe, Sonya L.; Hayden, Hillary S.; Radey, Matthew C.; Weiss, Eli J.; Damman, Christopher J.; Zisman, Timothy L.; Suskind, David L.; Miller, Samuel I.

    2016-01-01

    Background Comparative analysis of gut microbiomes in clinical studies of human diseases typically rely on identification and quantification of species or genes. In addition to exploring specific functional characteristics of the microbiome and potential significance of species diversity or expansion, microbiome similarity is also calculated to study change in response to therapies directed at altering the microbiome. Established ecological measures of similarity can be constructed from species abundances, however methods for calculating these commonly used ecological measures of similarity directly from whole genome shotgun (WGS) metagenomic sequence are lacking. Results We present an alignment-free method for calculating similarity of WGS metagenomic sequences that is analogous to the Bray–Curtis index for species, implemented by the General Utility for Testing Sequence Similarity (GUTSS) software application. This method was applied to intestinal microbiomes of healthy young children to measure developmental changes toward an adult microbiome during the first 3 years of life. We also calculate similarity of donor and recipient microbiomes to measure establishment, or engraftment, of donor microbiota in fecal microbiota transplantation (FMT) studies focused on mild to moderate Crohn's disease. We show how a relative index of similarity to donor can be calculated as a measure of change in a patient's microbiome toward that of the donor in response to FMT. Conclusion Because clinical efficacy of the transplant procedure cannot be fully evaluated without analysis methods to quantify actual FMT engraftment, we developed a method for detecting change in the gut microbiome that is independent of species identification and database bias, sensitive to changes in relative abundance of the microbial constituents, and can be formulated as an index for correlating engraftment success with clinical measures of disease. More generally, this method may be applied to clinical

  2. Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System

    PubMed Central

    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. PMID:26568953

  3. Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System.

    PubMed

    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. PMID:26568953

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

    PubMed

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

    2015-05-15

    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

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

    PubMed Central

    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

  6. Algorithms for Automatic Alignment of Arrays

    NASA Technical Reports Server (NTRS)

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

    1996-01-01

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

  7. Remarkably enhanced thermal transport based on a flexible horizontally-aligned carbon nanotube array film

    NASA Astrophysics Data System (ADS)

    Qiu, Lin; Wang, Xiaotian; Su, Guoping; Tang, Dawei; Zheng, Xinghua; Zhu, Jie; Wang, Zhiguo; Norris, Pamela M.; Bradford, Philip D.; Zhu, Yuntian

    2016-02-01

    It has been more than a decade since the thermal conductivity of vertically aligned carbon nanotube (VACNT) arrays was reported possible to exceed that of the best thermal greases or phase change materials by an order of magnitude. Despite tremendous prospects as a thermal interface material (TIM), results were discouraging for practical applications. The primary reason is the large thermal contact resistance between the CNT tips and the heat sink. Here we report a simultaneous sevenfold increase in in-plane thermal conductivity and a fourfold reduction in the thermal contact resistance at the flexible CNT-SiO2 coated heat sink interface by coupling the CNTs with orderly physical overlapping along the horizontal direction through an engineering approach (shear pressing). The removal of empty space rapidly increases the density of transport channels, and the replacement of the fine CNT tips with their cylindrical surface insures intimate contact at CNT-SiO2 interface. Our results suggest horizontally aligned CNT arrays exhibit remarkably enhanced in-plane thermal conductivity and reduced out-of-plane thermal conductivity and thermal contact resistance. This novel structure makes CNT film promising for applications in chip-level heat dissipation. Besides TIM, it also provides for a solution to anisotropic heat spreader which is significant for eliminating hot spots.

  8. Alignment based on a no adjustment philosophy for the Immersion Grating Infrared Spectrometer (IGRINS)

    NASA Astrophysics Data System (ADS)

    Han, Jeong-Yeol; Yuk, In-Soo; Ko, Kyeongyeon; Oh, Heeyoung; Nah, Jakyoung; Oh, Jae Sok; Park, Chan; Lee, Sungho; Kim, Kang-Min; Chun, Moo-Young; Jaffe, Daniel T.; Pak, Soojong; Gully-Santiago, Michael

    2012-12-01

    IGRINS, the Immersion GRating INfrared Spectrometer includes an immersion grating made of silicon and observes both H-band (1.49~1.80 μm) and K-band (1.96~2.46 μm), simultaneously. In order to align such an infrared optical system, the compensator in its optical components has been adjusted within tolerances at room temperature without vacuum environment. However, such a system will ultimately operate at low temperature and vacuum with no adjustment mechanism. Therefore a reasonable relationship between different environmental variations such as room and low temperature might provide useful knowledge to align the system properly. We are attempting to develop a new process to predict the Wave Front Error (WFE), and to produce correct mechanical control values when the optical system is perturbed by moving the lens at room temperature. The purpose is to provide adequate optical performance without making changes at operating temperature. In other words, WFE was measured at operating temperature without any modification but a compensator was altered correctly at room temperature to meet target performance. The `no adjustment' philosophy was achieved by deterministic mechanical adjustment at room temperature from a simulation that we developed. In this study, an achromatic doublet lens was used to substitute for the H and K band camera of IGRINS. This novel process exhibits accuracy predictability of about 0.002 λ rms WFE and can be applied to a cooled infrared optical systems.

  9. Remarkably enhanced thermal transport based on a flexible horizontally-aligned carbon nanotube array film.

    PubMed

    Qiu, Lin; Wang, Xiaotian; Su, Guoping; Tang, Dawei; Zheng, Xinghua; Zhu, Jie; Wang, Zhiguo; Norris, Pamela M; Bradford, Philip D; Zhu, Yuntian

    2016-01-01

    It has been more than a decade since the thermal conductivity of vertically aligned carbon nanotube (VACNT) arrays was reported possible to exceed that of the best thermal greases or phase change materials by an order of magnitude. Despite tremendous prospects as a thermal interface material (TIM), results were discouraging for practical applications. The primary reason is the large thermal contact resistance between the CNT tips and the heat sink. Here we report a simultaneous sevenfold increase in in-plane thermal conductivity and a fourfold reduction in the thermal contact resistance at the flexible CNT-SiO2 coated heat sink interface by coupling the CNTs with orderly physical overlapping along the horizontal direction through an engineering approach (shear pressing). The removal of empty space rapidly increases the density of transport channels, and the replacement of the fine CNT tips with their cylindrical surface insures intimate contact at CNT-SiO2 interface. Our results suggest horizontally aligned CNT arrays exhibit remarkably enhanced in-plane thermal conductivity and reduced out-of-plane thermal conductivity and thermal contact resistance. This novel structure makes CNT film promising for applications in chip-level heat dissipation. Besides TIM, it also provides for a solution to anisotropic heat spreader which is significant for eliminating hot spots. PMID:26880221

  10. Remarkably enhanced thermal transport based on a flexible horizontally-aligned carbon nanotube array film

    PubMed Central

    Qiu, Lin; Wang, Xiaotian; Su, Guoping; Tang, Dawei; Zheng, Xinghua; Zhu, Jie; Wang, Zhiguo; Norris, Pamela M.; Bradford, Philip D.; Zhu, Yuntian

    2016-01-01

    It has been more than a decade since the thermal conductivity of vertically aligned carbon nanotube (VACNT) arrays was reported possible to exceed that of the best thermal greases or phase change materials by an order of magnitude. Despite tremendous prospects as a thermal interface material (TIM), results were discouraging for practical applications. The primary reason is the large thermal contact resistance between the CNT tips and the heat sink. Here we report a simultaneous sevenfold increase in in-plane thermal conductivity and a fourfold reduction in the thermal contact resistance at the flexible CNT-SiO2 coated heat sink interface by coupling the CNTs with orderly physical overlapping along the horizontal direction through an engineering approach (shear pressing). The removal of empty space rapidly increases the density of transport channels, and the replacement of the fine CNT tips with their cylindrical surface insures intimate contact at CNT-SiO2 interface. Our results suggest horizontally aligned CNT arrays exhibit remarkably enhanced in-plane thermal conductivity and reduced out-of-plane thermal conductivity and thermal contact resistance. This novel structure makes CNT film promising for applications in chip-level heat dissipation. Besides TIM, it also provides for a solution to anisotropic heat spreader which is significant for eliminating hot spots. PMID:26880221

  11. Amino acid sequence alignment of bacterial and mammalian pancreatic serine proteases based on topological equivalences.

    PubMed

    James, M N; Delbaere, L T; Brayer, G D

    1978-06-01

    The three-dimensional structures of the bacterial serine proteases SGPA, SGPB, and alpha-lytic protease have been compared with those of the pancreatic enzymes alpha-chymotrypsin and elastase. This comparison shows that approximately 60% (55-64%) of the alpha-carbon atom positions of the bacterial serine proteases are topologically equivalent to the alpha-carbon atom positions of the pancreatic enzymes. The corresponding value for a comparison of the bacterial enzymes among themselves is approximately 84%. The results of these topological comparisons have been used to deduce an experimentally sound sequence alignment for these several enzymes. This alignment shows that there is extensive tertiary structural homology among the bacteria and pancreatic enzymes without significant primary sequence identity (less than 21%). The acquisition of a zymogen function by the pancreatic enzymes is accompanied by two major changes to the bacterial enzymes' architecture: an insertion of 9 residues to increase the length of the N-terminal loop, and one of 12 residues to a loop near the activation salt bridge. In addition, in these two enzyme families, the methionine loop (residues 164-182) adopts very different comformations which are associated with their altered substrate specificities. PMID:96920

  12. Triple-layered QSAR studies on substituted 1,2,4-trioxanes as potential antimalarial agents: superiority of the quantitative pharmacophore-based alignment over common substructure-based alignment.

    PubMed

    Gupta, A K; Saxena, A K

    2013-01-01

    This study reports the utilization of three approaches - pharmacophore, CoMFA/CoMSIA and HQSAR studies - to identify the essential structural requirements in 3D chemical space for the modulation of the antimalarial activity of substituted 1,2,4-trioxanes. The superiority of quantitative pharmacophore-based alignment (QuantitativePBA) over global minima energy conformer-based alignment (GMCBA) has been reported in CoMFA and CoMSIA studies. The developed models showed good statistical significance in internal validation (q(2), group cross-validation and bootstrapping) and performed very well in predicting the antimalarial activity of test set compounds. Structural features in terms of their steric, electrostatic and hydrophobic interactions in 3D space have been found to be important for the antimalarial activity of substituted 1,2,4-trioxanes. Further, the HQSAR studies based on the same training and test set acted as an additional tool to find the sub-structural fingerprints of substituted 1,2,4-trioxanes for their antimalarial activity. Together, these studies may facilitate the design and discovery of new substituted 1,2,4-trioxanes with potent antimalarial activity. PMID:23194465

  13. Comparison of landmark-based and automatic methods for cortical surface registration.

    PubMed

    Pantazis, Dimitrios; Joshi, Anand; Jiang, Jintao; Shattuck, David W; Bernstein, Lynne E; Damasio, Hanna; Leahy, Richard M

    2010-02-01

    Group analysis of structure or function in cerebral cortex typically involves, as a first step, the alignment of cortices. A surface-based approach to this problem treats the cortex as a convoluted surface and coregisters across subjects so that cortical landmarks or features are aligned. This registration can be performed using curves representing sulcal fundi and gyral crowns to constrain the mapping. Alternatively, registration can be based on the alignment of curvature metrics computed over the entire cortical surface. The former approach typically involves some degree of user interaction in defining the sulcal and gyral landmarks while the latter methods can be completely automated. Here we introduce a cortical delineation protocol consisting of 26 consistent landmarks spanning the entire cortical surface. We then compare the performance of a landmark-based registration method that uses this protocol with that of two automatic methods implemented in the software packages FreeSurfer and BrainVoyager. We compare performance in terms of discrepancy maps between the different methods, the accuracy with which regions of interest are aligned, and the ability of the automated methods to correctly align standard cortical landmarks. Our results show similar performance for ROIs in the perisylvian region for the landmark-based method and FreeSurfer. However, the discrepancy maps showed larger variability between methods in occipital and frontal cortex and automated methods often produce misalignment of standard cortical landmarks. Consequently, selection of the registration approach should consider the importance of accurate sulcal alignment for the specific task for which coregistration is being performed. When automatic methods are used, the users should ensure that sulci in regions of interest in their studies are adequately aligned before proceeding with subsequent analysis. PMID:19796696

  14. BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC

    PubMed Central

    Satija, Rahul; Novák, Ádám; Miklós, István; Lyngsø, Rune; Hein, Jotun

    2009-01-01

    Background We have previously combined statistical alignment and phylogenetic footprinting to detect conserved functional elements without assuming a fixed alignment. Considering a probability-weighted distribution of alignments removes sensitivity to alignment errors, properly accommodates regions of alignment uncertainty, and increases the accuracy of functional element prediction. Our method utilized standard dynamic programming hidden markov model algorithms to analyze up to four sequences. Results We present a novel approach, implemented in the software package BigFoot, for performing phylogenetic footprinting on greater numbers of sequences. We have developed a Markov chain Monte Carlo (MCMC) approach which samples both sequence alignments and locations of slowly evolving regions. We implement our method as an extension of the existing StatAlign software package and test it on well-annotated regions controlling the expression of the even-skipped gene in Drosophila and the α-globin gene in vertebrates. The results exhibit how adding additional sequences to the analysis has the potential to improve the accuracy of functional predictions, and demonstrate how BigFoot outperforms existing alignment-based phylogenetic footprinting techniques. Conclusion BigFoot extends a combined alignment and phylogenetic footprinting approach to analyze larger amounts of sequence data using MCMC. Our approach is robust to alignment error and uncertainty and can be applied to a variety of biological datasets. The source code and documentation are publicly available for download from PMID:19715598

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

    PubMed

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

    2016-08-01

    Stretchable supercapacitors that can sustain their performance under unpredictable tensile force are important elements for practical applications of various portable and wearable electronics. However, the stretchability of most reported supercapacitors was often lower than 100 % because of the limitation of the electrodes used. Herein we developed all-solid-state supercapacitors with a stretchability as high as 240 % by using aligned carbon nanotube composites with compact structure as electrodes. By combined with pseudocapacitive molybdenum disulfide nanosheets, the newly developed supercapacitor showed a specific capacitance of 13.16 F cm(-3) , and also showed excellent cycling retention (98 %) after 10 000 charge-discharge cycles. This work also presents a general and effective approach in developing high-performance electrodes for flexible and stretchable electronics. PMID:27328623

  16. Mechanochromic photonic-crystal fibers based on continuous sheets of aligned carbon nanotubes.

    PubMed

    Sun, Xuemei; Zhang, Jing; Lu, Xin; Fang, Xin; Peng, Huisheng

    2015-03-16

    A new family of mechanochromic photonic-crystal fibers exhibits tunable structural colors under stretching. This novel mechanochromic fiber is prepared by depositing polymer microspheres onto a continuous aligned-carbon-nanotube sheet that has been wound on an elastic poly(dimethylsiloxane) fiber, followed by further embedding in poly(dimethylsiloxane). The color of the fiber can be tuned by varying the size and the center-to-center distance of the polymer spheres. It further experiences reversible and rapid multicolor changes during the stretch and release processes, for example, between red, green, and blue. Both the high sensitivity and stability were maintained after 1000 deformation cycles. These elastic photonic-crystal fibers were woven into patterns and smart fabrics for various display and sensing applications. PMID:25728690

  17. Energy-effective frost-free coatings based on superhydrophobic aligned nanocones.

    PubMed

    Xu, Qian; Li, Juan; Tian, Jian; Zhu, Jie; Gao, Xuefeng

    2014-06-25

    We demonstrate the feasibility of superhydrophobic aligned nanocones as energy-effective frost-free coatings. Exemplified by Co(OH)2 nanocone films with condensed microdrop self-removal ability, their edge and whole-surface frosting time can be delayed to about 10 and 150 min, respectively. By using a Teflon gasket to shield edges, the samples can keep frost-free state over 90 min. Further, the lasting frost-free state can be realized by intermittent weak airflow heating, which is energy-effective in contrast to usual high-power heating for defrosting flat surfaces. These findings are significant to develop antifrosting nanotechnologies for energy-effective heat exchangers such as heat pumps and refrigerators. PMID:24912381

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

    PubMed

    Baumann, Michael; Mozer, Pierre; 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 and thus renders optimization efficient. The method was tested on 237 prostate volumes acquired from 14 different patients for 3D to 3D and 3D to orthogonal 2D slices registration. The 3D-3D version of the algorithm converged correctly in 96.7% of all cases in 6.5s with an accuracy of 1.41mm (r.m.s.) and 3.84mm (max). The 3D to slices method yielded a success rate of 88.9% in 2.3s with an accuracy of 1.37mm (r.m.s.) and 4.3mm (max). PMID:18044549

  19. A vertically aligned carbon nanotube-based impedance sensing biosensor for rapid and high sensitive detection of cancer cells.

    PubMed

    Abdolahad, Mohammad; Taghinejad, Mohammad; Taghinejad, Hossein; Janmaleki, Mohsen; Mohajerzadeh, Shams

    2012-03-21

    A novel vertically aligned carbon nanotube based electrical cell impedance sensing biosensor (CNT-ECIS) was demonstrated for the first time as a more rapid, sensitive and specific device for the detection of cancer cells. This biosensor is based on the fast entrapment of cancer cells on vertically aligned carbon nanotube arrays and leads to mechanical and electrical interactions between CNT tips and entrapped cell membranes, changing the impedance of the biosensor. CNT-ECIS was fabricated through a photolithography process on Ni/SiO(2)/Si layers. Carbon nanotube arrays have been grown on 9 nm thick patterned Ni microelectrodes by DC-PECVD. SW48 colon cancer cells were passed over the surface of CNT covered electrodes to be specifically entrapped on elastic nanotube beams. CNT arrays act as both adhesive and conductive agents and impedance changes occurred as fast as 30 s (for whole entrapment and signaling processes). CNT-ECIS detected the cancer cells with the concentration as low as 4000 cells cm(-2) on its surface and a sensitivity of 1.7 × 10(-3)Ω cm(2). Time and cell efficiency factor (TEF and CEF) parameters were defined which describe the sensor's rapidness and resolution, respectively. TEF and CEF of CNT-ECIS were much higher than other cell based electrical biosensors which are compared in this paper. PMID:22294045

  20. Diagnostic apparatus and method for use in the alignment of one or more laser means onto a fiber optics interface

    DOEpatents

    Johnson, Steve A.; Shannon, Robert R.

    1987-01-01

    Diagnostic apparatus for use in determining the proper alignment of a plurality of laser beams onto a fiber optics interface is disclosed. The apparatus includes a lens assembly which serves two functions, first to focus a plurality of laser beams onto the fiber optics interface, and secondly to reflect and image the interface using scattered light to a monitor means. The monitor means permits indirect observation of the alignment or focusing of the laser beams onto the fiber optics interface.

  1. Diagnostic apparatus and method for use in the alignment of one or more laser means onto a fiber optics interface

    DOEpatents

    Johnson, S.A.; Shannon, R.R.

    1985-01-18

    Diagnostic apparatus for use in determining the proper alignment of a plurality of laser beams onto a fiber optics interface is disclosed. The apparatus includes a lens assembly which serves two functions, first to focus a plurality of laser beams onto the fiber optics interface, and secondly to reflect and image the interface using scattered light to a monitor means. The monitor means permits indirect observation of the alignment or focusing of the laser beams onto the fiber optics interface.

  2. Automatic generation of alignments for 3D QSAR analyses.

    PubMed

    Jewell, N E; Turner, D B; Willett, P; Sexton, G J

    2001-01-01

    Many 3D QSAR methods require the alignment of the molecules in a dataset, which can require a fair amount of manual effort in deciding upon a rational basis for the superposition. This paper describes the use of FBSS, a program for field-based similarity searching in chemical databases, for generating such alignments automatically. The CoMFA and CoMSIA experiments with several literature datasets show that the QSAR models resulting from the FBSS alignments are broadly comparable in predictive performance with the models resulting from manual alignments. PMID:11774998

  3. Fully passive-alignment pluggable compact parallel optical interconnection modules based on a direct-butt-coupling structure for fiber-optic applications

    NASA Astrophysics Data System (ADS)

    Lim, Kwon-Seob; Park, Hyoung-Jun; Kang, Hyun Seo; Kim, Young Sun; Jang, Jae-Hyung

    2016-02-01

    A low-cost packaging method utilizing a fully passive optical alignment and surface-mounting method is demonstrated for pluggable compact and slim multichannel optical interconnection modules using a VCSEL/PIN-PD chip array. The modules are based on a nonplanar bent right-angle electrical signal path on a silicon platform and direct-butt-optical coupling without a bulky and expensive microlens array. The measured optical direct-butt-coupling efficiencies of each channel without any bulky optics are as high as 33% and 95% for the transmitter and receiver, respectively. Excellent lateral optical alignment tolerance of larger than 60 μm for both the transmitter and receiver module significantly reduces the manufacturing and material costs as well as the packaging time. The clear eye diagrams, extinction ratios higher than 8 dB at 10.3 Gbps for the transmitter module, and receiver sensitivity of better than -13.1 dBm at 10.3 Gbps and a bit error rate of 10-12 for all channels are demonstrated. Considering that the optical output power of the transmitter is greater than 0 dBm, the module has a sufficient power margin of about 13 dB for 10.3 Gbps operations for all channels.

  4. Beyond Scissors and Glue: Staff Developers Guide Teachers in Piecing Together a Vertically Aligned Curriculum and in Creating a Method to Get This Job Done

    ERIC Educational Resources Information Center

    Phelps, Vickie

    2005-01-01

    Layers and layers of curricula stuffed into vinyl binders were the norm in this Texas district until teachers sat down with scissors and glue to create a vertically aligned curriculum. They then created standards-based lessons to support the curriculum and put them into a database readily accessible by all.

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

    SciTech Connect

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

    2013-09-15

    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.

  6. Structural analysis of aligned RNAs.

    PubMed

    Voss, Björn

    2006-01-01

    The knowledge about classes of non-coding RNAs (ncRNAs) is growing very fast and it is mainly the structure which is the common characteristic property shared by members of the same class. For correct characterization of such classes it is therefore of great importance to analyse the structural features in great detail. In this manuscript I present RNAlishapes which combines various secondary structure analysis methods, such as suboptimal folding and shape abstraction, with a comparative approach known as RNA alignment folding. RNAlishapes makes use of an extended thermodynamic model and covariance scoring, which allows to reward covariation of paired bases. Applying the algorithm to a set of bacterial trp-operon leaders using shape abstraction it was able to identify the two alternating conformations of this attenuator. Besides providing in-depth analysis methods for aligned RNAs, the tool also shows a fairly well prediction accuracy. Therefore, RNAlishapes provides the community with a powerful tool for structural analysis of classes of RNAs and is also a reasonable method for consensus structure prediction based on sequence alignments. RNAlishapes is available for online use and download at http://rna.cyanolab.de. PMID:17020924

  7. Pairwise Sequence Alignment Library

    2015-05-20

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

  8. Pairwise Sequence Alignment Library

    SciTech Connect

    Jeff Daily, PNNL

    2015-05-20

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

  9. Ultra-stretchable conductors based on buckled super-aligned carbon nanotube films

    NASA Astrophysics Data System (ADS)

    Yu, Yang; Luo, Shu; Sun, Li; Wu, Yang; Jiang, Kaili; Li, Qunqing; Wang, Jiaping; Fan, Shoushan

    2015-05-01

    Ultra-stretchable conductors are fabricated by coating super-aligned carbon nanotube (SACNT) films on pre-strained polydimethylsiloxane (PDMS) substrates and forming buckled SACNT structures on PDMS after release of the pre-strain. The parallel SACNT/PDMS conductors demonstrate excellent stability with normalized resistance changes of only 4.1% under an applied strain as high as 200%. The SACNT/PDMS conductors prepared with cross-stacked SACNT films show even lower resistance variation. The parallel SACNT/PDMS conductors exhibit high durability with a resistance increase of less than 5% after 10 000 cycles at 150% strain. In situ microscopic observations demonstrate that the buckled SACNT structures are straightened during the stretching process with reversible morphology evolution and thus the continuous SACNT conductive network can be protected from fracture. Due to the excellent electrical and mechanical properties of SACNT films and the formation of the buckled structure, SACNT/PDMS films exhibit high stretchability and durability, possessing great potential for use as ultra-stretchable conductors for wearable electronics, sensors, and energy storage devices.Ultra-stretchable conductors are fabricated by coating super-aligned carbon nanotube (SACNT) films on pre-strained polydimethylsiloxane (PDMS) substrates and forming buckled SACNT structures on PDMS after release of the pre-strain. The parallel SACNT/PDMS conductors demonstrate excellent stability with normalized resistance changes of only 4.1% under an applied strain as high as 200%. The SACNT/PDMS conductors prepared with cross-stacked SACNT films show even lower resistance variation. The parallel SACNT/PDMS conductors exhibit high durability with a resistance increase of less than 5% after 10 000 cycles at 150% strain. In situ microscopic observations demonstrate that the buckled SACNT structures are straightened during the stretching process with reversible morphology evolution and thus the continuous

  10. Ultra-stretchable conductors based on buckled super-aligned carbon nanotube films.

    PubMed

    Yu, Yang; Luo, Shu; Sun, Li; Wu, Yang; Jiang, Kaili; Li, Qunqing; Wang, Jiaping; Fan, Shoushan

    2015-06-14

    Ultra-stretchable conductors are fabricated by coating super-aligned carbon nanotube (SACNT) films on pre-strained polydimethylsiloxane (PDMS) substrates and forming buckled SACNT structures on PDMS after release of the pre-strain. The parallel SACNT/PDMS conductors demonstrate excellent stability with normalized resistance changes of only 4.1% under an applied strain as high as 200%. The SACNT/PDMS conductors prepared with cross-stacked SACNT films show even lower resistance variation. The parallel SACNT/PDMS conductors exhibit high durability with a resistance increase of less than 5% after 10,000 cycles at 150% strain. In situ microscopic observations demonstrate that the buckled SACNT structures are straightened during the stretching process with reversible morphology evolution and thus the continuous SACNT conductive network can be protected from fracture. Due to the excellent electrical and mechanical properties of SACNT films and the formation of the buckled structure, SACNT/PDMS films exhibit high stretchability and durability, possessing great potential for use as ultra-stretchable conductors for wearable electronics, sensors, and energy storage devices. PMID:25985762

  11. Cell Alignment Driven by Mechanically Induced Collagen Fiber Alignment in Collagen/Alginate Coatings.

    PubMed

    Chaubaroux, Christophe; Perrin-Schmitt, Fabienne; Senger, Bernard; Vidal, Loïc; Voegel, Jean-Claude; Schaaf, Pierre; Haikel, Youssef; Boulmedais, Fouzia; Lavalle, Philippe; Hemmerlé, Joseph

    2015-09-01

    For many years it has been a major challenge to regenerate damaged tissues using synthetic or natural materials. To favor the healing processes after tendon, cornea, muscle, or brain injuries, aligned collagen-based architectures are of utmost interest. In this study, we define a novel aligned coating based on a collagen/alginate (COL/ALG) multilayer film. The coating exhibiting a nanofibrillar structure is cross-linked with genipin for stability in physiological conditions. By stretching COL/ALG-coated polydimethylsiloxane substrates, we developed a versatile method to align the collagen fibrils of the polymeric coating. Assays on cell morphology and alignment were performed to investigate the properties of these films. Microscopic assessments revealed that cells align with the stretched collagen fibrils of the coating. The degree of alignment is tuned by the stretching rate (i.e., the strain) of the COL/ALG-coated elastic substrate. Such coatings are of great interest for strategies that require aligned nanofibrillar biological material as a substrate for tissue engineering. PMID:25658028

  12. ALIGNING JIG

    DOEpatents

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

    1958-08-01

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

  13. Aligned and exchange-coupled L1{sub 0} (Fe,Co)Pt-based magnetic films

    SciTech Connect

    Liu, Y.; George, T. A.; Skomski, R.; Sellmyer, D. J.

    2012-04-01

    Films of aligned L1{sub 0}-structure (Fe,Co)Pt with fcc Fe(Co,Pt) are synthesized by co-sputtering Fe, Co, and Pt on an (001) MgO substrate with in situ heating at 830 deg. C. The nanostructures and magnetic properties of the films are characterized by X-ray diffraction (XRD), transmission electron microscopy (TEM), and superconducting quantum interference device (SQUID). The compositions of the samples (Fe,Co){sub x}Pt{sub 1-x} are designed to maintain an atomic Fe: Co ratio of 65: 35 while increasing the Fe,Co content in each successive sample. In samples with low Fe and Co concentration, the XRD patterns exhibit three strong peaks, namely L1{sub 0} (Fe,Co)Pt (001), L1{sub 0} (Fe,Co)Pt (002), and MgO (002). A fourth peak is observed in samples with high Fe and Co concentration and identified as fcc (002). The XRD patterns confirm the formation of L1{sub 0}-ordered (Fe,Co)Pt and its epitaxial growth on MgO. TEM shows that the (Fe,Co)Pt films form isolated magnetic grains of about 100 nm in diameter. Hysteresis-loop measurements show that the increase of the Fe,Co concentration from 57.3 to 68.3 at % enhances the saturation magnetization M{sub s} from 1245 emu/cm{sup 3} to 1416 emu/cm{sup 3}, and the coercivity decreases from 32 kOe to 8.9 kOe. The nominal maximum energy product per grain is 64 MGOe.

  14. Efficient alignment-free DNA barcode analytics

    PubMed Central

    Kuksa, Pavel; Pavlovic, Vladimir

    2009-01-01

    Background In this work we consider barcode DNA analysis problems and address them using alternative, alignment-free methods and representations which model sequences as collections of short sequence fragments (features). The methods use fixed-length representations (spectrum) for barcode sequences to measure similarities or dissimilarities between sequences coming from the same or different species. The spectrum-based representation not only allows for accurate and computationally efficient species classification, but also opens possibility for accurate clustering analysis of putative species barcodes and identification of critical within-barcode loci distinguishing barcodes of different sample groups. Results New alignment-free methods provide highly accurate and fast DNA barcode-based identification and classification of species with substantial improvements in accuracy and speed over state-of-the-art barcode analysis methods. We evaluate our methods on problems of species classification and identification using barcodes, important and relevant analytical tasks in many practical applications (adverse species movement monitoring, sampling surveys for unknown or pathogenic species identification, biodiversity assessment, etc.) On several benchmark barcode datasets, including ACG, Astraptes, Hesperiidae, Fish larvae, and Birds of North America, proposed alignment-free methods considerably improve prediction accuracy compared to prior results. We also observe significant running time improvements over the state-of-the-art methods. Conclusion Our results show that newly developed alignment-free methods for DNA barcoding can efficiently and with high accuracy identify specimens by examining only few barcode features, resulting in increased scalability and interpretability of current computational approaches to barcoding. PMID:19900305

  15. PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features.

    PubMed

    Gandhimathi, Arumugam; Ghosh, Pritha; Hariharaputran, Sridhar; Mathew, Oommen K; Sowdhamini, R

    2016-01-01

    Structure-based sequence alignment is an essential step in assessing and analysing the relationship of distantly related proteins. PASS2 is a database that records such alignments for protein domain superfamilies and has been constantly updated periodically. This update of the PASS2 version, named as PASS2.5, directly corresponds to the SCOPe 2.04 release. All SCOPe structural domains that share less than 40% sequence identity, as defined by the ASTRAL compendium of protein structures, are included. The current version includes 1977 superfamilies and has been assembled utilizing the structure-based sequence alignment protocol. Such an alignment is obtained initially through MATT, followed by a refinement through the COMPARER program. The JOY program has been used for structural annotations of such alignments. In this update, we have automated the protocol and focused on inclusion of new features such as mapping of GO terms, absolutely conserved residues among the domains in a superfamily and inclusion of PDBs, that are absent in SCOPe 2.04, using the HMM profiles from the alignments of the superfamily members and are provided as a separate list. We have also implemented a more user-friendly manner of data presentation and options for downloading more features. PASS2.5 version is available at http://caps.ncbs.res.in/pass2/. PMID:26553811

  16. PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features

    PubMed Central

    Gandhimathi, Arumugam; Ghosh, Pritha; Hariharaputran, Sridhar; Mathew, Oommen K.; Sowdhamini, R.

    2016-01-01

    Structure-based sequence alignment is an essential step in assessing and analysing the relationship of distantly related proteins. PASS2 is a database that records such alignments for protein domain superfamilies and has been constantly updated periodically. This update of the PASS2 version, named as PASS2.5, directly corresponds to the SCOPe 2.04 release. All SCOPe structural domains that share less than 40% sequence identity, as defined by the ASTRAL compendium of protein structures, are included. The current version includes 1977 superfamilies and has been assembled utilizing the structure-based sequence alignment protocol. Such an alignment is obtained initially through MATT, followed by a refinement through the COMPARER program. The JOY program has been used for structural annotations of such alignments. In this update, we have automated the protocol and focused on inclusion of new features such as mapping of GO terms, absolutely conserved residues among the domains in a superfamily and inclusion of PDBs, that are absent in SCOPe 2.04, using the HMM profiles from the alignments of the superfamily members and are provided as a separate list. We have also implemented a more user-friendly manner of data presentation and options for downloading more features. PASS2.5 version is available at http://caps.ncbs.res.in/pass2/. PMID:26553811

  17. Effectiveness of Using Fewer Implanted Fiducial Markers for Prostate Target Alignment

    SciTech Connect

    Kudchadker, Rajat J. Lee, Andrew K.; Yu Zhiqian; Johnson, Jennifer L.; Zhang Lifei; Zhang Yongbin; Amos, Richard A.; Nakanishi, Hiroyuki; Ochiai, Atsushi; Dong Lei

    2009-07-15

    Purpose: To evaluate the impact of the number and location of intraprostatic fiducial markers on the accuracy and reproducibility of daily prostate target alignment and to evaluate the migration of such markers. Methods and Materials: Three gold fiducial markers were implanted transrectally under ultrasound guidance near the apex, middle, and base of the prostate in 10 prostate cancer patients. The patients had pretreatment in-room computed tomography (CT) scans three times a week, for approximately 25 CT scans per patient during the 8-week treatment course. A total of 1280 alignments were performed using different alignment scenarios: whole-prostate soft tissue alignment (the gold standard), bone alignment, and seven permutations of alignments using one, two, or three fiducial markers. The results of bone alignment and fiducial alignment were compared with the results of whole-prostate alignment. Fiducial migration was also evaluated. Results: Single-fiducial-marker alignment was more accurate and reproducible than bone alignment. However, due to organ deformation, single fiducial markers did not always reliably represent the position of the entire prostate. The use of two-fiducial combinations was more accurate and reproducible than single-fiducial alignment, and use of all three fiducials was the best. Use of an apex fiducial together with a base fiducial rivaled the use of all three fiducials markers together. Fiducial migration was minimal. Conclusions: The number and the location of implanted fiducial markers affect the accuracy and reliability of daily prostate target alignment. The use of two or more fiducial markers is recommended.

  18. Method of casting pitch based foam

    DOEpatents

    Klett, James W.

    2002-01-01

    A process for producing molded pitch based foam is disclosed which minimizes cracking. The process includes forming a viscous pitch foam in a container, and then transferring the viscous pitch foam from the container into a mold. The viscous pitch foam in the mold is hardened to provide a carbon foam having a relatively uniform distribution of pore sizes and a highly aligned graphic structure in the struts.

  19. A Mixed-Method Analysis of the Alignment of Title I Achieving Schools' Professional Development to NCLB Professional Development Provisions

    ERIC Educational Resources Information Center

    Quinn, Kerry

    2013-01-01

    The improvement of schools has been a central discussion among educators, legislators, and stakeholders, with professional development being acknowledged as a fundamental topic for the success of the education system. Studying the alignment of professional development programs provided at Title I Achieving schools to NCLB research based…

  20. Substrate patterning for liquid crystal alignment by optical interference

    SciTech Connect

    Lu Xuemin; Lee, Fuk Kay; Sheng, Ping; Kwok, H.S.; Chigrinov, V.; Tsui, Ophelia K.C.

    2006-06-12

    Inhomogeneous liquid crystal (LC) alignment surfaces comprising a succession of microdomains favoring different LC alignment directions have been demonstrated for a number of optoelectronic applications. However, the prevalent method used to fabricate these surfaces is time consuming and produce functional areas that are too small for practical use. Here, we demonstrate a simple method based on photopatterning of an azodye layer with an interference pattern produced by intercepting two coherent UV beams. This method can produce alignment patterns within seconds with a practical size of {approx}(0.5 cm){sup 2}.

  1. Alignment analyses of a galvanometer-based scanner in free-space Fourier domain optical coherence tomography.

    PubMed

    Yuan, Qun; Zhu, Dan; Gao, Zhishan

    2015-11-10

    Free-space Fourier domain optical coherence tomography is adopted for biomedical imaging with ultrahigh resolution, in which the setup consists of an interferometer and a spectrometer. Two-dimensional lateral sampling in the sample arm of the interferometer is achieved by using a galvanometer-based scanner. Optical path difference (OPD) drift in the full scan field of view is observed in the assembly process of the scanner. A galvo mirror mount offset with respect to the rotation axis is demonstrated as the derivation of this OPD drift by both geometric analyses and model building. Then, an iterative assembly process of the scanner is proposed with the OPD drift taken as the alignment criteria. PMID:26560786

  2. Liquid-Crystal Biosensor Based on Nickel-Nanosphere-Induced Homeotropic Alignment for the Amplified Detection of Thrombin.

    PubMed

    Zhao, Dongyu; Peng, Yi; Xu, Lihong; Zhou, Wei; Wang, Qian; Guo, Lin

    2015-10-28

    A new liquid-crystal (LC)-based sensor operated by nickel nanosphere (NiNS)-induced homeotropic alignment for the label-free monitoring of thrombin was reported. When doped with NiNSs, a uniform vertical orientation of 4-cyano-4'-pentylbiphenyl (5CB) was easily obtained. A sandwich system of aptamer/thrombin/aptamer-functionalized gold nanoparticles (AuNPs) was fabricated, and AuNPs-aptamer conjugation caused the disruption of the 5CB orientation, leading to an obvious change of the optical appearance from a dark to a bright response to thrombin concentrations from 0.1 to 100 nM. This design also allowed quantitative detection of the thrombin concentration. This distinctive and sensitive thrombin LC sensor provides a new principle for building LC-sensing systems. PMID:26458050

  3. Preparation of a novel structured catalyst based on aligned carbon nanotube arrays for a microchannel Fischer-Tropsch synthesis reactor

    SciTech Connect

    Chin, Ya-Huei; Hu, Jianli; Cao, Chunshe; Gao, Yufei; Wang, Yong

    2005-12-15

    A novel catalyst microstructure based on aligned multiwall carbon nanotube arrays was synthesized. Its advanced heat and mass transport characteristics coupled with high surface area led to superior performances for Fischer-Tropsch synthesis in a microchannel chemical reactor. The fabrication of such a novel catalyst structure first involved metalorganic chemical vapor deposition (MOCVD) growth of a dense Al2O3 thin film over FeCrAlY foam substrate to enhance adhesion between catalyst layer and metal substrate. Aligned arrays of multiwall carbon nanotubes were grown over the substrate by catalytic decomposition of ethylene. These nanotube bundles were directly attached to the FeCrAlY substrate through a thin layer of oxide thin film. When the outer surfaces of nanobundles were coated with a catalyst layer, a unique hierarchical catalyst structure with nanoporous interstitials between the bundles was created. Thus, engineered catalysts based on such a novel hierarchical structure minimizes mass transfer encountered in the gas-liquid-solid three phase reactions. In addition, high thermal conductivity of carbon nanotube and the direct attachment of these nanobundles to the metal foam allow efficient heat removal from catalytic sites. The advanced heat and mass transfer on this novel structured catalyst was demonstrated in Fischer-Tropsch synthesis in a microchannel fixed bed reactor. The presence of carbon nanotube arrays improved dispersion of active metals and reduced mass transfer limitation, leading to a factor of four enhancement of Fischer-Tropsch synthesis activity. The improved temperature control with the carbon nanotube arrays also allows the Fischer-Tropsch synthesis being operated at temperatures as high as 265 C without reaction runaway favoring methane formation.

  4. Onorbit IMU alignment error budget

    NASA Technical Reports Server (NTRS)

    Corson, R. W.

    1980-01-01

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

  5. A Case Study of the Alignment between Curriculum and Assessment in the New York State Earth Science Standards-Based System

    NASA Astrophysics Data System (ADS)

    Contino, Julie

    2013-02-01

    In a standards-based system, it is important for all components of the system to align in order to achieve the intended goals. No Child Left Behind law mandates that assessments be fully aligned with state standards, be valid, reliable and fair, be reported to all stakeholders, and provide evidence that all students in the state are meeting the standards. This study reports an analysis of the alignment between the National Science Education Standards (NSES), New York State Physical Setting/Earth Science Core Curriculum (Core Curriculum) and New York State Physical Setting/Earth Science Regents Examination (Regents Exam)—the sources teachers use for creating Earth Science curricula in New York State. The NSES were found to have a 49 % overlap with the Core Curriculum and a 27 % overlap with the Regents Exam. The Core Curriculum and Regents Exam, represented by matrices consisting of performance indicators and cognitive demands, were compared using the Porter Alignment Index. The alignment was 0.35, categorized as slightly aligned, due to the different emphases on cognitive levels. The Core focused on cognitive skills of Understand and Apply while the Regents concentrated more on Apply followed by Understand and Remember. It is suggested that the NSES be revised and the Core updated to include quantifiable emphasis on the major understandings such as percentage of time.

  6. Transcription factor binding sites detection by using alignment-based approach.

    PubMed

    Mahdevar, Ghasem; Sadeghi, Mehdi; Nowzari-Dalini, Abbas

    2012-07-01

    Gene expression is the main cause for the existence of various phenotypes. Through this procedure, the information stored in DNA rises to the phenotype. Essentially, gene expression is dependent upon the successful binding of transcription factors (TFs) - a specific type of proteins - to explicit positions in its upstream, TF binding sites (TFBSs). Unfortunately, finding these TFBSs is costly and laborious; therefore, discovering TFBSs computationally is a significant problem that many researches endeavor to solve. In this paper, a new TFBS discovery method is presented by considering known biological facts about TFBSs. The input to this method includes sequences with arbitrary lengths and the output comprises positions that tend to be TFBS. Through the application of previous methods along with a method that focuses on biological and simulated datasets, it is shown that this method achieves higher accuracy in discovering TFBSs. PMID:22504445

  7. Aligning University-Based Teacher Preparation and New STEM Teacher Support

    ERIC Educational Resources Information Center

    Schuster, Dwight; Buckwalter, John; Marrs, Kathy; Pritchett, Sheila; Sebens, Jeremy; Hiatt, Bill

    2012-01-01

    This article is intended to help teacher educators, administrators, and mentor teachers envision how to support beginning STEM teachers as they transition from university-based preservice preparation into their first year of classroom teaching in high-need schools. Based on our experiences, and grounded in the associated research and literature,…

  8. Development of Research-Based Protocol Aligned to Predict High Levels of Teaching Quality

    ERIC Educational Resources Information Center

    Schumacher, Gary; Grigsby, Bettye; Vesey, Winona

    2011-01-01

    This study proposes a research-based teacher selection protocol. The protocol is intended to offer school district hiring authorities a tool to identify teacher candidates with the behaviors expected to predict effective teaching. It is hypothesized that a particular series of research-based interview questions focusing on teaching behaviors in…

  9. Conditional alignment random fields for multiple motion sequence alignment.

    PubMed

    Kim, Minyoung

    2013-11-01

    We consider the multiple time-series alignment problem, typically focusing on the task of synchronizing multiple motion videos of the same kind of human activity. Finding an optimal global alignment of multiple sequences is infeasible, while there have been several approximate solutions, including iterative pairwise warping algorithms and variants of hidden Markov models. In this paper, we propose a novel probabilistic model that represents the conditional densities of the latent target sequences which are aligned with the given observed sequences through the hidden alignment variables. By imposing certain constraints on the target sequences at the learning stage, we have a sensible model for multiple alignments that can be learned very efficiently by the EM algorithm. Compared to existing methods, our approach yields more accurate alignment while being more robust to local optima and initial configurations. We demonstrate its efficacy on both synthetic and real-world motion videos including facial emotions and human activities. PMID:24051737

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

    NASA Technical Reports Server (NTRS)

    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.

  11. Blazed vector grating liquid crystal cells with photocrosslinkable polymeric alignment films fabricated by one-step polarizer rotation method

    NASA Astrophysics Data System (ADS)

    Kawai, Kotaro; Kuzuwata, Mitsuru; Sasaki, Tomoyuki; Noda, Kohei; Kawatsuki, Nobuhiro; Ono, Hiroshi

    2014-12-01

    Blazed vector grating liquid crystal (LC) cells, in which the directors of low-molar-mass LCs are antisymmetrically distributed, were fabricated by one-step exposure of an empty glass cell inner-coated with a photocrosslinkable polymer LC (PCLC) to UV light. By adopting a LC cell structure, twisted nematic (TN) and homogeneous (HOMO) alignments were obtained in the blazed vector grating LC cells. Moreover, the diffraction efficiency of the blazed vector grating LC cells was greatly improved by increasing the thickness of the device in comparison with that of a blazed vector grating with a thin film structure obtained in our previous study. In addition, the diffraction efficiency and polarization states of ±1st-order diffracted beams from the resultant blazed vector grating LC cells were controlled by designing a blazed pattern in the alignment films, and these diffraction properties were well explained on the basis of Jones calculus and the elastic continuum theory of nematic LCs.

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

    PubMed Central

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

    2016-01-01

    ABSTRACT 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. PMID:26821742

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

    PubMed

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

    2016-03-01

    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. PMID:26821742

  14. An indirect method of studying band alignments in nBn photodetectors using off-axis electron holography

    SciTech Connect

    Shen, Xiao-Meng; He, Zhao-Yu; Liu, Shi; Lin, Zhi-Yuan; Zhang, Yong-Hang; Smith, David J.; McCartney, Martha R.

    2015-09-21

    Mid-wave and long-wave infrared nBn photodetectors with absorbers consisting of InAs/InAsSb superlattices and barriers consisting of InAs/AlGaSb(As) superlattices were grown using molecular beam epitaxy. High-resolution X-ray diffraction showing significant differences in Ga composition in the barrier layer, and different dark current behavior at 77 K, suggested the possibility of different types of band alignments between the barrier layer and the absorber for the mid- and long-wave infrared samples. Examination of the barrier layers using off-axis electron holography showed the presence of positive charge with an estimated density of 1.8 × 10{sup 17}/cm{sup 3} in the mid-wave sample as a result of a type-II band alignment, whereas negligible charge was detected in the long-wave sample, consistent with a type-I band alignment.

  15. RECOVERING FILTER-BASED MICROARRAY DATA FOR PATHWAYS ANALYSIS USING A MULTIPOINT ALIGNMENT STRATEGY

    EPA Science Inventory

    The use of commercial microarrays are rapidly becoming the method of choice for profiling gene expression and assessing various disease states. Research Genetics has provided a series of well defined biological and software tools to the research community for these analyses. Th...

  16. Towards Automatically Aligning German Compounds with English Word Groups in an Example-Based Translation System.

    ERIC Educational Resources Information Center

    Jones, Daniel; Alexa, Melina

    As part of the development of a completely sub-symbolic machine translation system, a method for automatically identifying German compounds was developed. Given a parallel bilingual corpus, German compounds are identified along with their English word groupings by statistical processing alone. The underlying principles and the design process are…

  17. Support Vector Training of Protein Alignment Models

    PubMed Central

    Joachims, Thorsten; Elber, Ron; Pillardy, Jaroslaw

    2008-01-01

    Abstract Sequence to structure alignment is an important step in homology modeling of protein structures. Incorporation of features such as secondary structure, solvent accessibility, or evolutionary information improve sequence to structure alignment accuracy, but conventional generative estimation techniques for alignment models impose independence assumptions that make these features difficult to include in a principled way. In this paper, we overcome this problem using a Support Vector Machine (SVM) method that provides a well-founded way of estimating complex alignment models with hundred of thousands of parameters. Furthermore, we show that the method can be trained using a variety of loss functions. In a rigorous empirical evaluation, the SVM algorithm outperforms the generative alignment method SSALN, a highly accurate generative alignment model that incorporates structural information. The alignment model learned by the SVM aligns 50% of the residues correctly and aligns over 70% of the residues within a shift of four positions. PMID:18707536

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

    ERIC Educational Resources Information Center

    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)…

  19. Alignment: Its Role in Standards-Based Reform and Prospects for the Common Core

    ERIC Educational Resources Information Center

    Massell, Diane; Perrault, Paul

    2014-01-01

    The Common Core State Standards (CCSS) of 2010 represent a new chapter in the 25-year history of standards-based reforms (SBR). The CCSS attempts to bring the system back to the principles of its founding--more rigorous, focused, academic content and performance expectations collectively embraced by the nation. The new standards depart…

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

    ERIC Educational Resources Information Center

    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…

  1. Aligning Theory and Web-Based Instructional Design Practice with Design Patterns.

    ERIC Educational Resources Information Center

    Frizell, Sherri S.; Hubscher, Roland

    Designing instructionally sound Web courses is a difficult task for instructors who lack experience in interaction and Web-based instructional design. Learning theories and instructional strategies can provide course designers with principles and design guidelines associated with effective instruction that can be utilized in the design of…

  2. IUS prerelease alignment

    NASA Technical Reports Server (NTRS)

    Evans, F. A.

    1978-01-01

    Space shuttle orbiter/IUS alignment transfer was evaluated. Although the orbiter alignment accuracy was originally believed to be the major contributor to the overall alignment transfer error, it was shown that orbiter alignment accuracy is not a factor affecting IUS alignment accuracy, if certain procedures are followed. Results are reported of alignment transfer accuracy analysis.

  3. Aligning cost assessment with community-based participatory research: the Kin KeeperSM intervention.

    PubMed

    Meghea, Cristian Ioan; Williams, Karen Patricia

    2015-04-01

    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(SM) Cancer Prevention Intervention, a female family-focused educational intervention for underserved women applied to increase breast and cervical cancer screening by enhancing cancer literacy. The cost analysis was performed from the perspective of a health organization with established community partnerships adding the Kin Keeper family intervention in the future to an existing community health worker program. The cost of delivering the Kin Keeper intervention, including two cancer education home visits, was $151/family. Kin Keeper is an inexpensive educational intervention delivered by community health workers to promote breast and cervical screening, with strong fidelity and quality. Prospecting cost evaluations of community-based interventions are needed for making informed timely decisions on the adaptation and expansion of such programs. PMID:25394822

  4. Alignment of Nephrology Training with Workforce, Patient, and Educational Needs: An Evidence Based Proposal

    PubMed Central

    Brown, Mark

    2011-01-01

    Summary Background and objectives Competency-based training programs focus on the product of training rather than the process with the desired attributes and skills set of the specialist directing the training program. These ideal skills and qualities have yet to be formally identified for nephrology training. The objectives of our study were: (1) to define the attributes of a “high quality” nephrologist from the perspectives of the trainer (nephrologist), trainee, and renal patient and (2) identify components and relative frequencies of nephrologists' work practice. Design, setting, participants, & measurements Four substudies were undertaken, utilizing a combined quantitative and qualitative approach: (1) a national nephrology workforce study, (2) in-depth interviews of nephrology patients, (3) in-depth interviews of nephrology trainees, and (4) in-depth interviews of practicing nephrologists. Results Patients value good communication skills above other attributes. Nephrologists and trainees identify particular personal attributes, a holistic and evidence-based approach to patient care, and good clinical skills as paramount. Although nephrologists spend most of their time in clinical practice, substantial time is also spent in research, teaching, and administrative work. Conclusions For the first time, an evidence-based approach has been used to help define qualities desired in a practicing nephrologist. Along with training and assessment in clinical practice, this research supports nephrology training programs incorporating training in basic interventions, research skill acquisition, administration, and teaching. Training toward high standards in advanced communication and the maintenance of a holistic approach to patient care are necessary. PMID:21980186

  5. Improvement in device performance from a mixture of a liquid crystal and photosensitive acrylic prepolymer with the photoinduced vertical alignment method

    NASA Astrophysics Data System (ADS)

    Ho, Czung-Yu; Lin, Fa-Hsin; Tao, Yu-Tai; Lee, Jiunn-Yih

    2011-12-01

    In a multicomponent nematic liquid crystal (NLC) mixture of a liquid crystal (negative-type NLC) and a photosensitive acrylic prepolymer, photopolymerization upon UV irradiation induces the separation of the LC and photosensitive acrylic prepolymer layers, thereby leading to a vertical arrangement of LC molecules. In this study, we propose a simple vertical alignment method for LC molecules, by adding a chiral smectic A (SmA*) liquid crystal having homeotropic texture characteristics to an NLC mixture solution. Measurements of electro-optical properties revealed that the addition of the SmA* LC not only strengthened the anchoring force of the copolymer alignment film surface, but also significantly enhanced the contrast ratio (~73%), response time and grayscale switching performance of the device.

  6. Well-pump alignment system

    DOEpatents

    Drumheller, Douglas S.

    1998-01-01

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

  7. On the alignment of quasars

    NASA Astrophysics Data System (ADS)

    Zhu, X.-F.

    1986-06-01

    Taking the two Savage-Bolton 5 deg x 5 deg regions of optical quasar patrol as samples, a systematic analysis of the number of aligned quasars was made and compared with the random data generated by Monte Carlo method. The statistical result is that, at least for these two samples, there is no clear evidence for alignment.

  8. On the alignment of quasars

    NASA Astrophysics Data System (ADS)

    Zhu, Xing-fen

    1986-06-01

    Taking the two Savage-Bolton 5° × 5° regions of optical quasar patrol as samples, I made a systematic analysis of the number of aligned quasars and compared with the random data generated by Monte Carlo method. The statistical result is that, at least for these two samples, there is no clear evidence for alignment.

  9. LCLS Undulator Commissioning, Alignment, and Performance

    SciTech Connect

    Nuhn, Heinz-Dieter

    2009-10-30

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

  10. Heterogeneous Data Fusion via Space Alignment Using Nonmetric Multidimensional Scaling

    SciTech Connect

    Choo, Jaegul; Bohn, Shawn J.; Nakamura, Grant C.; White, Amanda M.; Park, Haesun

    2012-04-26

    Heterogeneous data sets are typically represented in different feature spaces, making it difficult to analyze relationships spanning different data sets even when they are semantically related. Data fusion via space alignment can remedy this task by integrating multiple data sets lying in different spaces into one common space. Given a set of reference correspondence data that share the same semantic meaning across different spaces, space alignment attempts to place the corresponding reference data as close together as possible, and accordingly, the entire data are aligned in a common space. Space alignment involves optimizing two potentially conflicting criteria: minimum deformation of the original relationships and maximum alignment between the different spaces. To solve this problem, we provide a novel graph embedding framework for space alignment, which converts each data set into a graph and assigns zero distance between reference correspondence pairs resulting in a single graph. We propose a graph embedding method for fusion based on nonmetric multidimensional scaling (MDS). Its criteria using the rank order rather than the distance allows nonmetric MDS to effectively handle both deformation and alignment. Experiments using parallel data sets demonstrate that our approach works well in comparison to existing methods such as constrained Laplacian eigenmaps, Procrustes analysis, and tensor decomposition. We also present standard cross-domain information retrieval tests as well as interesting visualization examples using space alignment.

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

    NASA Astrophysics Data System (ADS)

    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.

  12. DISPLACEMENT BASED SEISMIC DESIGN METHODS.

    SciTech Connect

    HOFMAYER,C.MILLER,C.WANG,Y.COSTELLO,J.

    2003-07-15

    A research effort was undertaken to determine the need for any changes to USNRC's seismic regulatory practice to reflect the move, in the earthquake engineering community, toward using expected displacement rather than force (or stress) as the basis for assessing design adequacy. The research explored the extent to which displacement based seismic design methods, such as given in FEMA 273, could be useful for reviewing nuclear power stations. Two structures common to nuclear power plants were chosen to compare the results of the analysis models used. The first structure is a four-story frame structure with shear walls providing the primary lateral load system, referred herein as the shear wall model. The second structure is the turbine building of the Diablo Canyon nuclear power plant. The models were analyzed using both displacement based (pushover) analysis and nonlinear dynamic analysis. In addition, for the shear wall model an elastic analysis with ductility factors applied was also performed. The objectives of the work were to compare the results between the analyses, and to develop insights regarding the work that would be needed before the displacement based analysis methodology could be considered applicable to facilities licensed by the NRC. A summary of the research results, which were published in NUREGICR-6719 in July 2001, is presented in this paper.

  13. MUSE optical alignment procedure

    NASA Astrophysics Data System (ADS)

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

    2012-09-01

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

  14. Amperometric Non-Enzymatic Hydrogen Peroxide Sensor Based on Aligned Zinc Oxide Nanorods

    PubMed Central

    Al-Hardan, Naif H.; Abdul Hamid, Muhammad Azmi; Shamsudin, Roslinda; Othman, Norinsan Kamil; Kar Keng, Lim

    2016-01-01

    Zinc oxide (ZnO) nanorods (NRs) have been synthesized via the hydrothermal process. The NRs were grown over a conductive glass substrate. A non-enzymatic electrochemical sensor for hydrogen peroxide (H2O2), based on the prepared ZnO NRs, was examined through the use of current-voltage measurements. The measured currents, as a function of H2O2 concentrations ranging from 10 μM to 700 μM, revealed two distinct behaviours and good performance, with a lower detection limit (LOD) of 42 μM for the low range of H2O2 concentrations (first region), and a LOD of 143.5 μM for the higher range of H2O2 concentrations (second region). The prepared ZnO NRs show excellent electrocatalytic activity. This enables a measurable and stable output current. The results were correlated with the oxidation process of the H2O2 and revealed a good performance for the ZnO NR non-enzymatic H2O2 sensor. PMID:27367693

  15. Fabrication and characterization of Mach–Zehnder interferometer based on a hollow optical fiber filled with radial-aligned liquid crystal

    NASA Astrophysics Data System (ADS)

    Ho, Bo-Yan; Peng, Fenglin; Wu, Shin-Tson; Hwang, Shug-June

    2016-07-01

    We demonstrate a high sensitivity all-fiber Mach–Zehnder interferometer (MZI) based on radial-aligned liquid crystal (LC) in a hollow optical fiber (HOF). The transmission spectrum of the liquid crystal-filled fiber MZI (LCF-MZI) was measured at different temperatures, and the thermal-induced wavelength shift of the interference spectrum probed. The experimental results indicate that the LC alignment and refractive indices inside the hollow capillary are significantly influenced by the temperature, which in turn changes the optical properties of LCF-MZI. Our experimental data on notch wavelength shift agree well with the measured refractive index temperature gradient.

  16. Homeotropic alignment and director structures in thin films of triphenylamine-based discotic liquid crystals controlled by supporting nanostructured substrates and surface confinement.

    PubMed

    Choudhury, Trirup Dutta; Rao, Nandiraju V S; Tenent, Robert; Blackburn, Jeffrey; Gregg, Brian; Smalyukh, Ivan I

    2011-02-01

    We explore the effects of nanoscale morphology of supporting solid substrates on alignment, defects, and director structures exhibited by thin films of triphenylamine-based discotic liquid crystals. Fluorescence confocal polarizing microscopy and intrinsic polarized fluorescence properties of studied molecules are used to visualize three-dimensional director fields in the liquid crystal films. We demonstrate that, by controlling surface anchoring on supporting or confining solid substrates such as those of carbon nanotube electrodes on glass plates, both uniform homeotropic and in-plane (edge-on) alignment and nonuniform structures with developable domains can be achieved for the same discotic liquid crystal material. PMID:21214228

  17. Gold Alignment and Internal Dissipation

    NASA Astrophysics Data System (ADS)

    Lazarian, A.

    1997-07-01

    The measures of mechanical alignment are obtained for both prolate and oblate grains whose temperatures are comparable to the grain kinetic energy divided by k, the Boltzmann constant. For such grains, the alignment of angular momentum, J, with the axis of maximal inertia, a, is only partial, which substantially alters the mechanical alignment as compared with the results obtained by Lazarian and Roberge, Hanany, & Messinger under the assumption of perfect alignment. We also describe Gold alignment when the Barnett dissipation is suppressed and derive an analytical expression that relates the measure of alignment to the parameters of grain nonsphericity and the direction of the gas-grain drift. This solution provides the lower limit for the measure of alignment, while the upper limit is given by the method derived by Lazarian. Using the results of a recent study of incomplete internal relaxation by Lazarian & Roberge, we find measures of alignment for the whole range of ratios of grain rotational energy to kTs, where Ts is the grain temperature. To describe alignment for mildly supersonic drifts, we suggest an analytical approach that provides good correspondence with the results of direct numerical simulations by Roberge, Hanany, & Messinger. We also extend our approach to account for simultaneous action of the Gold and Davis-Greenstein mechanisms.

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

    PubMed

    Menke, Matthew; Berger, Bonnie; Cowen, Lenore

    2008-01-01

    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 and average root

  19. Direct analytical method of contact position effects on the energy-level alignments at organic semiconductor/electrode interfaces using photoemission spectroscopy combined with Ar gas cluster ion beam sputtering

    NASA Astrophysics Data System (ADS)

    Yun, Dong-Jin; Chung, JaeGwan; Kim, Seong Heon; Kim, Yongsu; Park, SungHoon; Seol, Minsu; Heo, Sung

    2015-11-01

    Poly(3, 4-ethylenedioxythiophene) (PEDOT) polymerized with poly(4-styrenesulfonate) (PSS) is one of the most widely used conducting organic electrodes owing to its outstanding optical/electrical properties and high work function. Because its work function depends significantly on the molecular arrangements between PEDOT and PSS molecules on the surface, the contact position of PEDOT:PSS films on organic semiconductors (OSCs) must also be an essential consideration. However, existing analysis methods based on in situ deposition/analysis are limited in their ability to accurately investigate the electronic structures of the buried interface regions under the solution-processed electrode or OSC layer in organic devices. Therefore, to overcome such limitations, we propose a top-down method based on photoemission spectroscopy analysis combined with Ar gas cluster ion beam (GCIB) sputtering. Through this method, both energy-level alignments and molecular distributions at various OSC/electrode interfaces can be successfully characterized without reference to any deposition process.

  20. Aligning Astronomical Telescopes via Identification of Stars

    NASA Technical Reports Server (NTRS)

    Whorton, Mark

    2010-01-01

    A proposed method of automated, precise alignment of a ground-based astronomical telescope would eliminate the need for initial manual alignment. The method, based on automated identification of known stars and other celestial objects in the telescope field of view, would also eliminate the need for an initial estimate of the aiming direction. The method does not require any equipment other than a digital imaging device such as a charge-coupled-device digital imaging camera and control computers of the telescope and camera, all of which are standard components in professional astronomical telescope systems and in high-end amateur astronomical telescope systems. The method could be implemented in software running in the telescope or camera control computer or in an external computer communicating with the telescope pointing mount and camera control computers.