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Sample records for alignment method based

  1. Optical center alignment technique based on inner profile measurement method

    NASA Astrophysics Data System (ADS)

    Wakayama, Toshitaka; Yoshizawa, Toru

    2014-05-01

    Center alignment is important technique to tune up the spindle of various precision machines in manufacturing industry. Conventionally such a tool as a dial indicator has been used to adjust and to position the axis by manual operations of a technical worker. However, it is not easy to precisely control its axis. In this paper, we developed the optical center alignment technique based on inner profile measurement using a ring beam device. In this case, the center position of the cylinder hole can be determined from circular profile detected by optical sectioning method using a ring beam device. In our trials, the resolution of the center position is proved less than 10 micrometers in extreme cases. This technique is available for practical applications in machine tool industry.

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

    PubMed Central

    Terashi, Genki; Takeda-Shitaka, Mayuko

    2015-01-01

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

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

    PubMed

    Terashi, Genki; Takeda-Shitaka, Mayuko

    2015-01-01

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

  4. 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.

  5. 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.

  6. Iris-based cyclotorsional image alignment method for wavefront registration.

    PubMed

    Chernyak, Dimitri A

    2005-12-01

    In refractive surgery, especially wavefront-guided refractive surgery, correct registration of the treatment to the cornea is of paramount importance. The specificity of the custom ablation formula requires that the ablation be applied to the cornea only when it has been precisely aligned with the mapped area. If, however, the eye has rotated between measurement and ablation, and this cyclotorsion is not compensated for, the rotational misalignment could impair the effectiveness of the refractive surgery. To achieve precise registration, a noninvasive method for torsional rotational alignment of the captured wavefront image to the patient's eyes at surgery has been developed. This method applies a common coordinate system to the wavefront and the eye. Video cameras on the laser and wavefront devices precisely establish the spatial relationship between the optics of the eye and the natural features of the iris, enabling the surgeon to identify and compensate for cyclotorsional eye motion, whatever its cause.

  7. A new graph-based method for pairwise global network alignment

    PubMed Central

    Klau, Gunnar W

    2009-01-01

    Background In addition to component-based comparative approaches, network alignments provide the means to study conserved network topology such as common pathways and more complex network motifs. Yet, unlike in classical sequence alignment, the comparison of networks becomes computationally more challenging, as most meaningful assumptions instantly lead to NP-hard problems. Most previous algorithmic work on network alignments is heuristic in nature. Results We introduce the graph-based maximum structural matching formulation for pairwise global network alignment. We relate the formulation to previous work and prove NP-hardness of the problem. Based on the new formulation we build upon recent results in computational structural biology and present a novel Lagrangian relaxation approach that, in combination with a branch-and-bound method, computes provably optimal network alignments. The Lagrangian algorithm alone is a powerful heuristic method, which produces solutions that are often near-optimal and – unlike those computed by pure heuristics – come with a quality guarantee. Conclusion Computational experiments on the alignment of protein-protein interaction networks and on the classification of metabolic subnetworks demonstrate that the new method is reasonably fast and has advantages over pure heuristics. Our software tool is freely available as part of the LISA library. PMID:19208162

  8. 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.

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

    PubMed Central

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

    2015-01-01

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

  10. Novel method based on DDE technology for computer-aided alignment

    NASA Astrophysics Data System (ADS)

    Huang, Yifan; Li, Lin

    2008-03-01

    A new method based on Dynamic Data Exchange (DDE) technology for computer-aided alignment is put forward in this paper. It is adopted to realize the automatic data transferring between Matlab and Zemax optical software. Based on the analysis of CAA and its procedure, a self-made program is developed to perform all the CAA steps under Matlab environment. Flow process of this program is shown in this paper. A Gregorian system is adopted as an example to verify the feasibility of the program. Comparisons of the image quality between the misaligned system and the post-aligned system are presented. Results show that this program is very effective.

  11. In-motion coarse alignment method based on reconstructed observation vectors

    NASA Astrophysics Data System (ADS)

    Xu, Xiang; Xu, Xiaosu; Yao, Yiqing; Wang, Zhicheng

    2017-03-01

    In this paper, an in-motion coarse alignment method is proposed based on the reconstructed observation vectors. Since the complicated noises are contained in the outputs of the inertial sensors, the components of measurement observation vectors, which are constructed by the sensors' outputs, are analyzed in detail. To suppress the high-frequency noises, an effective digital filter based on the Infinite Impulse Response technology is employed. On the basis of the parameter models of the observation vectors, a new form Kalman filter, which is also an adaptive filter, is designed for the recognition of the parameter matrix. Furthermore, a robust filter technology, which is based on the Huber's M-estimation, is employed to suppress the gross outliers, which are caused by the movement of the carrier. Simulation test and field trial are designed to verify the proposed method. All the alignment results demonstrate that the performance of the proposed method is superior to the conventional optimization-based alignment and the digital filter alignment, which are the current popular methods.

  12. 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.

  13. FLASHFLOOD: A 3D Field-based similarity search and alignment method for flexible molecules

    NASA Astrophysics Data System (ADS)

    Pitman, Michael C.; Huber, Wolfgang K.; Horn, Hans; Krämer, Andreas; Rice, Julia E.; Swope, William C.

    2001-07-01

    A three-dimensional field-based similarity search and alignment method for flexible molecules is introduced. The conformational space of a flexible molecule is represented in terms of fragments and torsional angles of allowed conformations. A user-definable property field is used to compute features of fragment pairs. Features are generalizations of CoMMA descriptors (Silverman, B.D. and Platt, D.E., J. Med. Chem., 39 (1996) 2129.) that characterize local regions of the property field by its local moments. The features are invariant under coordinate system transformations. Features taken from a query molecule are used to form alignments with fragment pairs in the database. An assembly algorithm is then used to merge the fragment pairs into full structures, aligned to the query. Key to the method is the use of a context adaptive descriptor scaling procedure as the basis for similarity. This allows the user to tune the weights of the various feature components based on examples relevant to the particular context under investigation. The property fields may range from simple, phenomenological fields, to fields derived from quantum mechanical calculations. We apply the method to the dihydrofolate/methotrexate benchmark system, and show that when one injects relevant contextual information into the descriptor scaling procedure, better results are obtained more efficiently. We also show how the method works and include computer times for a query from a database that represents approximately 23 million conformers of seventeen flexible molecules.

  14. Method for alignment of microwires

    DOEpatents

    Beardslee, Joseph A.; Lewis, Nathan S.; Sadtler, Bryce

    2017-01-24

    A method of aligning microwires includes modifying the microwires so they are more responsive to a magnetic field. The method also includes using a magnetic field so as to magnetically align the microwires. The method can further include capturing the microwires in a solid support structure that retains the longitudinal alignment of the microwires when the magnetic field is not applied to the microwires.

  15. An efficient method for multiple sequence alignment

    SciTech Connect

    Kim, J.; Pramanik, S.

    1994-12-31

    Multiple sequence alignment has been a useful method in the study of molecular evolution and sequence-structure relationships. This paper presents a new method for multiple sequence alignment based on simulated annealing technique. Dynamic programming has been widely used to find an optimal alignment. However, dynamic programming has several limitations to obtain optimal alignment. It requires long computation time and cannot apply certain types of cost functions. We describe detail mechanisms of simulated annealing for multiple sequence alignment problem. It is shown that simulated annealing can be an effective approach to overcome the limitations of dynamic programming in multiple sequence alignment problem.

  16. Shuttle onboard IMU alignment methods

    NASA Technical Reports Server (NTRS)

    Henderson, D. M.

    1976-01-01

    The current approach to the shuttle IMU alignment is based solely on the Apollo Deterministic Method. This method is simple, fast, reliable and provides an accurate estimate for the present cluster to mean of 1,950 transformation matrix. If four or more star sightings are available, the application of least squares analysis can be utilized. The least squares method offers the next level of sophistication to the IMU alignment solution. The least squares method studied shows that a more accurate estimate for the misalignment angles is computed, and the IMU drift rates are a free by-product of the analysis. Core storage requirements are considerably more; estimated 20 to 30 times the core required for the Apollo Deterministic Method. The least squares method offers an intermediate solution utilizing as much data that is available without a complete statistical analysis as in Kalman filtering.

  17. A Coarse Alignment Method Based on Digital Filters and Reconstructed Observation Vectors.

    PubMed

    Xu, Xiang; Xu, Xiaosu; Zhang, Tao; Li, Yao; Wang, Zhicheng

    2017-03-29

    In this paper, a coarse alignment method based on apparent gravitational motion is proposed. Due to the interference of the complex situations, the true observation vectors, which are calculated by the apparent gravity, are contaminated. The sources of the interference are analyzed in detail, and then a low-pass digital filter is designed in this paper for eliminating the high-frequency noise of the measurement observation vectors. To extract the effective observation vectors from the inertial sensors' outputs, a parameter recognition and vector reconstruction method are designed, where an adaptive Kalman filter is employed to estimate the unknown parameters. Furthermore, a robust filter, which is based on Huber's M-estimation theory, is developed for addressing the outliers of the measurement observation vectors due to the maneuver of the vehicle. A comprehensive experiment, which contains a simulation test and physical test, is designed to verify the performance of the proposed method, and the results show that the proposed method is equivalent to the popular apparent velocity method in swaying mode, but it is superior to the current methods while in moving mode when the strapdown inertial navigation system (SINS) is under entirely self-contained conditions.

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

    PubMed

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

    2011-01-01

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

  19. 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

  20. 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.

  1. 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.

  2. 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

  3. An improved self-alignment method for strapdown inertial navigation system based on gravitational apparent motion and dual-vector.

    PubMed

    Liu, Xixiang; Zhao, Yu; Liu, Xianjun; Yang, Yan; Song, Qing; Liu, Zhipeng

    2014-12-01

    Analysis and simulation results indicate that two problems should be solved when the self-alignment method based on gravitational apparent motion and dual-vector can be used for Strapdown Inertial Navigation System. The first one is how to identify the apparent motion from accelerometer measurement containing random noise and the second is how to avoid the collinear problem between two vectors used in alignment solution. In this paper, a parameter identification and reconstruction algorithm is proposed to solve the first problem and simulation results indicate that proposed algorithm can identify apparent motion from accelerometer measurements effectively; and reconstruction algorithm based on current identified parameters for dual-vector is designed in detail to solve the second problem which can make full use of newest identification and avoid collinear problem completely. Simulation and turntable results show that the proposed alignment method can fulfill self-alignment in a swinging condition and the alignment accuracy can reach the theoretical values determined by the sensor precision.

  4. Practical alignment method for X-ray spectral measurement in micro-CT system based on 3D printing technology.

    PubMed

    Ren, Liqiang; Wu, Di; Li, Yuhua; Zheng, Bin; Chen, Yong; Yang, Kai; Liu, Hong

    2016-06-01

    This study presents a practical alignment method for X-ray spectral measurement in a rotating gantry based micro-computed tomography (micro-CT) system using three-dimensional (3D) printing technology. In order to facilitate the spectrometer placement inside the gantry, supporting structures including a cover and a stand were dedicatedly designed and printed using a 3D printer. According to the relative position between the spectrometer and the stand, the upright projection of the spectrometer collimator onto the stand was determined and then marked by a tungsten pinhole. Thus, a visible alignment indicator of the X-ray central beam and the spectrometer collimator represented by the pinhole was established in the micro-CT live mode. Then, a rough alignment could be achieved through repeatedly adjusting and imaging the stand until the pinhole was located at the center of the acquired projection image. With the spectrometer being positioned back onto the stand, the precise alignment was completed by slightly translating the spectrometer-stand assembly around the rough location, until finding a "sweet spot" with the highest photon rate and proper distribution of the X-ray photons in the resultant spectrum. The spectra were acquired under precise alignment and misalignment of approximately 0.2, 0.5, and 1.0mm away from the precise alignment position, and then were compared in qualitative and quantitative analyses. Qualitative analysis results show that, with slight misalignment, the photon rate is reduced from 1302 to 1098, 1031, and 416 photons/second (p/s), respectively, and the characteristic peaks in the acquired spectra are gradually deteriorated. Quantitative analysis indicates that the energy resolutions for characteristic peak of Kα1 were calculated as 1.56% for precise alignment, while were 1.84% and 2.40% for slight misalignment of 0.2mm and 0.5mm. The mean energies were reduced from 43.93keV under precise alignment condition to 40.97, 39.63 and 37.78keV when

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  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. 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.

  11. A method to avoid errors associated with the analysis of hypermutated viral sequences by alignment-based methods.

    PubMed

    Alinejad-Rokny, Hamid; Ebrahimi, Diako

    2015-12-01

    The human genome encodes for a family of editing enzymes known as APOBEC3 (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like3). They induce context dependent G-to-A changes, referred to as "hypermutation", in the genome of viruses such as HIV, SIV, HBV and endogenous retroviruses. Hypermutation is characterized by aligning affected sequences to a reference sequence. We show that indels (insertions/deletions) in the sequences lead to an incorrect assignment of APOBEC3 targeted and non-target sites. This can result in an incorrect identification of hypermutated sequences and erroneous biological inferences made based on hypermutation analysis.

  12. Image Correlation Method for DNA Sequence Alignment

    PubMed Central

    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. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2012-06-01

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

  15. Switchable Fresnel lens based on micropatterned alignment.

    PubMed

    Wang, Xiao-Qian; Srivastava, Abhishek K; Chigrinov, Vladimir G; Kwok, Hoi-Sing

    2013-06-01

    In this Letter we disclose a method to fabricate a liquid crystal (LC) Fresnel zone lens (FZL) with higher efficiency. The LCFZL, based on alternate twisted nematic (TN) and planar aligned (PA) regions, has been prepared by means of a two-step photo-alignment process. The FZL profile for both optical regimes, i.e., in TN and PA alignment domains, generates the same focal length (f). Thus, the proposed LCFZL manifests double light intensity at the focal point and therefore offers double the efficiency of existing FZLs. Moreover, because of lower driving voltage and fast response, these elements could find application in many modern devices.

  16. A New Analytic Alignment Method for a SINS.

    PubMed

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

    2015-11-04

    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.

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

    NASA Astrophysics Data System (ADS)

    Sippl, Wolfgang

    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 ( r 2 = 0.617, q 2 LOO = 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 ( r 2 = 0.991, q 2 LOO = 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 ( r 2 = 0.951, q 2 LOO = 0.796) indicates that the combination of receptor-based and 3D QSAR methods is able to improve the quality of the underlying model.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

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

    PubMed

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

    2015-10-05

    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.

  5. Control rod housing alignment and repair method

    SciTech Connect

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

    1992-04-07

    This patent describes a method for underwater welding of a control rod drive housing inserted through a stub tube to maintain requisite alignment and elevation of the top of the control rod drive housing to an overlying and corresponding aperture in a core plate as measured by an alignment device which determines the relative elevation and angularity with respect to the aperture. It comprises providing a welding cylinder dependent from the alignment device such that the elevation of the top of the welding cylinder is in a fixed relationship to the alignment device and is gas-proof; pressurizing the welding cylinder with inert welding gas sufficient to maintain the interior of the welding cylinder dry; lowering the welding cylinder through the aperture in the core plate by depending the cylinder with respect to the alignment device, the lowering including lowering through and adjusting the elevation relationship of the welding cylinder to the alignment device such that when the alignment device is in position to measure the elevation and angularity of the new control rod drive housing, the lower distal end of the welding cylinder extends below the upper periphery of the stub where welding is to occur; inserting a new control rod drive housing through the stub tube and positioning the control rod drive housing to a predetermined relationship to the anticipated final position of the control rod drive housing; providing welding implements transversely rotatably mounted interior of the welding cylinder relative to the alignment device such that the welding implements may be accurately positioned for dispensing weldment around the periphery of the top of the stub tube and at the side of the control rod drive housing; measuring the elevation and angularity of the control rod drive housing; and dispensing weldment along the top of the stub tube and at the side of the control rod drive housing.

  6. Improved accuracy for noncoplanar radiotherapy: an EPID-based method for submillimeter alignment of linear accelerator table rotation with MV isocenter.

    PubMed

    Nyflot, Matthew J; Cao, Ning; Meyer, Juergen; Ford, Eric C

    2014-03-06

    Accurate alignment of linear accelerator table rotational axis with radiation isocenter is critical for noncoplanar radiotherapy applications. The purpose of the present study is to develop a method to align the table rotation axis and the MV isocenter to submillimeter accuracy. We developed a computerized method using electronic portal imaging device (EPID) and measured alignment stability over time. Mechanical and radiation isocenter coincidence was measured by placing a steel ball bearing at radiation isocenter using existing EPID techniques. Then, EPID images were acquired over the range of table rotation. A MATLAB script was developed to calculate the center of rotation, as well as the necessary adjustment to move the table rotational axis to MV isocenter. Adjustment was applied via torque to screws at the base of the linac table. Stability of rotational alignment was measured with 49 measurements over 363 days on four linacs. Initial rotational misalignment from radiation isocenter ranged from 0.91-2.11 mm on the four tested linacs. Linac-A had greatest error (> 2 mm) and was adjusted with the described method. After adjustment, the error was significantly decreased to 0.40 ± 0.12 mm. The adjustment was stable over the course of 15 measurements over 231 days. Linac-B was not adjusted, but tracked from time of commissioning with 27 measurements over 363 days. No discernible shift in couch characteristics was observed (mean error 1.40 ± 0.22 mm). The greater variability for Linac-B may relate to the interchangeable two-piece couch, which allows more lateral movement than the one-piece Linac-A couch. Submillimeter isocenter alignment was achieved by applying a precision correction to the linac table base. Table rotational characteristics were shown to be stable over the course of twelve months. The accuracy and efficiency of this method may make it suitable for acceptance testing, annual quality assurance, or commissioning of highly-conformal noncoplanar

  7. Alignment method for spectrograms of DNA sequences.

    PubMed

    Bucur, Anca; van Leeuwen, Jasper; Dimitrova, Nevenka; Mittal, Chetan

    2010-01-01

    DNA spectrograms express the periodicities of each of the four nucleotides A, T, C, and G in one or several genomic sequences to be analyzed. DNA spectral analysis can be applied to systematically investigate DNA patterns, which may correspond to relevant biological features. As opposed to looking at nucleotide sequences, spectrogram analysis may detect structural characteristics in very long sequences that are not identifiable by sequence alignment. Alignment of DNA spectrograms can be used to facilitate analysis of very long sequences or entire genomes at different resolutions. Standard clustering algorithms have been used in spectral analysis to find strong patterns in spectra. However, as they use a global distance metric, these algorithms can only detect strong patterns coexisting in several frequencies. In this paper, we propose a new method and several algorithms for aligning spectra suitable for efficient spectral analysis and allowing for the easy detection of strong patterns in both single frequencies and multiple frequencies.

  8. 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.

  9. A Novel Method for Alignment-free DNA Sequence Similarity Analysis Based on the Characterization of Complex Networks

    PubMed Central

    Zhou, Jie; Zhong, Pianyu; Zhang, Tinghui

    2016-01-01

    Determination of sequence similarity is one of the major steps in computational phylogenetic studies. One of the major tasks of computational biologists is to develop novel mathematical descriptors for similarity analysis. DNA clustering is an important technology that automatically identifies inherent relationships among large-scale DNA sequences. The comparison between the DNA sequences of different species helps determine phylogenetic relationships among species. Alignment-free approaches have continuously gained interest in various sequence analysis applications such as phylogenetic inference and metagenomic classification/clustering, particularly for large-scale sequence datasets. Here, we construct a novel and simple mathematical descriptor based on the characterization of cis sequence complex DNA networks. This new approach is based on a code of three cis nucleotides in a gene that could code for an amino acid. In particular, for each DNA sequence, we will set up a cis sequence complex network that will be used to develop a characterization vector for the analysis of mitochondrial DNA sequence phylogenetic relationships among nine species. The resulting phylogenetic relationships among the nine species were determined to be in agreement with the actual situation. PMID:27746676

  10. A Novel Method for Alignment-free DNA Sequence Similarity Analysis Based on the Characterization of Complex Networks.

    PubMed

    Zhou, Jie; Zhong, Pianyu; Zhang, Tinghui

    2016-01-01

    Determination of sequence similarity is one of the major steps in computational phylogenetic studies. One of the major tasks of computational biologists is to develop novel mathematical descriptors for similarity analysis. DNA clustering is an important technology that automatically identifies inherent relationships among large-scale DNA sequences. The comparison between the DNA sequences of different species helps determine phylogenetic relationships among species. Alignment-free approaches have continuously gained interest in various sequence analysis applications such as phylogenetic inference and metagenomic classification/clustering, particularly for large-scale sequence datasets. Here, we construct a novel and simple mathematical descriptor based on the characterization of cis sequence complex DNA networks. This new approach is based on a code of three cis nucleotides in a gene that could code for an amino acid. In particular, for each DNA sequence, we will set up a cis sequence complex network that will be used to develop a characterization vector for the analysis of mitochondrial DNA sequence phylogenetic relationships among nine species. The resulting phylogenetic relationships among the nine species were determined to be in agreement with the actual situation.

  11. An Improved Method for Completely Uncertain Biological Network Alignment

    PubMed Central

    Shen, Bin; Zhao, Muwei; Zhong, Wei; He, Jieyue

    2015-01-01

    With the continuous development of biological experiment technology, more and more data related to uncertain biological networks needs to be analyzed. However, most of current alignment methods are designed for the deterministic biological network. Only a few can solve the probabilistic network alignment problem. However, these approaches only use the part of probabilistic data in the original networks allowing only one of the two networks to be probabilistic. To overcome the weakness of current approaches, an improved method called completely probabilistic biological network comparison alignment (C_PBNA) is proposed in this paper. This new method is designed for complete probabilistic biological network alignment based on probabilistic biological network alignment (PBNA) in order to take full advantage of the uncertain information of biological network. The degree of consistency (agreement) indicates that C_PBNA can find the results neglected by PBNA algorithm. Furthermore, the GO consistency (GOC) and global network alignment score (GNAS) have been selected as evaluation criteria, and all of them proved that C_PBNA can obtain more biologically significant results than those of PBNA algorithm. PMID:26000284

  12. 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

  13. A sequence alignment-independent method for protein classification.

    PubMed

    Vries, John K; Munshi, Rajan; Tobi, Dror; Klein-Seetharaman, Judith; Benos, Panayiotis V; Bahar, Ivet

    2004-01-01

    Annotation of the rapidly accumulating body of sequence data relies heavily on the detection of remote homologues and functional motifs in protein families. The most popular methods rely on sequence alignment. These include programs that use a scoring matrix to compare the probability of a potential alignment with random chance and programs that use curated multiple alignments to train profile hidden Markov models (HMMs). Related approaches depend on bootstrapping multiple alignments from a single sequence. However, alignment-based programs have limitations. They make the assumption that contiguity is conserved between homologous segments, which may not be true in genetic recombination or horizontal transfer. Alignments also become ambiguous when sequence similarity drops below 40%. This has kindled interest in classification methods that do not rely on alignment. An approach to classification without alignment based on the distribution of contiguous sequences of four amino acids (4-grams) was developed. Interest in 4-grams stemmed from the observation that almost all theoretically possible 4-grams (20(4)) occur in natural sequences and the majority of 4-grams are uniformly distributed. This implies that the probability of finding identical 4-grams by random chance in unrelated sequences is low. A Bayesian probabilistic model was developed to test this hypothesis. For each protein family in Pfam-A and PIR-PSD, a feature vector called a probe was constructed from the set of 4-grams that best characterised the family. In rigorous jackknife tests, unknown sequences from Pfam-A and PIR-PSD were compared with the probes for each family. A classification result was deemed a true positive if the probe match with the highest probability was in first place in a rank-ordered list. This was achieved in 70% of cases. Analysis of false positives suggested that the precision might approach 85% if selected families were clustered into subsets. Case studies indicated that the 4

  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. Machinery alignment tables: Face-OD and reverse indicator methods

    SciTech Connect

    Buck, G.S.

    1984-01-01

    Many alignment techniques are too complex for practical use, and guessing never provides the needed precision. The face-OD (face-rim) and reverse indicator methods are the two most popular techniques experienced millwrights use, but both methods require time-consuming calculations. These tables replace the graphs, formulas, and calculations used to determine shim requirements. Contents: Face-OD method and reverse indicator method: Setting up Data forms. Equations and calculations. Examples. Alignment Tolerances. Errors in taking data. Typical alignment tolerances. Indicator sag. Cause of indicator sag. Correction of indicator sag. Typical values of indicator sag. Hot alignment. References.

  16. 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.

  17. Remarks on the Methods of Investigations of Alignment of Galaxies

    NASA Astrophysics Data System (ADS)

    Godłowski, Włodzimierz

    2012-03-01

    In the 1975 Hawley and Peebles proposed the use of three statistical tests for investigations of galaxy orientations in the large structures. Nowadays, it is considered as the standard method of searching for galactic alignments. In the present paper we analyzed the tests in detail and proposed a few improvements. Based on the improvements, a new method of analysis of the alignment of galaxies in clusters is proposed. The power of this method is demonstrated on the sample of 247 Abell clusters with at least 100 objects in each. The distributions of the position angles for galaxies in each cluster are analyzed using statistical tests: χ2, Fourier, autocorrelation, and Kolmogorov test. The mean value of analyzed statistics is compared with theoretical predictions as well as with results obtained from numerical simulations. We performed 1000 simulations of 247 fictitious clusters, each with the numbers of galaxies the same as in the real clusters. We found that orientations of galaxies in analyzed clusters are not random, i.e., that there exists an alignment of galaxies in rich Abell galaxy clusters.

  18. Fast Fiber-Laser Alignment: Beam Spot-Size Method

    NASA Astrophysics Data System (ADS)

    Zhang, Rong; Guo, Jingyan; Shi, Frank G.

    2005-03-01

    A novel fast and cost-effective method is introduced for the active alignment of a fiber to a laser diode: only four easy laser beam spot-size measurements are required for moving the fiber tip from the far field to the proximity of the optimal alignment position, thus dramatically reducing the total alignment time (at least five times faster than a conventional method),as experimentally confirmed. Moreover, in contrast to the existing methods,the new method is failure-proof. The principle of the proposed method can be applied generally to any type of packages and is illustrated by an example of a butterfly package.

  19. L-GRAAL: Lagrangian graphlet-based network aligner

    PubMed Central

    Malod-Dognin, Noël; Pržulj, Nataša

    2015-01-01

    Motivation: Discovering and understanding patterns in networks of protein–protein interactions (PPIs) is a central problem in systems biology. Alignments between these networks aid functional understanding as they uncover important information, such as evolutionary conserved pathways, protein complexes and functional orthologs. A few methods have been proposed for global PPI network alignments, but because of NP-completeness of underlying sub-graph isomorphism problem, producing topologically and biologically accurate alignments remains a challenge. Results: We introduce a novel global network alignment tool, Lagrangian GRAphlet-based ALigner (L-GRAAL), which directly optimizes both the protein and the interaction functional conservations, using a novel alignment search heuristic based on integer programming and Lagrangian relaxation. We compare L-GRAAL with the state-of-the-art network aligners on the largest available PPI networks from BioGRID and observe that L-GRAAL uncovers the largest common sub-graphs between the networks, as measured by edge-correctness and symmetric sub-structures scores, which allow transferring more functional information across networks. We assess the biological quality of the protein mappings using the semantic similarity of their Gene Ontology annotations and observe that L-GRAAL best uncovers functionally conserved proteins. Furthermore, we introduce for the first time a measure of the semantic similarity of the mapped interactions and show that L-GRAAL also uncovers best functionally conserved interactions. In addition, we illustrate on the PPI networks of baker's yeast and human the ability of L-GRAAL to predict new PPIs. Finally, L-GRAAL's results are the first to show that topological information is more important than sequence information for uncovering functionally conserved interactions. Availability and implementation: L-GRAAL is coded in C++. Software is available at: http://bio-nets.doc.ic.ac.uk/L-GRAAL/. Contact: n

  20. Alignment method of off-axis RC reflective optical system

    NASA Astrophysics Data System (ADS)

    Xue-min, Zhang; Xing, Song; Zhi-jun, Zhang; Hou, Xiao-hua

    2016-10-01

    Off-axis optical system has a wide application in space optics and remote detective area. The high surface shape accuracy can be ensured with the development of advanced manufacture technique. So the only condition which limits the wide application of off-axis optical system is how to realize the precise alignment of it. Based on a RC reflective optical system whose diameter is 400mm, the alignment method which combines the high resolution initial placement and computer-aided alignment is introduced. By designing a system which can measure the off-axis fabrication and off-axis angle precisely, the high resolution initial placement of off-axis mirror can be ensured with a measurement accuracy of +/-0.05mm and +/-10". The good initial placement can give a good initial state, so the computer-aided model can be converged well. The experiment shows that a system which has a good initial placement could have a good wave aberration of 0.04λ after three times iteration adjustment.

  1. 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.

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

    PubMed

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

    2012-05-16

    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.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. Physically motivated global alignment method for electron tomography

    DOE PAGES

    Sanders, Toby; Prange, Micah; Akatay, Cem; ...

    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

  8. 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.

  9. TM-align: a protein structure alignment algorithm based on the TM-score

    PubMed Central

    Zhang, Yang; Skolnick, Jeffrey

    2005-01-01

    We have developed TM-align, a new algorithm to identify the best structural alignment between protein pairs that combines the TM-score rotation matrix and Dynamic Programming (DP). The algorithm is ∼4 times faster than CE and 20 times faster than DALI and SAL. On average, the resulting structure alignments have higher accuracy and coverage than those provided by these most often-used methods. TM-align is applied to an all-against-all structure comparison of 10 515 representative protein chains from the Protein Data Bank (PDB) with a sequence identity cutoff <95%: 1996 distinct folds are found when a TM-score threshold of 0.5 is used. We also use TM-align to match the models predicted by TASSER for solved non-homologous proteins in PDB. For both folded and misfolded models, TM-align can almost always find close structural analogs, with an average root mean square deviation, RMSD, of 3 Å and 87% alignment coverage. Nevertheless, there exists a significant correlation between the correctness of the predicted structure and the structural similarity of the model to the other proteins in the PDB. This correlation could be used to assist in model selection in blind protein structure predictions. The TM-align program is freely downloadable at . PMID:15849316

  10. 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.

  11. 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.

  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. 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.

  14. 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

    2014-12-10

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

  15. 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

  16. 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.

  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

    2016-01-08

    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.

  18. The Stonehenge technique. A method for aligning coherent bremsstrahlung radiators

    NASA Astrophysics Data System (ADS)

    Livingston, Ken

    2009-05-01

    This paper describes a technique for the alignment of crystal radiators used to produce high energy, linearly polarized photons via coherent bremsstrahlung scattering at electron beam facilities. In these experiments the crystal is mounted on a goniometer which is used to adjust its orientation relative to the electron beam. The angles and equations which relate the crystal lattice, goniometer and electron beam direction are presented here, and the method of alignment is illustrated with data taken at MAMI (the Mainz microtron). A practical guide to setting up a coherent bremsstrahlung facility and installing new crystals using this technique is also included.

  19. webPRC: the Profile Comparer for alignment-based searching of public domain databases.

    PubMed

    Brandt, Bernd W; Heringa, Jaap

    2009-07-01

    Profile-profile methods are well suited to detect remote evolutionary relationships between protein families. Profile Comparer (PRC) is an existing stand-alone program for scoring and aligning hidden Markov models (HMMs), which are based on multiple sequence alignments. Since PRC compares profile HMMs instead of sequences, it can be used to find distant homologues. For this purpose, PRC is used by, for example, the CATH and Pfam-domain databases. As PRC is a profile comparer, it only reports profile HMM alignments and does not produce multiple sequence alignments. We have developed webPRC server, which makes it straightforward to search for distant homologues or similar alignments in a number of domain databases. In addition, it provides the results both as multiple sequence alignments and aligned HMMs. Furthermore, the user can view the domain annotation, evaluate the PRC hits with the Jalview multiple alignment editor and generate logos from the aligned HMMs or the aligned multiple alignments. Thus, this server assists in detecting distant homologues with PRC as well as in evaluating and using the results. The webPRC interface is available at http://www.ibi.vu.nl/programs/prcwww/.

  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. 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…

  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.

  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. 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.

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

    PubMed Central

    2010-01-01

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

  6. fMRI alignment based on local functional connectivity patterns

    NASA Astrophysics Data System (ADS)

    Jiang, Di; Du, Yuhui; Cheng, Hewei; Jiang, Tianzi; Fan, Yong

    2012-02-01

    In functional neuroimaging studies, the inter-subject alignment of functional magnetic resonance imaging (fMRI) data is a necessary precursor to improve functional consistency across subjects. Traditional structural MRI based registration methods cannot achieve accurate inter-subject functional consistency in that functional units are not necessarily consistently located relative to anatomical structures due to functional variability across subjects. Although spatial smoothing commonly used in fMRI data preprocessing can reduce the inter-subject functional variability, it may blur the functional signals and thus lose the fine-grained information. In this paper we propose a novel functional signal based fMRI image registration method which aligns local functional connectivity patterns of different subjects to improve the inter-subject functional consistency. Particularly, the functional connectivity is measured using Pearson correlation. For each voxel of an fMRI image, its functional connectivity to every voxel in its local spatial neighborhood, referred to as its local functional connectivity pattern, is characterized by a rotation and shift invariant representation. Based on this representation, the spatial registration of two fMRI images is achieved by minimizing the difference between their corresponding voxels' local functional connectivity patterns using a deformable image registration model. Experiment results based on simulated fMRI data have demonstrated that the proposed method is more robust and reliable than the existing fMRI image registration methods, including maximizing functional correlations and minimizing difference of global connectivity matrices across different subjects. Experiment results based on real resting-state fMRI data have further demonstrated that the proposed fMRI registration method can statistically significantly improve functional consistency across subjects.

  7. 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.

  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 Kalman Filter for SINS Self-Alignment Based on Vector Observation

    PubMed Central

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

    2017-01-01

    In this paper, a self-alignment method for strapdown inertial navigation systems based on the q-method is studied. In addition, an improved method based on integrating gravitational apparent motion to form apparent velocity is designed, which can reduce the random noises of the observation vectors. For further analysis, a novel self-alignment method using a Kalman filter based on adaptive filter technology is proposed, which transforms the self-alignment procedure into an attitude estimation using the observation vectors. In the proposed method, a linear psuedo-measurement equation is adopted by employing the transfer method between the quaternion and the observation vectors. Analysis and simulation indicate that the accuracy of the self-alignment is improved. Meanwhile, to improve the convergence rate of the proposed method, a new method based on parameter recognition and a reconstruction algorithm for apparent gravitation is devised, which can reduce the influence of the random noises of the observation vectors. Simulations and turntable tests are carried out, and the results indicate that the proposed method can acquire sound alignment results with lower standard variances, and can obtain higher alignment accuracy and a faster convergence rate. PMID:28146059

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

    PubMed

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

    2017-01-29

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

  11. 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

  12. Applications of alignment-free methods in epigenomics.

    PubMed

    Pinello, Luca; Lo Bosco, Giosuè; Yuan, Guo-Cheng

    2014-05-01

    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.

  13. 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.

  14. System and method for 2D workpiece alignment

    DOEpatents

    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.

  15. 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

  16. Comparing alignment methods for inferring the history of the new world lizard genus Mabuya (Squamata: Scincidae).

    PubMed

    Whiting, Alison S; Sites, Jack W; Pellegrino, Katia C M; Rodrigues, Miguel T

    2006-03-01

    The rapid increase in the ability to generate molecular data, and the focus on model-based methods for tree reconstruction have greatly advanced the use of phylogenetics in many fields. The recent flurry of new analytical techniques has focused almost solely on tree reconstruction, whereas alignment issues have received far less attention. In this paper, we use a diverse sampling of gene regions from lizards of the genus Mabuya to compare the impact, on phylogeny estimation, of new maximum likelihood alignment algorithms with more widely used methods. Sequences aligned under different optimality criteria are analyzed using partitioned Bayesian analysis with independent models and parameter settings for each gene region, and the most strongly supported phylogenetic hypothesis is then used to test the hypothesis of two colonizations of the New World by African scincid lizards. Our results show that the consistent use of model-based methods in both alignment and tree reconstruction leads to trees with more optimal likelihood scores than the use of independent criteria in alignment and tree reconstruction. We corroborate and extend earlier evidence for two independent colonizations of South America by scincid lizards. Relationships within South American Mabuya are found to be in need of taxonomic revision, specifically complexes under the names M. heathi, M. agilis, and M. bistriata (sensu, M.T. Rodrigues, Papeis Avulsos de Zoologia 41 (2000) 313).

  17. 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.

  18. 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.

  19. 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.

  20. nDSE-based overlay alignment: enabling technology for nano metrology and fabrication

    NASA Astrophysics Data System (ADS)

    Gao, Jun; Picciotto, Carl; Wu, Wei; Park, Inkyu; Tong, William M.

    2006-03-01

    Displacement sensing and estimation (DSE) is important preprocessing task for many image-based processing systems that extract information from multiple images. In last two years, we gained significant insight of the nature of DSE and developed theory and algorithm framework named nanoscale displacement sensing and estimation (nDSE). We also build procedures to apply nDSE to overlay alignment down to the nanoscale. We will introduce two basic theories: Phase Delay Detection (PDD) and Derivatives-based Maximum Likelihood Estimation (DML) and associated DSE algorithms, noticeably Near-Neighbor-Navigation (N-Cubed) algorithm. We presented our best nDSE experimental result of 1 nm (1σ) while tracking 5 nm stepping. To develop nDSE-based nanoscale alignment, we introduced our definition of displacement, alignment and pseudo-displacement. We presented both theoretical and practical procedures to use nDSE to achieve nano-alignment down to the 10s of nano-meters and beyond. Then we compared nDSE-based nano-alignment to other industry standard alignment method and attempt to show the substantial advantages of nDSE based alignment in terms of cost and simplicity of the system design.

  1. A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives

    PubMed Central

    Thompson, Julie D.; Linard, Benjamin; Lecompte, Odile; Poch, Olivier

    2011-01-01

    Multiple comparison or alignmentof protein sequences has become a fundamental tool in many different domains in modern molecular biology, from evolutionary studies to prediction of 2D/3D structure, molecular function and inter-molecular interactions etc. By placing the sequence in the framework of the overall family, multiple alignments can be used to identify conserved features and to highlight differences or specificities. In this paper, we describe a comprehensive evaluation of many of the most popular methods for multiple sequence alignment (MSA), based on a new benchmark test set. The benchmark is designed to represent typical problems encountered when aligning the large protein sequence sets that result from today's high throughput biotechnologies. We show that alignmentmethods have significantly progressed and can now identify most of the shared sequence features that determine the broad molecular function(s) of a protein family, even for divergent sequences. However,we have identified a number of important challenges. First, the locally conserved regions, that reflect functional specificities or that modulate a protein's function in a given cellular context,are less well aligned. Second, motifs in natively disordered regions are often misaligned. Third, the badly predicted or fragmentary protein sequences, which make up a large proportion of today's databases, lead to a significant number of alignment errors. Based on this study, we demonstrate that the existing MSA methods can be exploited in combination to improve alignment accuracy, although novel approaches will still be needed to fully explore the most difficult regions. We then propose knowledge-enabled, dynamic solutions that will hopefully pave the way to enhanced alignment construction and exploitation in future evolutionary systems biology studies. PMID:21483869

  2. 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

  3. 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 Hyoun; 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. PACS numbers: 87.56.Fc, 87.53.Bn, 87.53.Kn, 87.53.Ly, 87.55.Gh.

  4. Calibration method for lumbosacral dimensions in wearable sensor system of lumbar alignment.

    PubMed

    Tsuchiya, Yoshio; Kusaka, Takashi; Tanaka, Takayuki; Matsuo, Yoshikazu; Oda, Makoto; Sasaki, Tsukasa; Kamishima, Tamotsu; Yamanaka, Masanori

    2015-01-01

    Anteflexion of the spine is essential for many physical activities in everyday life. However, this motion places the lumbar disks under heavy load due to changes in the shape of the lumbar spine and can lead to low back pain. With the aim of reducing low back pain, here we developed a wearable sensor system that can estimate lumbosacral alignment and lumbar load by measuring the shape of the lumbar skin when the lumbosacral alignment changes. In addition, we used this system to measure the parameters of anteflexion and studied the change in dimensions of the lumbar spine from changes in posture. By determining the dimensions of the lumbosacral spine on an X-ray image, a lumbosacral dimensions calibration method based on body surface area and height was developed. By using this method, lumbosacral alignment and lumbar load could be accurately estimated using the wearable sensor system.

  5. 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.

  6. 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.

  7. Structure-based evaluation of sequence comparison and fold recognition alignment accuracy.

    PubMed

    Domingues, F S; Lackner, P; Andreeva, A; Sippl, M J

    2000-04-07

    The biological role, biochemical function, and structure of uncharacterized protein sequences is often inferred from their similarity to known proteins. A constant goal is to increase the reliability, sensitivity, and accuracy of alignment techniques to enable the detection of increasingly distant relationships. Development, tuning, and testing of these methods benefit from appropriate benchmarks for the assessment of alignment accuracy.Here, we describe a benchmark protocol to estimate sequence-to-sequence and sequence-to-structure alignment accuracy. The protocol consists of structurally related pairs of proteins and procedures to evaluate alignment accuracy over the whole set. The set of protein pairs covers all the currently known fold types. The benchmark is challenging in the sense that it consists of proteins lacking clear sequence similarity. Correct target alignments are derived from the three-dimensional structures of these pairs by rigid body superposition. An evaluation engine computes the accuracy of alignments obtained from a particular algorithm in terms of alignment shifts with respect to the structure derived alignments. Using this benchmark we estimate that the best results can be obtained from a combination of amino acid residue substitution matrices and knowledge-based potentials.

  8. 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.

  9. Active optical alignment of off-axis telescopes based on nodal aberration theory.

    PubMed

    Zhang, Xiaobin; Zhang, Dong; Xu, Shuyan; Ma, Hongcai

    2016-11-14

    Our paper mainly separates the specific aberration contributions of third-order astigmatism and third-order coma from the total aberration fields, on the framework of the modified nodal aberration theory (NAT), for the perturbed off-axis telescope. Based on the derived aberration functions, two alignment models for the same off-axis two-mirror telescope are established and compared. Among them, one is based on third-order NAT, the other is based on fifth-order NAT. By comparison, it is found that the calculated perturbations based on fifth-order NAT are more accurate. It illustrates that third-order astigmatism and third-order coma contributed from fifth-order aberrations can't be neglected in the alignment process. Then the fifth-order NAT is used for the alignment of off-axis three-mirror telescopes. After simulation, it is found that the perturbed off-axis three-mirror telescope can be perfectly aligned as well. To further demonstrate the application of the alignment method based on fifth-order NAT (simplified as NAT method), Monte-Carlo simulations for both off-axis two-mirror telescope and off-axis three-mirror telescope are conducted in the end. Meantime, a comparison between NAT method and sensitivity table method is also conducted. It is proven that the computation accuracy of NAT method is much higher, especially in poor conditions.

  10. Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method

    PubMed Central

    Nielsen, Morten; Lundegaard, Claus; Lund, Ole

    2007-01-01

    Background Antigen presenting cells (APCs) sample the extra cellular space and present peptides from here to T helper cells, which can be activated if the peptides are of foreign origin. The peptides are presented on the surface of the cells in complex with major histocompatibility class II (MHC II) molecules. Identification of peptides that bind MHC II molecules is thus a key step in rational vaccine design and developing methods for accurate prediction of the peptide:MHC interactions play a central role in epitope discovery. The MHC class II binding groove is open at both ends making the correct alignment of a peptide in the binding groove a crucial part of identifying the core of an MHC class II binding motif. Here, we present a novel stabilization matrix alignment method, SMM-align, that allows for direct prediction of peptide:MHC binding affinities. The predictive performance of the method is validated on a large MHC class II benchmark data set covering 14 HLA-DR (human MHC) and three mouse H2-IA alleles. Results The predictive performance of the SMM-align method was demonstrated to be superior to that of the Gibbs sampler, TEPITOPE, SVRMHC, and MHCpred methods. Cross validation between peptide data set obtained from different sources demonstrated that direct incorporation of peptide length potentially results in over-fitting of the binding prediction method. Focusing on amino terminal peptide flanking residues (PFR), we demonstrate a consistent gain in predictive performance by favoring binding registers with a minimum PFR length of two amino acids. Visualizing the binding motif as obtained by the SMM-align and TEPITOPE methods highlights a series of fundamental discrepancies between the two predicted motifs. For the DRB1*1302 allele for instance, the TEPITOPE method favors basic amino acids at most anchor positions, whereas the SMM-align method identifies a preference for hydrophobic or neutral amino acids at the anchors. Conclusion The SMM-align method was

  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. Magnetic alignment of mesophase pitch-based carbon fibers

    NASA Astrophysics Data System (ADS)

    Matthews, M. J.; Dresselhaus, M. S.; Dresselhaus, G.; Endo, M.; Nishimura, Y.; Hiraoka, T.; Tamaki, N.

    1996-07-01

    Mesophase pitch-based carbon fibers (MPCFs) have recently been developed for use as high performance anode materials in Li ion secondary batteries, having a microscopic as well as macroscopic structure especially suitable for Li storage. Because of the highly anisotropic diamagnetic moment observed between 50 and 310 K in pristine milled MPCF segments, they can easily be oriented parallel to an applied magnetic field, as observed by scanning electron microscopy. A simple model is proposed to explain both the observed alignment of undoped fibers and the suppression of alignment in B-doped MPCFs for relatively small applied magnetic fields, because of their smaller diamagnetic moment.

  13. Advanced Multifunctional Properties of Aligned Carbon Nanotube-Epoxy Composites from Carbon Nanotube Aerogel Method

    NASA Astrophysics Data System (ADS)

    Tran, Thang; Liu, Peng; Fan, Zeng; Ngern, Nigel; Duong, Hai

    2015-03-01

    Unlike previous methods of making carbon nanotube (CNT) thin films, aligned CNT thin films in this work are synthesized directly from CNT aerogels in a CVD process. CH4/H2/He gases and ferrocene/thiophene catalysts are mixed and reacted in the reactor at 1200 °C to form CNT aerogel socks. By pulling out the socks with a metal rod, CNT thin films with 15-nm diameter MWNTs are aligned and produced continuously at a speed of a few meters per minute. The number of the aligned CNT thin film layers/ thickness can also be controlled well. The as-synthesized aligned CNT films are further condensed by acetone spray and post-treated by UV light. The aligned CNT films without any above post-treatment have a high electrical conductivity of 400S/cm. We also develop aligned CNT-epoxy composites by infiltrating epoxy into the above aligned CNT thin films using Vacuum Assisted Resin Transfer Molding (VARTM) method. Our cost-effective fabrication method of the aligned CNT films is more advanced for developing the composites having CNT orientation control. The mechanical, electrical and optical properties of the aligned CNT epoxy composites are measured. About 2% of the aligned CNTs can enhance significantly the electrical conductivity and hardness of aligned CNT-epoxy composite films. Effects of morphologies, volume fraction, and alignment of the CNTs on the advanced multifunctional properties of the aligned CNT-epoxy composites are also quantified.

  14. Alignment method for fabricating a parallel flat-field grating used in soft x-ray region.

    PubMed

    Wang, Qingbo; Liu, Zhengkun; Zheng, Yanchang; Chen, Huoyao; Wang, Yu; Liu, Ying; Hong, Yilin

    2015-06-20

    Parallel flat-field gratings consist of two flat-field gratings lying on one substrate, one for 5-20 nm and the other for 2-5 nm spectral regions, and thus can be widely used in various fields to record broader spectra in the soft x-ray region. The alignment of two subgratings directly determines the resolving power of parallel flat-field gratings. The theoretical resolving power is evaluated by means of the ray-tracing method and the maximal allowable alignment error is 0.366°. Alignment is based on diffraction patterns and moiré fringes and the total alignment error in our experiment is within 0.234°. The results demonstrate that this alignment method is an effective way for fabricating parallel flat-field gratings.

  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. 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.

  17. A direct method for computing extreme value (Gumbel) parameters for gapped biological sequence alignments.

    PubMed

    Quinn, Terrance; Sinkala, Zachariah

    2014-01-01

    We develop a general method for computing extreme value distribution (Gumbel, 1958) parameters for gapped alignments. Our approach uses mixture distribution theory to obtain associated BLOSUM matrices for gapped alignments, which in turn are used for determining significance of gapped alignment scores for pairs of biological sequences. We compare our results with parameters already obtained in the literature.

  18. Terahertz detectors arrays based on orderly aligned InN nanowires

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

    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.

  19. Dynamics of field-aligned currents reconstructed by the ground-based and satellite data

    NASA Astrophysics Data System (ADS)

    Nikolaeva, V. D.; Kotikov, A. L.; Sergienko, T. I.

    2014-09-01

    Parameters of field-aligned currents reconstructed by ground-based measurements of magnetic field in the Scandinavian countries (IMAGE) and ionospheric conductivity for specific events of the 6 and 8 December 2004 are represented here. Ionospheric conductivity was calculated from precipitating electron flux measured at DMSP-13 satellite and electron density EISCAT incoherent scattering radar direct measurements. There is a high correlation between field-aligned currents, calculated from DMSP-13 satellite data and field-aligned currents calculated from radar measurements for the December 6, 2004 in the presence of developed ionospheric current system. The comparison of field-aligned currents, reconstructed by the proposed method, with the currents calculated by the variation of magnetic field on the DMSP satellites, confirms correctness of the offered algorithm.

  20. 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

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

    NASA Astrophysics Data System (ADS)

    Bai, Lijian; Wang, Yue

    2017-03-01

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

  2. 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.

  3. 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.

  4. 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.

  5. Incremental Window-based Protein Sequence Alignment Algorithms

    DTIC Science & Technology

    2006-03-23

    Huzefa Rangwala and George Karypis March 23, 2006 Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the collection of... Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 Incremental Window-based Protein Sequence Alignment Algorithms Huzefa Rangwala and George Karypis...Then it per- forms a series of iterations in which it performs the following three steps: First, it extracts from ’ the residue-pair with the highest

  6. 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.

  7. 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.

  8. 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.

  9. A new method for improving functional-to-structural MRI alignment using local Pearson correlation.

    PubMed

    Saad, Ziad S; Glen, Daniel R; Chen, Gang; Beauchamp, Michael S; Desai, Rutvik; Cox, Robert W

    2009-02-01

    Accurate registration of Functional Magnetic Resonance Imaging (FMRI) T2-weighted volumes to same-subject high-resolution T1-weighted structural volumes is important for Blood Oxygenation Level Dependent (BOLD) FMRI and crucial for applications such as cortical surface-based analyses and pre-surgical planning. Such registration is generally implemented by minimizing a cost functional, which measures the mismatch between two image volumes over the group of proper affine transformations. Widely used cost functionals, such as mutual information (MI) and correlation ratio (CR), appear to yield decent alignments when visually judged by matching outer brain contours. However, close inspection reveals that internal brain structures are often significantly misaligned. Poor registration is most evident in the ventricles and sulcal folds, where CSF is concentrated. This observation motivated our development of an improved modality-specific cost functional which uses a weighted local Pearson coefficient (LPC) to align T2- and T1-weighted images. In the absence of an alignment gold standard, we used three human observers blinded to registration method to provide an independent assessment of the quality of the registration for each cost functional. We found that LPC performed significantly better (p<0.001) than generic cost functionals including MI and CR. Generic cost functionals were very often not minimal near the best alignment, thereby suggesting that optimization is not the cause of their failure. Lastly, we emphasize the importance of precise visual inspection of alignment quality and present an automated method for generating composite images that help capture errors of misalignment.

  10. Integrated web service for improving alignment quality based on segments comparison

    PubMed Central

    Plewczynski, Dariusz; Rychlewski, Leszek; Ye, Yuzhen; Jaroszewski, Lukasz; Godzik, Adam

    2004-01-01

    Background Defining blocks forming the global protein structure on the basis of local structural regularity is a very fruitful idea, extensively used in description, and prediction of structure from only sequence information. Over many years the secondary structure elements were used as available building blocks with great success. Specially prepared sets of possible structural motifs can be used to describe similarity between very distant, non-homologous proteins. The reason for utilizing the structural information in the description of proteins is straightforward. Structural comparison is able to detect approximately twice as many distant relationships as sequence comparison at the same error rate. Results Here we provide a new fragment library for Local Structure Segment (LSS) prediction called FRAGlib which is integrated with a previously described segment alignment algorithm SEA. A joined FRAGlib/SEA server provides easy access to both algorithms, allowing a one stop alignment service using a novel approach to protein sequence alignment based on a network matching approach. The FRAGlib used as secondary structure prediction achieves only 73% accuracy in Q3 measure, but when combined with the SEA alignment, it achieves a significant improvement in pairwise sequence alignment quality, as compared to previous SEA implementation and other public alignment algorithms. The FRAGlib algorithm takes ~2 min. to search over FRAGlib database for a typical query protein with 500 residues. The SEA service align two typical proteins within circa ~5 min. All supplementary materials (detailed results of all the benchmarks, the list of test proteins and the whole fragments library) are available for download on-line at . Conclusions The joined FRAGlib/SEA server will be a valuable tool both for molecular biologists working on protein sequence analysis and for bioinformaticians developing computational methods of structure prediction and alignment of proteins. PMID:15271224

  11. Alignment of trans-tibial prostheses based on roll-over shape principles.

    PubMed

    Hansen, A H; Meier, M R; Sam, M; Childress, D S; Edwards, M L

    2003-08-01

    The authors examined the roll-over shape alignment hypothesis, which states that prosthetic feet are aligned by matching their roll-over shapes with an "ideal" shape. The "ideal" shape was considered to be the roll-over shape of the able-bodied foot-ankle system. An alignment algorithm and computational alignment system were developed to set trans-tibial alignments based on this hypothesis. Three prosthetic feet with considerably different roll-over shapes were either aligned using the alignment system or not aligned (i.e. used previous foot's alignment), and then were aligned by a team of prosthetists. No significant differences were found between roll-over shapes aligned by the computational alignment system and those based on standard clinical techniques (p = 0.944). Significant differences were found between the "no alignment" shapes and the prosthetist alignment shapes (p = 0.006), and between the "no alignment" shapes and the computational alignment system shapes (p = 0.024). The results of the experiment support the hypothesis that the goal of alignment is to match the prosthetic foot's roll-over shape, as closely as possible, with an "ideal" shape. The hypothesis is also supported by its ability to explain the results of previous studies. Using an "ideal" roll-over shape or surface as a goal for prosthetic alignment could lead to a priori alignment, eliminating the need for alignment hardware in some cases. Being able to build the alignment into a prosthesis without special hardware could be beneficial in low-income countries and in the fabrication of lightweight prostheses for the elderly.

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

    PubMed Central

    Vu, Trung Nghia; Laukens, Kris

    2013-01-01

    One of the most significant challenges in the comparative analysis of Nuclear Magnetic Resonance (NMR) metabolome profiles is the occurrence of shifts between peaks across different spectra, for example caused by fluctuations in pH, temperature, instrument factors and ion content. Proper alignment of spectral peaks is therefore often a crucial preprocessing step prior to downstream quantitative analysis. Various alignment methods have been developed specifically for this purpose. Other methods were originally developed to align other data types (GC, LC, SELDI-MS, etc.), but can also be applied to NMR data. This review discusses the available methods, as well as related problems such as reference determination or the evaluation of alignment quality. We present a generic alignment framework that allows for comparison and classification of different alignment approaches according to their algorithmic principles, and we discuss their performance. PMID:24957991

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. Metabarcoding of marine nematodes – evaluation of similarity scores used in alignment-based taxonomy assignment approach

    PubMed Central

    2016-01-01

    Abstract Background The diversity of organisms is being commonly accessed using metabarcoding of environmental samples. Reliable identification of barcodes is one of the critical steps in the process and several taxonomy assignment methods were proposed to accomplish this task, including alignment-based approach that uses Basic Local Alignment Search Tool (BLAST) algorithm. This publication evaluates the variability of 5' end of 18S rRNA barcoding region as expressed by similarity scores (alignment score and identity score) produced by BLAST, and its impact on barcode identification to family-level taxonomic categories. New information In alignment-based taxonomy assignment approach, reliable identification of anonymous OTUs to supraspecific taxa depends on the correct application of similarity thresholds. Since various taxa show different level of genetic variation, practical application of alignment-based approach requires the determination and use of taxon-specific similarity thresholds. PMID:27932928

  18. Hyperspectral face recognition using improved inter-channel alignment based on qualitative prediction models.

    PubMed

    Cho, Woon; Jang, Jinbeum; Koschan, Andreas; Abidi, Mongi A; Paik, Joonki

    2016-11-28

    A fundamental limitation of hyperspectral imaging is the inter-band misalignment correlated with subject motion during data acquisition. One way of resolving this problem is to assess the alignment quality of hyperspectral image cubes derived from the state-of-the-art alignment methods. In this paper, we present an automatic selection framework for the optimal alignment method to improve the performance of face recognition. Specifically, we develop two qualitative prediction models based on: 1) a principal curvature map for evaluating the similarity index between sequential target bands and a reference band in the hyperspectral image cube as a full-reference metric; and 2) the cumulative probability of target colors in the HSV color space for evaluating the alignment index of a single sRGB image rendered using all of the bands of the hyperspectral image cube as a no-reference metric. We verify the efficacy of the proposed metrics on a new large-scale database, demonstrating a higher prediction accuracy in determining improved alignment compared to two full-reference and five no-reference image quality metrics. We also validate the ability of the proposed framework to improve hyperspectral face recognition.

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

    PubMed Central

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

    2017-01-01

    In airborne MEMS SINS transfer alignment, the error of MEMS IMU is highly environment-dependent and the parameters of the system model are also uncertain, which may lead to large error and bad convergence of the Kalman filter. In order to solve this problem, an improved adaptive incremental Kalman filter (AIKF) algorithm is proposed. First, the model of SINS transfer alignment is defined based on the “Velocity and Attitude” matching method. Then the detailed algorithm progress of AIKF and its recurrence formulas are presented. The performance and calculation amount of AKF and AIKF are also compared. Finally, a simulation test is designed to verify the accuracy and the rapidity of the AIKF algorithm by comparing it with KF and AKF. The results show that the AIKF algorithm has better estimation accuracy and shorter convergence time, especially for the bias of the gyroscope and the accelerometer, which can meet the accuracy and rapidity requirement of transfer alignment. PMID:28098829

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

    PubMed

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

    2017-01-14

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

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

    PubMed

    Rani, R Ranjani; Ramyachitra, D

    2016-12-01

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

  2. 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.

  3. 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

  4. Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point

    PubMed Central

    Ilyin, Valentin A.; Abyzov, Alexej; Leslin, Chesley M.

    2004-01-01

    Similarity of protein structures has been analyzed using three-dimensional Delaunay triangulation patterns derived from the backbone representation. It has been found that structurally related proteins have a common spatial invariant part, a set of tetrahedrons, mathematically described as a common spatial subgraph volume of the three-dimensional contact graph derived from Delaunay tessellation (DT). Based on this property of protein structures, we present a novel common volume superimposition (TOPOFIT) method to produce structural alignments. Structural alignments usually evaluated by a number of equivalent (aligned) positions (Ne) with corresponding root mean square deviation (RMSD). The superimposition of the DT patterns allows one to uniquely identify a maximal common number of equivalent residues in the structural alignment. In other words, TOPOFIT identifies a feature point on the RMSD Ne curve, a topomax point, until which the topologies of two structures correspond to each other, including backbone and interresidue contacts, whereas the growing number of mismatches between the DT patterns occurs at larger RMSD (Ne) after the topomax point. It has been found that the topomax point is present in all alignments from different protein structural classes; therefore, the TOPOFIT method identifies common, invariant structural parts between proteins. The alignments produced by the TOPOFIT method have a good correlation with alignments produced by other current methods. This novel method opens new opportunities for the comparative analysis of protein structures and for more detailed studies on understanding the molecular principles of tertiary structure organization and functionality. The TOPOFIT method also helps to detect conformational changes, topological differences in variable parts, which are particularly important for studies of variations in active/ binding sites and protein classification. PMID:15215530

  5. Synthesis of vertically aligned boron nitride nanosheets using CVD method

    SciTech Connect

    Zhang, Chao; Hao, Xiaopeng; Wu, Yongzhong; Du, Miao

    2012-09-15

    Highlights: ► The synthesized boron nitride nanosheets (BNNSs) are vertically aligned and very thin. ► No electrical field is applied in the CVD process. ► The thin BNNSs show a low turn-on field of 6.5 V μm{sup −1} and emit strong UV light. -- Abstract: Boron nitride nanosheets (BNNSs) protruding from boron nitride (BN) films were synthesized on silicon substrates by chemical vapor deposition technique from a gas mixture of BCl{sub 3}–NH{sub 3}–H{sub 2}–N{sub 2}. Parts of the as-grown nanosheets were vertically aligned on the BN films. The morphology and structure of the synthesized BNNSs were characterized by scanning electron microscopy, transmission electron microscopy, and Fourier transformation infrared spectroscopy. The chemical composition was studied by energy dispersive spectroscopy and X-ray photoelectron spectroscopy. Cathodoluminescence spectra revealed that the product emitted strong UV light with a broad band ranging from 250 to 400 nm. Field-emission characteristic of the product shows a low turn-on field of 6.5 V μm{sup −1}.

  6. 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.

  7. Calibration method of tilt and azimuth angles for alignment of TEM tomographic tilt series

    NASA Astrophysics Data System (ADS)

    Hayashida, Misa; Terauchi, Shinya; Fujimoto, Toshiyuki

    2011-10-01

    This paper describes the calibration method of the tilt and azimuth angles of specimen using a digital protractor and a laser autocollimator for alignment of electron tomography. It also suggests an easy method to check whether the specimen is tilted by 180.0°, and whether the azimuth angle is 0.0°; the method involves the use of two images of a rod-shaped specimen collected before and after a 180.0° tilt. The method is based on the assumption that these images are symmetric about the tilt axis when the azimuth angle is 0.0°. In addition, we used an experiment to demonstrate the effect of the incorrect angles on reconstructed images and simulated the image quality against distance away from tilt axis.

  8. Does pilates-based exercise improve postural alignment in adult women?

    PubMed

    Cruz-Ferreira, Ana; Fernandes, Jorge; Kuo, Yi-Liang; Bernardo, Lisa Marie; Fernandes, Orlando; Laranjo, Luís; Silva, António

    2013-01-01

    A randomized, controlled trial was conducted to determine the effect of Pilates-based exercise on postural alignment. Seventy-four adult women (mean age ± SD, 34.9 ± 16.4 years) were randomized to a Pilates-based mat class (n = 40) or a control group (n = 34). Pilates-based exercise participants were taught the Initial Mat of Body Control Pilates for 6 months, twice a week, for 60 minutes per session; the control group received no exercise intervention. Repeated measurements were performed at baseline, 3 months, and 6 months of the frontal alignment of the thoracolumbar spine, shoulder, and pelvis, and sagittal alignment of the head and pelvis. No differences were found in either group, over time, on frontal alignment of the thoracolumbar spine and pelvis. The experimental group showed significant improvements in frontal alignment of the shoulder and sagittal alignment of the head and pelvis at 6 months. The Pilates-based exercise enhanced some parameters of the postural alignment of women, as measured by frontal alignment of the shoulder and sagittal alignment of the head and pelvis. The significant improvement in sagittal alignment of the head may imply that 6 months of Pilates-based exercise enhances sagittal alignment of the cervical or thoracic spine.

  9. 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

  10. 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

  11. DETECTORS AND EXPERIMENTAL METHODS: Software alignment of the BESIII main drift chamber using the Kalman Filter method

    NASA Astrophysics Data System (ADS)

    Wang, Ji-Ke; Mao, Ze-Pu; Bian, Jian-Ming; Cao, Guo-Fu; Cao, Xue-Xiang; Chen, Shen-Jian; Deng, Zi-Yan; Fu, Cheng-Dong; Gao, Yuan-Ning; He, Kang-Lin; He, Miao; Hua, Chun-Fei; Huang, Bin; Huang, Xing-Tao; Ji, Xiao-Bin; Li, Fei; Li, Hai-Bo; Li, Wei-Dong; Liang, Yu-Tie; Liu, Chun-Xiu; Liu, Huai-Min; Liu, Suo; Liu, Ying-Jie; Ma, Qiu-Mei; Ma, Xiang; Mao, Ya-Jun; Mo, Xiao-Hu; Pan, Ming-Hua; Pang, Cai-Ying; Ping, Rong-Gang; Qin, Ya-Hong; Qiu, Jin-Fa; Sun, Sheng-Sen; Sun, Yong-Zhao; Wang, Liang-Liang; Wen, Shuo-Pin; Wu, Ling-Hui; Xie, Yu-Guang; Xu, Min; Yan, Liang; You, Zheng-Yun; Yuan, Chang-Zheng; Yuan, Ye; Zhang, Bing-Yun; Zhang, Chang-Chun; Zhang, Jian-Yong; Zhang, Xue-Yao; Zhang, Yao; Zheng, Yang-Heng; Zhu, Ke-Jun; Zhu, Yong-Sheng; Zhu, Zhi-Li; Zou, Jia-Heng

    2009-03-01

    Software alignment is quite important for a tracking detector to reach its ultimate position accuracy and momentum resolution. We developed a new alignment algorithm for the BESIII Main Drift Chamber using the Kalman Filter method. Two different types of data which are helix tracks and straight tracks are used to test this algorithm, and the results show that the design and implementation is successful.

  12. A fast initial alignment of MIMU in the two-dimension trajectory correction fuze for spinning projectile on stationary base

    NASA Astrophysics Data System (ADS)

    Wang, Qin; Li, Shi-yi; Xiao, Hong-bing; Li, Hu-quan

    2008-03-01

    In the paper, a fast initial alignment of strapdown MIMU used in the two-dimension trajectory correction fuze was analyzed. According to the situation that MIMU can't work normally because of high shock on shrapnel of Compound Extended Range by Base Bleed and Rocket at firing, the MIMU in initial alignment with Bar-Itzhack and Berman's error model is presented and the observability was analyzed. It shows that the observability of MIMU on stationary base is poor. The selection of unobservable states was discussed. A Kalman filter estimation algorithm was provided, but the azimuth error converges very slowly in initial alignment. A fast estimation method of the azimuth error was proposed. It reveals that the azimuth error can be entirely estimated from the estimates of leveling error and leveling error rate without gyro output signal. It shows that the method can realize the rapid initial alignment of MIMU.

  13. Study on computer-aided alignment method of reflective zoom systems

    NASA Astrophysics Data System (ADS)

    Zhou, Jide; Chang, Jun; Xie, Guijuan; Zhang, Ke

    2015-08-01

    Computer-aided alignment is an effective method to improve the imaging quality of high-precision, complex, and off-axis optical systems. However, how to determine the misalignment quickly, exactly and constantly is essential to the technology of computer-aided alignment. Owing to the varying optical characteristics of a zoom system, sensitivity matrices are used in the alignment rather than a single matrix. Thus, the processing of sensitivity matrices is important for the computer-aided alignment of the reflective zoom system. So, the total least squares is proposed in order to solve the problems of the numerical instability and the result inaccuracy which result from the solution of the least squares method directly. Finally, the simulant calculation is processed using the numerical analysis model established in the essay. The results demonstrate that the computation method is rational and effective.

  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. The stonehenge technique: a new method of crystal alignment for coherent bremsstrahlung experiments

    NASA Astrophysics Data System (ADS)

    Livingston, Kenneth

    2005-08-01

    In the coherent bremsstrahlung technique a thin diamond crystal oriented correctly in an electron beam can produce photons with a high degree of linear polarization.1 The crystal is mounted on a goniometer to control its orientation and it is necessary to measure the angular offsets a) between the crystal axes and the goniometer axes and b) between the goniometer and the electron beam axis. A method for measuring these offsets and aligning the crystal was developed by Lohman et al, and has been used successfully in Mainz.2 However, recent attempts to investigate new crystals have shown that this approach has limitations which become more serious at higher beam energies where more accurate setting of the crystal angles, which scale with l/Ebeam, is required. (Eg. the recent installation of coherent bremsstrahlung facility at Jlab, with Ebeam = 6 GeV ) This paper describes a new, more general alignment technique, which overcomes these limitations. The technique is based on scans where the horizontal and vertical rotation axes of the goniometer are adjusted in a series of steps to make the normal to the crystal describe a cone of a given angle. For each step in the scan, the photon energy spectrum is measured using a tagging spectrometer, and the offsets between the electron beam and the crystal lattice are inferred from the resulting 2D plot. Using this method, it is possible to align the crystal with the beam quickly, and hence to set any desired orientation of the crystal relative to the beam. This is essential for any experiment requiring linearly polarized photons produced via coherent bremsstrahlung, and is also required for a systematic study of the channeling radiation produced by the electron beam incident on the crystal.

  16. 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

  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

    2015-08-31

    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.

  18. Method for accurate optical alignment using diffraction rings from lenses with spherical aberration.

    PubMed

    Gwynn, R B; Christensen, D A

    1993-03-01

    A useful alignment method is presented that exploits the closely spaced concentric fringes that form in the longitudinal spherical aberration region of positive spherical lenses imaging a point source. To align one or more elements to a common axis, spherical lenses are attached precisely to the elements and the resulting diffraction rings are made to coincide. We modeled the spherical aberration of the lenses by calculating the diffraction patterns of converging plane waves passing through concentric narrow annular apertures. The validity of the model is supported by experimental data and is determined to be accurate for a prototype penumbral imaging alignment system developed at Lawrence Livermore National Laboratory.

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

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

  20. 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

  1. Large aperture laser beam alignment system based on far field sampling technique

    NASA Astrophysics Data System (ADS)

    Zhang, J. C.; Liu, D. Z.; Ouyang, X. P.; Kang, J.; Xie, X. L.; Zhou, J.; Gong, L.; Zhu, B. Q.

    2016-11-01

    Laser beam alignment is very important for high-power laser facility. Long laser path and large-aperture lens for alignment are generally used, while the proposed alignment system with a wedge by far-field sampling technique reduces both space and cost requirements. General alignment system for large-aperture laser beam is long in distance and large in volum because of taking near-field sampling technique. With the development of laser fusion facilities, the space for alignment system is limited. A new alignment system for large-aperture laser beam is designed to save space and reduce operating costs. The new alignment for large-aperture laser beam with a wedge is based on far-field sampling technique. The wedge is placed behind the spatial filter to reflect some laser beam as signal light for alignment. Therefore, laser beam diameter in alignment system is small, which can save space for the laser facility. Comparing to general alignment system for large-aperture laser beam, large-aperture lenses for near-field and far-field sampling, long distance laser path are unnecessary for proposed alignment system, which saves cost and space greatly. This alignment system for large-aperture laser beam has been demonstrated well on the Muliti-PW Facility which uses the 7th beam of the SG-Ⅱ Facility as pump source. The experimental results indicate that the average near-field alignment error is less than 1% of reference, and the average far-filed alignment error is less than 5% of spatial filter pinhole diameter, which meet the alignment system requirements for laser beam of Multi-PW Facility.

  2. 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

  3. Individually addressable vertically aligned carbon nanofiber-based electrochemical probes

    NASA Astrophysics Data System (ADS)

    Guillorn, M. A.; McKnight, T. E.; Melechko, A.; Merkulov, V. I.; Britt, P. F.; Austin, D. W.; Lowndes, D. H.; Simpson, M. L.

    2002-03-01

    In this paper we present the fabrication and initial testing results of high aspect ratio vertically aligned carbon nanofiber (VACNF)-based electrochemical probes. Electron beam lithography was used to define the catalytic growth sites of the VACNFs. Following catalyst deposition, VACNF were grown using a plasma enhanced chemical vapor deposition process. Photolithography was performed to realize interconnect structures. These probes were passivated with a thin layer of SiO2, which was then removed from the tips of the VACNF, rendering them electrochemically active. We have investigated the functionality of completed devices using cyclic voltammetry (CV) of ruthenium hexammine trichloride, a highly reversible, outer sphere redox system. The faradaic current obtained during CV potential sweeps shows clear oxidation and reduction peaks at magnitudes that correspond well with the geometry of these nanoscale electrochemical probes. Due to the size and the site-specific directed synthesis of the VACNFs, these probes are ideally suited for characterizing electrochemical phenomena with an unprecedented degree of spatial resolution.

  4. Mixing Interview and Questionnaire Methods: Practical Problems in Aligning Data

    ERIC Educational Resources Information Center

    Harris, Lois R.; Brown, Gavin T. L.

    2010-01-01

    Structured questionnaires and semi-structured interviews are often used in mixed method studies to generate confirmatory results despite differences in methods of data collection, analysis, and interpretation. A review of 19 questionnaire-interview comparison studies found that consensus and consistency statistics were generally weak between…

  5. Fabrication of aligned nanofibers by electric-field-controlled electrospinning: insulating-block method.

    PubMed

    Hwang, Wontae; Pang, Changhyun; Chae, Heeyeop

    2016-10-28

    Aligned nanofiber arrays and mats were fabricated with an electrospinning process by manipulating the electric field. The electric field was modified by insulating blocks (IBs) that were installed between the nozzle and the substrate as guiding elements to control the trajectory of the electrospinning jet flow. Simulation results showed that the electric field was deformed near the IBs, resulting in confinement of the electrospinning jet between the blocks. The balance of the electric field in the vertical direction and the repulsive force by space charges in the confined electrified jet stream was attributed to the aligned motion of the jet. Aligned arrays of 200 nm thick polyethylene oxide nanofibers were obtained, exhibiting wave-shaped and cross patterns as well as rectilinear patterns. In addition, 40 μm thick quasi-aligned carbon-nanofiber mats with anisotropic electrical property were also attained by this method.

  6. Fabrication of aligned nanofibers by electric-field-controlled electrospinning: insulating-block method

    NASA Astrophysics Data System (ADS)

    Hwang, Wontae; Pang, Changhyun; Chae, Heeyeop

    2016-10-01

    Aligned nanofiber arrays and mats were fabricated with an electrospinning process by manipulating the electric field. The electric field was modified by insulating blocks (IBs) that were installed between the nozzle and the substrate as guiding elements to control the trajectory of the electrospinning jet flow. Simulation results showed that the electric field was deformed near the IBs, resulting in confinement of the electrospinning jet between the blocks. The balance of the electric field in the vertical direction and the repulsive force by space charges in the confined electrified jet stream was attributed to the aligned motion of the jet. Aligned arrays of 200 nm thick polyethylene oxide nanofibers were obtained, exhibiting wave-shaped and cross patterns as well as rectilinear patterns. In addition, 40 μm thick quasi-aligned carbon-nanofiber mats with anisotropic electrical property were also attained by this method.

  7. AlexSys: a knowledge-based expert system for multiple sequence alignment construction and analysis.

    PubMed

    Aniba, Mohamed Radhouene; Poch, Olivier; Marchler-Bauer, Aron; Thompson, Julie Dawn

    2010-10-01

    Multiple sequence alignment (MSA) is a cornerstone of modern molecular biology and represents a unique means of investigating the patterns of conservation and diversity in complex biological systems. Many different algorithms have been developed to construct MSAs, but previous studies have shown that no single aligner consistently outperforms the rest. This has led to the development of a number of 'meta-methods' that systematically run several aligners and merge the output into one single solution. Although these methods generally produce more accurate alignments, they are inefficient because all the aligners need to be run first and the choice of the best solution is made a posteriori. Here, we describe the development of a new expert system, AlexSys, for the multiple alignment of protein sequences. AlexSys incorporates an intelligent inference engine to automatically select an appropriate aligner a priori, depending only on the nature of the input sequences. The inference engine was trained on a large set of reference multiple alignments, using a novel machine learning approach. Applying AlexSys to a test set of 178 alignments, we show that the expert system represents a good compromise between alignment quality and running time, making it suitable for high throughput projects. AlexSys is freely available from http://alnitak.u-strasbg.fr/∼aniba/alexsys.

  8. 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.

  9. 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

  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. Pharmacophore alignment search tool: influence of scoring systems on text-based similarity searching.

    PubMed

    Hähnke, Volker; Schneider, Gisbert

    2011-06-01

    The text-based similarity searching method Pharmacophore Alignment Search Tool is grounded on pairwise comparisons of potential pharmacophoric points between a query and screening compounds. The underlying scoring matrix is of critical importance for successful virtual screening and hit retrieval from large compound libraries. Here, we compare three conceptually different computational methods for systematic deduction of scoring matrices: assignment-based, alignment-based, and stochastic optimization. All three methods resulted in optimized pharmacophore scoring matrices with significantly superior retrospective performance in comparison with simplistic scoring schemes. Computer-generated similarity matrices of pharmacophoric features turned out to agree well with a manually constructed matrix. We introduce the concept of position-specific scoring to text-based similarity searching so that knowledge about specific ligand-receptor binding patterns can be included and demonstrate its benefit for hit retrieval. The approach was also used for automated pharmacophore elucidation in agonists of peroxisome proliferator activated receptor gamma, successfully identifying key interactions for receptor activation.

  12. Field induced UV-alignment method for a zero pre-tilt liquid crystal cell

    NASA Astrophysics Data System (ADS)

    Oh, Seung-Won; Park, Jun-Hee; Yoon, Tae-Hoon

    2016-09-01

    Recently, photo-alignment technology has been the focus of research efforts because lowering the pre-tilt angle is essential for complete elimination of the off-axis light leakage. However, even though photo-alignment can provide zero pre-tilt angle, it has not yet been widely applied in mass production because of its weak surface anchoring, high curing energy, and strong image sticking. In this paper, we demonstrate that the zero pre-tilt angle can be obtained by employing the field-induced UV-alignment method. We have shown electro-optical characteristics and parameters related to the image quality of a fringe-field switching cell fabricated using the proposed method as functions of the monomer concentration and the UV irradiation time.

  13. 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.

  14. Distant homology detection using a LEngth and STructure-based sequence Alignment Tool (LESTAT).

    PubMed

    Lee, Marianne M; Bundschuh, Ralf; Chan, Michael K

    2008-05-15

    A new machine learning algorithm, LESTAT (LEngth and STructure-based sequence Alignment Tool) has been developed for detecting protein homologs having low-sequence identity. LESTAT is an iterative profile-based method that runs without reliance on a predefined library and incorporates several novel features that enhance its ability to identify remote sequences. To overcome the inherent bias associated with a single starting model, LESTAT utilizes three structural homologs to create a profile consisting of structurally conserved positions and block separation distances. Subsequent profiles are refined iteratively using sequence information obtained from previous cycles. Additionally, the refinement process incorporates a "lock-in" feature to retain the high-scoring sequences involved in previous alignments for subsequent model building and an enhancement factor to complement the weighting scheme used to build the position specific scoring matrix. A comparison of the performance of LESTAT against PSI-BLAST for seven systems reveals that LESTAT exhibits increased sensitivity and specificity over PSI-BLAST in six of these systems, based on the number of true homologs detected and the number of families these homologs covered. Notably, many of the hits identified are unique to each method, presumably resulting from the distinct differences in the two approaches. Taken together, these findings suggest that LESTAT is a useful complementary method to PSI-BLAST in the detection of distant homologs.

  15. Alignment, segmentation and 3-D reconstruction of serial sections based on automated algorithm

    NASA Astrophysics Data System (ADS)

    Bian, Weiguo; Tang, Shaojie; Xu, Qiong; Lian, Qin; Wang, Jin; Li, Dichen

    2012-12-01

    A well-defined three-dimensional (3-D) reconstruction of bone-cartilage transitional structures is crucial for the osteochondral restoration. This paper presents an accurate, computationally efficient and fully-automated algorithm for the alignment and segmentation of two-dimensional (2-D) serial to construct the 3-D model of bone-cartilage transitional structures. Entire system includes the following five components: (1) image harvest, (2) image registration, (3) image segmentation, (4) 3-D reconstruction and visualization, and (5) evaluation. A computer program was developed in the environment of Matlab for the automatic alignment and segmentation of serial sections. Automatic alignment algorithm based on the position's cross-correlation of the anatomical characteristic feature points of two sequential sections. A method combining an automatic segmentation and an image threshold processing was applied to capture the regions and structures of interest. SEM micrograph and 3-D model reconstructed directly in digital microscope were used to evaluate the reliability and accuracy of this strategy. The morphology of 3-D model constructed by serial sections is consistent with the results of SEM micrograph and 3-D model of digital microscope.

  16. Wrinkled, wavelength-tunable graphene-based surface topographies for directing cell alignment and morphology

    PubMed Central

    Wang, Zhongying; Tonderys, Daniel; Leggett, Susan E.; Williams, Evelyn Kendall; Kiani, Mehrdad T.; Steinberg, Ruben Spitz; Qiu, Yang; Wong, Ian Y.; Hurt, Robert H.

    2015-01-01

    Textured surfaces with periodic topographical features and long-range order are highly attractive for directing cell-material interactions. They mimic physiological environments more accurately than planar surfaces and can fundamentally alter cell alignment, shape, gene expression, and cellular assembly into superstructures or microtissues. Here we demonstrate for the first time that wrinkled graphene-based surfaces are suitable as textured cell attachment substrates, and that engineered wrinkling can dramatically alter cell alignment and morphology. The wrinkled surfaces are fabricated by graphene oxide wet deposition onto pre-stretched elastomers followed by relaxation and mild thermal treatment to stabilize the films in cell culture medium. Multilayer graphene oxide films form periodic, delaminated buckle textures whose wavelengths and amplitudes can be systematically tuned by variation in the wet deposition process. Human and murine fibroblasts attach to these textured films and remain viable, while developing pronounced alignment and elongation relative to those on planar graphene controls. Compared to lithographic patterning of nanogratings, this method has advantages in the simplicity and scalability of fabrication, as well as the opportunity to couple the use of topographic cues with the unique conductive, adsorptive, or barrier properties of graphene materials for functional biomedical devices. PMID:25848137

  17. 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.

  18. Self-aligning LED-based optical link

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

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

    PubMed

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

    2016-12-13

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

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

    PubMed Central

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

    2016-01-01

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

  1. 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.

  2. 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…

  3. Method and apparatus for aligning a solar concentrator using two lasers

    DOEpatents

    Diver Jr., Richard Boyer

    2003-07-22

    A method and apparatus are provided for aligning the facets of a solar concentrator. A first laser directs a first laser beam onto a selected facet of the concentrator such that a target board positioned adjacent to the first laser at approximately one focal length behind the focal point of the concentrator is illuminated by the beam after reflection thereof off of the selected facet. A second laser, located adjacent to the vertex of the optical axis of the concentrator, is used to direct a second laser beam onto the target board at a target point thereon. By adjusting the selected facet to cause the first beam to illuminate the target point on the target board produced by the second beam, the selected facet can be brought into alignment with the target point. These steps are repeated for other selected facets of the concentrator, as necessary, to provide overall alignment of the concentrator.

  4. 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.

  5. 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.

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

    PubMed

    Qu, Jianliang; Chen, Weihai; Zhang, Jianbin

    2014-09-01

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

  7. 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.

  8. Multiple sequence alignment with hierarchical clustering.

    PubMed Central

    Corpet, F

    1988-01-01

    An algorithm is presented for the multiple alignment of sequences, either proteins or nucleic acids, that is both accurate and easy to use on microcomputers. The approach is based on the conventional dynamic-programming method of pairwise alignment. Initially, a hierarchical clustering of the sequences is performed using the matrix of the pairwise alignment scores. The closest sequences are aligned creating groups of aligned sequences. Then close groups are aligned until all sequences are aligned in one group. The pairwise alignments included in the multiple alignment form a new matrix that is used to produce a hierarchical clustering. If it is different from the first one, iteration of the process can be performed. The method is illustrated by an example: a global alignment of 39 sequences of cytochrome c. PMID:2849754

  9. 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

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

    PubMed

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

    2016-04-29

    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.

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

    PubMed

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

    2017-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

  13. 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.

  14. IBBOMSA: An Improved Biogeography-based Approach for Multiple Sequence Alignment

    PubMed Central

    Yadav, Rohit Kumar; Banka, Haider

    2016-01-01

    In bioinformatics, multiple sequence alignment (MSA) is an NP-hard problem. Hence, nature-inspired techniques can better approximate the solution. In the current study, a novel biogeography-based optimization (NBBO) is proposed to solve an MSA problem. The biogeography-based optimization (BBO) is a new paradigm for optimization. But, there exists some deficiencies in solving complicated problems such as low population diversity and slow convergence rate. NBBO is an enhanced version of BBO, in which, a new migration operation is proposed to overcome the limitations of BBO. The new migration adopts more information from other habitats, maintains population diversity, and preserves exploitation ability. In the performance analysis, the proposed and existing techniques such as VDGA, MOMSA, and GAPAM are tested on publicly available benchmark datasets (ie, Bali base). It has been observed that the proposed method shows the superiority/competitiveness with the existing techniques. PMID:27812276

  15. The online estimation of relative alignments for multiple heads star tracker based on the invariability of inter-star angle principle

    NASA Astrophysics Data System (ADS)

    Xiong, Ya-zhou; Wu, Yan-peng; Cheng, Hui-yan; Liu, Da

    2016-11-01

    In this paper, a real-time calibration method for relative alignments between multiple heads star tracker (MHST) heads based on the invariability of inter-star angle principle is presented. Firstly, the ill effects of relative misalignments on accuracy of MHST attitude based on star-fusion are analyzed. Then, the invariability of inter-star angle principle and the changing feature of relative alignments are applied to build a kalman filtering model to estimate the errors. Finally, a simulation is used to illustrate that the method meets well the real-time requirement of accurate relative alignments of MHST.

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

    PubMed

    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).

  17. 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.

  18. 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.

  19. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

  1. Computer-aided alignment method of optical lens with high accuracy

    NASA Astrophysics Data System (ADS)

    Xing, Song; Hou, Xiao-hua; Zhang, Xue-min; Ji, Bin-dong

    2016-09-01

    With the development of space and aviation industry, the optical systems with high resolution and better imaging quality are required. According to the alignment technical process, the factors of every step which have big influence to the imaging quality are analyzed. It is detected that the micro-stress assembly of the optical unit and the high co-axial precision of the entire optical system are the two important factors which are supposed to determine how well the imaging quality of the optical system is; also the technical methods are discussed to ensure these two factors from the engineering view. The reflective interference testing method to measure the surface figure and the transitive interference testing method to measure the wave aberration of the optical unit are combined to ensure the micro-stress assembly of the optical unit, so it will not bring astigmatism to the whole system imaging quality. Optical alignment machining and precision alignment are combined to ensure the high co-axial precision of the optical system. An optical lens of high accuracy is assembled by using these methods; the final wave aberration of optical lens is 0.022λ.

  2. Flash imprint lithography using a mask aligner: a method for printing nanostructures in photosensitive hydrogels

    NASA Astrophysics Data System (ADS)

    Fozdar, David Y.; Zhang, Wande; Palard, Marylene; Patrick, Charles W., Jr.; Chen, Shaochen

    2008-05-01

    In this paper, we report a general method for imprinting nanometer-scale features in low-viscosity photosensitive hydrogels using conventional optical mask aligner technology. We call this method flash imprint lithography using a mask aligner (FILM). The FILM process makes it possible to fabricate nanometer-scale features in ultraviolet (UV)-curable hydrogels quickly, inexpensively and reproducibly. We believe that the FILM process will be useful in many areas of research but is particularly applicable to tissue engineering. Accordingly, we demonstrate the FILM process by imprinting dense arrays of nanostructures in polyethylene glycol dimethacrylate (PEGDMA), a material commonly utilized as a substrate in micro-and nanoscale tissue scaffolds; finite element modeling and contact angle analysis are employed to characterize pattern transfer of low-viscosity polymers (e.g. PEGDMA) in the FILM process.

  3. 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

  4. Theory of electrical conductivity and dielectric permittivity of highly aligned graphene-based nanocomposites.

    PubMed

    Xia, Xiaodong; Hao, Jia; Wang, Yang; Zhong, Zheng; Weng, George J

    2017-03-24

    Highly aligned graphene-based nanocomposites are of great interest due to their excellent electrical properties along the aligned direction. Graphene fillers in these composites are not necessarily perfectly aligned, but their orientations are highly confined to a certain angle, with 90-degree giving rise to the randomly oriented state and 0-degree to the perfectly aligned one. Recent experiments have shown that electrical conductivity and dielectric permittivity of highly aligned graphene-polymer nanocomposites are strongly dependent on this distribution angle, but at present no theory seems to exist to address this issue. In this work we present a new effective-medium theory that is derived from the underlying physical process including the effects of graphene orientation, filler loading, aspect ratio, percolation threshold, interfacial tunneling, and Maxwell-Wagner-Sillars polarization, to determine these two properties. The theory is formulated in the context of preferred orientational average. We highlight this new theory with an application to rGO/epoxy nanocomposites, and demonstrate that the calculated in-plane and out-of-plane conductivity and permittivity are in agreement with the experimental data as the range of graphene orientations changes from the randomly oriented to the highly aligned state. We also show that the percolation thresholds of highly aligned graphene nanocomposites are in general different along the planar and the normal directions, but they converge into a single one when the statistical distribution of graphene fillers is spherically symmetric.

  5. 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.

  6. Objective method for estimating asymptotic parameters, with an application to sequence alignment

    NASA Astrophysics Data System (ADS)

    Sheetlin, Sergey; Park, Yonil; Spouge, John L.

    2011-09-01

    Sequence alignment is an indispensable computational tool in modern molecular biology. The model underlying biological sequence alignment is of interest to physicists because it approximates the statistical mechanics of DNA and protein annealing, while bearing an intimate relationship to models of directed polymers in random media. Recent methods for determining the statistics of random sequence alignments have reduced the computation time to less than 1 s, opening up some interesting possibilities for online computation with biological search engines. Before implementation, however, the methods required an objective technique for computing regression coefficients pertinent to an asymptotic regime. Typically, physicists estimate parameters pertinent to an asymptotic regime subjectively: They eyeball their data; estimate the asymptotic regime where the regression model holds with reasonable accuracy; and then regress data only within the estimated asymptotic regime. Our publicly available computer program arrp replaces the subjective assessment of the asymptotic regime with an objective change-point detection method, increasing confidence in the scientific objectivity of the parameter estimates. Asymptotic regression has potential applications across most of physics.

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

    NASA Astrophysics Data System (ADS)

    Chattaraj, Suvendu; Mukherjee, Abhik

    2016-07-01

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

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

    PubMed

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

    2008-01-01

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

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

    PubMed

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

    2012-03-15

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

  10. Ingenious method of external fixator use to maintain alignment for nailing a proximal tibial shaft fracture.

    PubMed

    Behera, Prateek; Aggarwal, Sameer; Kumar, Vishal; Kumar Meena, Umesh; Saibaba, Balaji

    2015-09-01

    Fractures of the tibia are one of the most commonly seen orthopedic injuries. Most of them result from a high velocity trauma. While intramedullary nailing of tibial diaphyseal fractures is considered as the golden standard form of treatment for such cases, many metaphyseal and metaphyseal-diaphyseal junction fractures can also be managed by nailing. Maintenance of alignment of such fractures during surgical procedure is often challenging as the pull of patellar tendon tends to extend the proximal fragment as soon as one flexes the knee for the surgical procedure. Numerous technical modifications have been described in the literature for successfully nailing such fractures including semi extended nailing, use of medial plates and external fixators among others. In this study, it was aimed to report two cases in which we used our ingenious method of applying external fixator for maintaining alignment of the fracture and aiding in the entire process of closed intramedullary nailing of metaphyseal tibial fractures by the conventional method. We were able to get good alignment during and after the closed surgery as observed on post-operative radiographs and believe that further evaluation of this technique may be of help to surgeons who want to avoid other techniques.

  11. Enhanced method of magnetic powder alignment for production of PLP Nd-Fe-B magnets

    NASA Astrophysics Data System (ADS)

    Popov, A. G.; Golovnia, O. A.; Protasov, A. V.

    2017-04-01

    It is demonstrated how the high degree of powder alignment in PLP magnets can be achieved by loading the powder into a container placed in a magnetic field of moderate strength. The strip-cast alloy with a composition of 30.00 Nd, 1.95 Dy, 66.42 Fe, 0.99 B, 0.54 Co, 0.1 Ga (wt%) was subjected to hydrogen decrepitation and then milled in a vibratory mill in toluene to an average particle size of 2.9 μm determined by the FSSS method. The powder was compacted in the magnetic field of 0.2 - 1.2 T to the filling density 2.6 - 3.2×103 kg/m3. It is shown that loading the powder into a container placed in a magnetic field enhances the degree of powder alignment in sintered Nd-Fe-B magnets produced from non-pressed powder. At the filling density less than 3.2×103 kg/m3, the density of magnets is high but insufficient, because of the formation of magnetostatic chains of particles, which impedes the powder compaction. The simulation by the discrete-element method qualitatively proves that the magnetostatic interaction of the chains of particles that are formed in the course of loading in the magnetic field stimulates a decrease in the density of the sintered magnets and its non-uniform distribution over the sample. As a result of the optimization of the parameters of the alignment and compaction of the powder loaded in a magnetic field, PLP magnets with Br ≥1.34 T, Нc ≥950 kA/m, (BH)max ≥340 kJ/m3, and the degree of alignment exceeding 96% were produced.

  12. 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…

  13. Identification of Ligand Templates using Local Structure Alignment for Structure-based Drug Design

    PubMed Central

    Lee, Hui Sun; Im, Wonpil

    2012-01-01

    With a rapid increase in the number of high-resolution protein-ligand structures, the known protein-ligand structures can be used to gain insight into ligand-binding modes in a target protein. Based on the fact that the structurally similar binding sites share information about their ligands, we have developed a local structure alignment tool, G-LoSA (Graph-based Local Structure Alignment). In G-LoSA, the known protein-ligand binding-site structure library is searched to detect binding-site structures with similar geometry and physicochemical properties to a query binding-site structure regardless of sequence continuity and protein fold. Then, the ligands in the identified complexes are used as templates (i.e., template ligands) to predict/design a ligand for the target protein. The performance of G-LoSA is validated against 76 benchmark targets from the Astex diverse set. Using the currently available protein-ligand structure library, G-LoSA is able to identify a single template ligand (from a non-homologous protein complex) that is highly similar to the target ligand in more than half of the benchmark targets. In addition, our benchmark analyses show that an assembly of structural fragments from multiple template ligands with partial similarity to the target ligand can be used to design novel ligand structures specific to the target protein. This study clearly indicates that a template-based ligand modeling has potential for de novo ligand design and can be a complementary approach to the receptor structure based methods. PMID:22978550

  14. 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.

  15. 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.

  16. Alignment method of optical registration for multi-channel CCD camera

    NASA Astrophysics Data System (ADS)

    Xin, Jia; Yue, Guo

    2016-10-01

    The mapping satellite is use of the multichip CCD assemble technology to meet the precision landscape positioning requirements. The size of a single CCD cannot meet the requirements of modern optical system. High cost and special technology are required for the resolution. In order to apply space camera to the measurement in large field of view and high resolution, the technology of optical assembly with several CCD is discussed. And a reflector based butting system was adopted. To extend the field of view, an optical butting system is proposed. Aiming at the problems of vignette and decline of modulation transfer function caused by butting, a reflector based butting system which has nine mirrors was investigated. This paper introduced the structure design of a long array and the principle of optical butting. The basic idea of this system is to split the optical image into several parts, so that they can be detected by different sensors. The mirror is used in conventional imaging system; divide the optical image into two parts. To eliminate the vignette distortion caused by the optical system and keep high signal to noise ratio, the sensors receiving the two focal image parts are placed with a little overlapping so that they can compensate each other. In order to ensure the key techniques of mirror location accuracy, a new alignment method was proposed about locating conversation components, mainly aimed at enhancing assembly accuracy of linear array CCD.A high quality image can be obtained by butting the two image parts. Its principle, methods of adjusting and testing as well as the structure of focal plane are described. The assembly with nine TDICCDs is finished on the facility which is composed of a long work-distance microscope and a precise X-Y rail, using the method in which the mechanical adjusting is applied. Compared with convention system, this method can satisfy the linearity accuracy and overlapping pixels tolerance of 0.2 detector pixel sizes. And can

  17. A unified model for transfer alignment at random misalignment angles based on second-order EKF

    NASA Astrophysics Data System (ADS)

    Cui, Xiao; Mei, Chunbo; Qin, Yongyuan; Yan, Gongmin; Liu, Zhenbo

    2017-04-01

    In the transfer alignment process of inertial navigation systems (INSs), the conventional linear error model based on the small misalignment angle assumption cannot be applied to large misalignment situations. Furthermore, the nonlinear model based on the large misalignment angle suffers from redundant computation with nonlinear filters. This paper presents a unified model for transfer alignment suitable for arbitrary misalignment angles. The alignment problem is transformed into an estimation of the relative attitude between the master INS (MINS) and the slave INS (SINS), by decomposing the attitude matrix of the latter. Based on the Rodriguez parameters, a unified alignment model in the inertial frame with the linear state-space equation and a second order nonlinear measurement equation are established, without making any assumptions about the misalignment angles. Furthermore, we employ the Taylor series expansions on the second-order nonlinear measurement equation to implement the second-order extended Kalman filter (EKF2). Monte-Carlo simulations demonstrate that the initial alignment can be fulfilled within 10 s, with higher accuracy and much smaller computational cost compared with the traditional unscented Kalman filter (UKF) at large misalignment angles.

  18. 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.

  19. 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.

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

    NASA Astrophysics Data System (ADS)

    Hara, Kazuo; Shimbo, Masashi; Matsumoto, Yuji

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

  1. An IMU-to-Body Alignment Method Applied to Human Gait Analysis.

    PubMed

    Vargas-Valencia, Laura Susana; Elias, Arlindo; Rocon, Eduardo; Bastos-Filho, Teodiano; Frizera, Anselmo

    2016-12-10

    This paper presents a novel calibration procedure as a simple, yet powerful, method to place and align inertial sensors with body segments. The calibration can be easily replicated without the need of any additional tools. The proposed method is validated in three different applications: a computer mathematical simulation; a simplified joint composed of two semi-spheres interconnected by a universal goniometer; and a real gait test with five able-bodied subjects. Simulation results demonstrate that, after the calibration method is applied, the joint angles are correctly measured independently of previous sensor placement on the joint, thus validating the proposed procedure. In the cases of a simplified joint and a real gait test with human volunteers, the method also performs correctly, although secondary plane errors appear when compared with the simulation results. We believe that such errors are caused by limitations of the current inertial measurement unit (IMU) technology and fusion algorithms. In conclusion, the presented calibration procedure is an interesting option to solve the alignment problem when using IMUs for gait analysis.

  2. An IMU-to-Body Alignment Method Applied to Human Gait Analysis

    PubMed Central

    Vargas-Valencia, Laura Susana; Elias, Arlindo; Rocon, Eduardo; Bastos-Filho, Teodiano; Frizera, Anselmo

    2016-01-01

    This paper presents a novel calibration procedure as a simple, yet powerful, method to place and align inertial sensors with body segments. The calibration can be easily replicated without the need of any additional tools. The proposed method is validated in three different applications: a computer mathematical simulation; a simplified joint composed of two semi-spheres interconnected by a universal goniometer; and a real gait test with five able-bodied subjects. Simulation results demonstrate that, after the calibration method is applied, the joint angles are correctly measured independently of previous sensor placement on the joint, thus validating the proposed procedure. In the cases of a simplified joint and a real gait test with human volunteers, the method also performs correctly, although secondary plane errors appear when compared with the simulation results. We believe that such errors are caused by limitations of the current inertial measurement unit (IMU) technology and fusion algorithms. In conclusion, the presented calibration procedure is an interesting option to solve the alignment problem when using IMUs for gait analysis. PMID:27973406

  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. Controlled growth of well-aligned ZnO nanorod arrays by hydrothermal method

    NASA Astrophysics Data System (ADS)

    Mihailova, I.; Gerbreders, V.; Bulanovs, A.; Tamanis, E.; Sledevskis, E.; Ogurcovs, A.; Sarajevs, P.

    2014-10-01

    The application prospect of zinc oxide (ZnO) nanostructures largely relies on the ability to grow nanoobjects with necessary geometry. In this study well-aligned ZnO nanorod arrays with a high density and uniformity were successfully synthesized on the glass substrates by a hydrothermal method at low-temperature. The aqueous solutions of zinc nitrate hexahydrate and hexamethylenetetramine was used. The effect of seed layer (obtained by electrochemical method and by vacuum deposition method) on the alignment of ZnO nanorods has been investigated. The morphological properties of the ZnO nanorods were also examined in accordance with varying the magnetron sputtering angle for ZnO seeds deposition. It is also shown that the electric field can control the direction of the growth of ZnO nanorods. Morphological, structural and compositional characterizations of obtained films were carried out by scanning electron microscopy, energy-dispersive X-ray spectroscopy and X-ray diffraction analysis methods.

  5. 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/ .

  6. Research on the method of precise alignment technology of atmospheric laser communication

    NASA Astrophysics Data System (ADS)

    Chen, Wen-jian; Gao, Wei; Duan, Yuan-yuan; Ma, Shi-wei; Chen, Jian

    2016-10-01

    Atmosphere laser communication takes advantage of laser as the carrier transmitting the voice, data, and image information in the atmosphere. Because of its high reliability, strong anti-interference ability, the advantages of easy installation, it has great potential and development space in the communications field. In the process of establish communication, the capture, targeting and tracking of the communication signal is the key technology. This paper introduce a method of targeting the signal spot in the process of atmosphere laser communication, which through the way of making analog signal addition and subtraction directly and normalized to obtain the target azimuth information to drive the servo system to achieve precise alignment of tracking.

  7. A method for quantitatively analyzing the angle of direction for arbitral c-axis alignment with retardation measurements

    NASA Astrophysics Data System (ADS)

    Shimoi, Norihiro; Tanaka, Yasumitsu

    2015-01-01

    c-axis alignment in a polymer or crystal structure has drawn attention in numerous scientific and technological applications, including crystals, thin film growth, electro-optic devices, and phase difference optics. We here demonstrate a new approach based on retardation measurement that can obtain the direction of the c-axis alignment. This is employed to visualize the three-dimensional direction of continuous crystals as a thin optical film utilizing a liquid crystal panel, using retardation analysis equipment with high resolution measurement capability. The direction of the c-axis alignment is shown so as to allow a detailed characterization of the direction perpendicular to the plane. In this analysis, the direction of the c-axis alignment is identified, and differences between molecules at inequivalent sites are quantified. The results suggest that the excellent lubrication properties of the c-axis alignment may be due to a significant localization in lateral directions.

  8. Use laser-optics for machinery alignment

    SciTech Connect

    Bloch, H.P.

    1987-10-01

    Many sources attribute most bearing overload and destructive vibration in industrial machinery to shaft misalignment. There is considerable disagreement as to the alignment quality required. There is also little agreement on suitable calculation methods and achievable accuracy for anticipated thermal growth of machinery (necessary if running alignment is to remain acceptable). This article examines existing alignment quality guidelines for relevance and consistency, and reviews the application of laser-optic alignment systems based on three years of field experience.

  9. 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.

  10. 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.

  11. 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

  12. 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].

  13. 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.

  14. 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.

  15. RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits

    PubMed Central

    Teeling, Hanno; Gloeckner, Frank Oliver

    2006-01-01

    Background Until today, analysis of 16S ribosomal RNA (rRNA) sequences has been the de-facto gold standard for the assessment of phylogenetic relationships among prokaryotes. However, the branching order of the individual phlya is not well-resolved in 16S rRNA-based trees. In search of an improvement, new phylogenetic methods have been developed alongside with the growing availability of complete genome sequences. Unfortunately, only a few genes in prokaryotic genomes qualify as universal phylogenetic markers and almost all of them have a lower information content than the 16S rRNA gene. Therefore, emphasis has been placed on methods that are based on multiple genes or even entire genomes. The concatenation of ribosomal protein sequences is one method which has been ascribed an improved resolution. Since there is neither a comprehensive database for ribosomal protein sequences nor a tool that assists in sequence retrieval and generation of respective input files for phylogenetic reconstruction programs, RibAlign has been developed to fill this gap. Results RibAlign serves two purposes: First, it provides a fast and scalable database that has been specifically adapted to eubacterial ribosomal protein sequences and second, it provides sophisticated import and export capabilities. This includes semi-automatic extraction of ribosomal protein sequences from whole-genome GenBank and FASTA files as well as exporting aligned, concatenated and filtered sequence files that can directly be used in conjunction with the PHYLIP and MrBayes phylogenetic reconstruction programs. Conclusion Up to now, phylogeny based on concatenated ribosomal protein sequences is hampered by the limited set of sequenced genomes and high computational requirements. However, hundreds of full and draft genome sequencing projects are on the way, and advances in cluster-computing and algorithms make phylogenetic reconstructions feasible even with large alignments of concatenated marker genes. RibAlign

  16. Collinearity alignment of probe beams in a laser-based Faraday effect diagnostica)

    NASA Astrophysics Data System (ADS)

    Lin, L.; Ding, W. X.; Brower, D. L.

    2012-10-01

    Two counter-rotating circularly polarized beams are used in a laser-based polarimetry diagnostic providing a phase measurement of the Faraday effect. Collinearity of these beams is a key issue that affects measurement accuracy. Spatial offset from even small misalignment induces systematic error due to density gradient and path length difference. Here, we report an alignment technique using a rotating dielectric wedge, which is capable of reducing spatial offset of two probe beams below 0.1 mm for beams with 40 mm diameter. With optimized alignment, 0.05° Faraday effect fluctuations associated with global tearing modes are resolved with an uncertainty below 0.01°.

  17. Fast switchable grating based on orthogonal photo alignments of ferroelectric liquid crystals

    NASA Astrophysics Data System (ADS)

    Srivastava, A. K.; Hu, Wei; Chigrinov, V. G.; Kiselev, A. D.; Lu, Yan-Qing

    2012-07-01

    We demonstrate a fast switchable grating based on ferroelectric liquid crystals and orthogonal planar alignment by means of photo alignments. Both 1D and 2D gratings have been constructed. The proposed diffracting element provides fast response time of around 20 μs, contrast of 7000:1 and high diffraction efficiency, at the electric field of 6 V/μm. The saturated electro-optical (EO) states up to very high frequency (≈5 kHz) are the real advantage of the proposed switchable grating, which opens several opportunities to improve the quality of existing devices and to find new applications.

  18. 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…

  19. Nova laser alignment control system

    SciTech Connect

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

    1984-03-29

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

  20. 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

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

    PubMed

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

    2010-02-01

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

  2. Novel analytical methods for stratus OCT: alignment of the scan circle.

    PubMed

    Marín-Franch, Iván; Swanson, William H; Adams, Brittany R; Zhu, Haogang; Crabb, David P

    2012-12-01

    Measurement of retinal nerve fiber layer (RNFL) thickness using optical coherence tomography (OCT) is commonly used in the detection and management of glaucoma. The Stratus OCT (Carl Zeiss Meditec, Inc., Dublin, CA) is widely used, but image acquisition is subject to artifacts, such as those caused by normal fixational eye movements, and this leads to unreliable measurements. Novel analytical methods have been developed to estimate the amount of misalignment of the circular scanning protocol used by the Stratus OCT. A computer program with a graphical user interface implementing these methods has been written by some of the authors. A case example is presented in this report that shows the effect that vertical displacements of the OCT scan have on measured RNFL thickness. The example is used to demonstrate how the software can be used for estimating the positional alignment of the scan circle. This software can potentially improve the identification of unreliable RNFL thickness measurements and is freely available from the authors.

  3. Simple method for the stretching and alignment of single adsorbed synthetic polycations.

    PubMed

    Bocharova, Vera; Kiriy, Anton; Stamm, Manfred; Stoffelbach, Francois; Jérôme, Robert; Detrembleur, Christophe

    2006-07-01

    Spin-coating of isolated positively charged macromolecules onto mica in the presence of octylamine was found to be a simple and general method of stretching and aligning the macromolecular chains. The contour length and molar mass for the stretched macromolecules can be directly measured by atomic force microscopy, which makes this method a very useful analytical tool. Moreover, the molecular height is increased by co-deposition with octylamine, which drastically improves the molecular resolution and allows even ultrathin polycations to be visualized. The reason for the key role of the octylamine is found in the formation of an ultrathin liquidlike alkylamine film, which reduces the surface energy of mica and weakens the interactions between the surface and the charged macromolecules.

  4. Using optimization methods to align food production and biodiversity conservation beyond land sharing and land sparing.

    PubMed

    Butsic, Van; Kuemmerle, Tobias

    2015-04-01

    Aligning food production with biodiversity conservation is one of the greatest challenges of our time. One framing of this challenge is the land-sharing vs. land-sparing debate. Much empirical research has focused on identifying the relationship between agricultural yields and species populations, and using the relative number of species with particular relationships to inform landscape-level management. We feel this is misguided, as such an approach does not guarantee the existence of every species of conservation concern. Here, we show that constrained optimization methods can be used to identify landscape-level solutions which maximize agricultural yields and populations for any number of species. Our results suggest that the relative number of species with particular yield-density curves is not a good indicator as to how landscapes should be managed. Likewise, choosing between blanket sharing or sparing strategies leads to suboptimal outcomes at the landscape scale in many cases. Our framework makes maximum use of the rich information contained in yield-density curves to move beyond black-and-white choices and toward more nuanced, context-specific solutions to aligning biodiversity conservation and agricultural production. Such optimal landscapes will likely have features of both sharing and sparing strategies.

  5. 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

  6. Elucidation of the Enantiodiscrimination Properties of a Nonracemic Chiral Alignment Medium through Gel‐based Capillary Electrochromatography: Separation of the Mefloquine Stereoisomers

    PubMed Central

    Al‐Massaedh, “Ayat Allah”; Schmidt, Manuel

    2016-01-01

    Abstract Enantiodiscrimination and enantioseparation are two highly important processes in chemistry, often performed by using NMR spectroscopy and chromatography. For a better understanding of the mechanistic details, the same system should be studied by both methods. In addition, isotropic and anisotropic NMR parameters should be obtained, the latter using alignment media so that residual dipolar couplings and chemical‐shift anisotropies can be measured. Consequently, a chiral alignment medium was used for the first time in chiral gel‐based capillary electrochromatography with the four stereoisomers of the antimalaria drug mefloquine as test compounds. Chromatographic data verify that enantiodiscrimination obtained with this alignment gel is caused by differences in the equilibrium constants related to associate formation. Hence, the chromatographic separation provides physicochemical data that form a basis for the understanding and optimization of alignment processes, and vice versa. PMID:27777838

  7. 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

  8. 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

  9. Alignment of Helical Membrane Protein Sequences Using AlignMe

    PubMed Central

    Khafizov, Kamil; Forrest, Lucy R.

    2013-01-01

    Few sequence alignment methods have been designed specifically for integral membrane proteins, even though these important proteins have distinct evolutionary and structural properties that might affect their alignments. Existing approaches typically consider membrane-related information either by using membrane-specific substitution matrices or by assigning distinct penalties for gap creation in transmembrane and non-transmembrane regions. Here, we ask whether favoring matching of predicted transmembrane segments within a standard dynamic programming algorithm can improve the accuracy of pairwise membrane protein sequence alignments. We tested various strategies using a specifically designed program called AlignMe. An updated set of homologous membrane protein structures, called HOMEP2, was used as a reference for optimizing the gap penalties. The best of the membrane-protein optimized approaches were then tested on an independent reference set of membrane protein sequence alignments from the BAliBASE collection. When secondary structure (S) matching was combined with evolutionary information (using a position-specific substitution matrix (P)), in an approach we called AlignMePS, the resultant pairwise alignments were typically among the most accurate over a broad range of sequence similarities when compared to available methods. Matching transmembrane predictions (T), in addition to evolutionary information, and secondary-structure predictions, in an approach called AlignMePST, generally reduces the accuracy of the alignments of closely-related proteins in the BAliBASE set relative to AlignMePS, but may be useful in cases of extremely distantly related proteins for which sequence information is less informative. The open source AlignMe code is available at https://sourceforge.net/projects/alignme/, and at http://www.forrestlab.org, along with an online server and the HOMEP2 data set. PMID:23469223

  10. 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.

  11. 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.

  12. 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

  13. Aligned carbon nanotube-based flexible gel substrates for engineering bio-hybrid tissue actuators.

    PubMed

    Shin, Su Ryon; Shin, Courtney; Memic, Adnan; Shadmehr, Samaneh; Miscuglio, Mario; Jung, Hyun Young; Jung, Sung Mi; Bae, Hojae; Khademhosseini, Ali; Tang, Xiaowu Shirley; Dokmeci, Mehmet R

    2015-07-20

    Muscle-based biohybrid actuators have generated significant interest as the future of biorobotics but so far they move without having much control over their actuation behavior. Integration of microelectrodes into the backbone of these systems may enable guidance during their motion and allow precise control over these actuators with specific activation patterns. Here, we addressed this challenge by developing aligned CNT forest microelectrode arrays and incorporated them into scaffolds for stimulating the cells. Aligned CNTs were successfully embedded into flexible and biocompatible hydrogel exhibiting excellent anisotropic electrical conductivity. Bioactuators were then engineered by culturing cardiomyocytes on the CNT microelectrode-integrated hydrogel constructs. The resulting cardiac tissue showed homogeneous cell organization with improved cell-to-cell coupling and maturation, which was directly related to the contractile force of muscle tissue. This centimeter-scale bioactuator has excellent mechanical integrity, embedded microelectrodes and is capable of spontaneous actuation behavior. Furthermore, we demonstrated that a biohybrid machine can be controlled by an external electrical field provided by the integrated CNT microelectrode arrays. In addition, due to the anisotropic electrical conductivity of the electrodes provided from aligned CNTs, significantly different excitation thresholds were observed in different configurations such as the ones in parallel vs. perpendicular direction to the CNT alignment.

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

    PubMed Central

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

    2015-01-01

    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. PMID:26023248

  16. Device study, chemical doping, and logic circuits based on transferred aligned single-walled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Wang, Chuan; Ryu, Koungmin; Badmaev, Alexander; Patil, Nishant; Lin, Albert; Mitra, Subhasish; Wong, H.-S. Philip; Zhou, Chongwu

    2008-07-01

    In this paper, high-performance back-gated carbon nanotube field-effect transistors based on transferred aligned carbon nanotubes were fabricated and studies found that the on/off ratio can reach 107 and the current density can reach 1.6μA/μm after electrical breakdown. In addition, chemical doping with hydrazine was used to convert the p-type aligned nanotube devices into n-type. These devices were further utilized to demonstrate various logic circuits, including p-type metal-oxide-semiconductor inverters, diode-loaded inverters, complementary metal-oxide-semiconductor inverters, NAND, and NOR gates. This approach could work as the platform for future nanotube-based nanoelectronics.

  17. 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…

  18. The AAG's ALIGNED Toolkit: A Place-based Approach to Fostering Diversity in the Geosciences

    NASA Astrophysics Data System (ADS)

    Rodrigue, C. M.

    2012-12-01

    Where do we look to attract a more diverse group of students to academic programs in geography and the geosciences? What do we do once we find them? This presentation introduces the ALIGNED Toolkit developed by the Association of American Geographers, with funding from the NSF's Opportunities to Enhance Diversity in the Geosciences (OEDG) Program. ALIGNED (Addressing Locally-tailored Information Infrastructure and Geoscience Needs for Enhancing Diversity) seeks to align the needs of university departments and underrepresented students by drawing upon the intellectual wealth of geography and spatial science to provide better informed, knowledge-based action to enhance diversity in higher education and the geoscience workforce. The project seeks to inform and transform the ways in which departments and programs envision and realize their own goals to enhance diversity, promote inclusion, and broaden participation. We also seek to provide the data, information, knowledge, and best practices needed in order to enhance the recruitment and retention of underrepresented students. The ALIGNED Toolkit is currently in a beta release, available to 13 pilot departments and 50 testing departments of geography/geosciences. It consolidates a variety of data from departments, the U.S. Census Bureau, and the U.S. Department of Education's National Center for Education Statistics to provide interactive, GIS-based visualizations across multiple scales. It also incorporates a place-based, geographic perspective to support departments in their efforts to enhance diversity. A member of ALIGNED's senior personnel, who is also a representative of one of the pilot departments, will provide an overview and preview of the tool while sharing her department's experiences in progressing toward its diversity goals. A brief discussion on how geoscience departments might benefit from the ALIGNED approach and resources will follow. Undergraduate advisors, graduate program directors, department

  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. 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

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

    PubMed

    Kim, Byungwoo; Chung, Haegeun; Kim, Woong

    2012-04-20

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

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

    PubMed

    Ishii, Satoshi; Kadota, Koji; Senoo, Keishi

    2009-09-01

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

  4. GS-align for glycan structure alignment and similarity measurement

    PubMed Central

    Lee, Hui Sun; Jo, Sunhwan; Mukherjee, Srayanta; Park, Sang-Jun; Skolnick, Jeffrey; Lee, Jooyoung; Im, Wonpil

    2015-01-01

    Motivation: Glycans play critical roles in many biological processes, and their structural diversity is key for specific protein-glycan recognition. Comparative structural studies of biological molecules provide useful insight into their biological relationships. However, most computational tools are designed for protein structure, and despite their importance, there is no currently available tool for comparing glycan structures in a sequence order- and size-independent manner. Results: A novel method, GS-align, is developed for glycan structure alignment and similarity measurement. GS-align generates possible alignments between two glycan structures through iterative maximum clique search and fragment superposition. The optimal alignment is then determined by the maximum structural similarity score, GS-score, which is size-independent. Benchmark tests against the Protein Data Bank (PDB) N-linked glycan library and PDB homologous/non-homologous N-glycoprotein sets indicate that GS-align is a robust computational tool to align glycan structures and quantify their structural similarity. GS-align is also applied to template-based glycan structure prediction and monosaccharide substitution matrix generation to illustrate its utility. Availability and implementation: http://www.glycanstructure.org/gsalign. Contact: wonpil@ku.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25857669

  5. Computational approaches for protein function prediction: a combined strategy from multiple sequence alignment to molecular docking-based virtual screening.

    PubMed

    Pierri, Ciro Leonardo; Parisi, Giovanni; Porcelli, Vito

    2010-09-01

    The functional characterization of proteins represents a daily challenge for biochemical, medical and computational sciences. Although finally proved on the bench, the function of a protein can be successfully predicted by computational approaches that drive the further experimental assays. Current methods for comparative modeling allow the construction of accurate 3D models for proteins of unknown structure, provided that a crystal structure of a homologous protein is available. Binding regions can be proposed by using binding site predictors, data inferred from homologous crystal structures, and data provided from a careful interpretation of the multiple sequence alignment of the investigated protein and its homologs. Once the location of a binding site has been proposed, chemical ligands that have a high likelihood of binding can be identified by using ligand docking and structure-based virtual screening of chemical libraries. Most docking algorithms allow building a list sorted by energy of the lowest energy docking configuration for each ligand of the library. In this review the state-of-the-art of computational approaches in 3D protein comparative modeling and in the study of protein-ligand interactions is provided. Furthermore a possible combined/concerted multistep strategy for protein function prediction, based on multiple sequence alignment, comparative modeling, binding region prediction, and structure-based virtual screening of chemical libraries, is described by using suitable examples. As practical examples, Abl-kinase molecular modeling studies, HPV-E6 protein multiple sequence alignment analysis, and some other model docking-based characterization reports are briefly described to highlight the importance of computational approaches in protein function prediction.

  6. 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.

  7. 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.

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

    NASA Astrophysics Data System (ADS)

    Brown, Malachi

    2017-01-01

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

  9. Thin film nanotube transistors based on self-assembled, aligned, semiconducting carbon nanotube arrays.

    PubMed

    Engel, Michael; Small, Joshua P; Steiner, Mathias; Freitag, Marcus; Green, Alexander A; Hersam, Mark C; Avouris, Phaedon

    2008-12-23

    Thin film transistors (TFTs) are now poised to revolutionize the display, sensor, and flexible electronics markets. However, there is a limited choice of channel materials compatible with low-temperature processing. This has inhibited the fabrication of high electrical performance TFTs. Single-walled carbon nanotubes (CNTs) have very high mobilities and can be solution-processed, making thin film CNT-based TFTs a natural direction for exploration. The two main challenges facing CNT-TFTs are the difficulty of placing and aligning CNTs over large areas and low on/off current ratios due to admixture of metallic nanotubes. Here, we report the self-assembly and self-alignment of CNTs from solution into micron-wide strips that form regular arrays of dense and highly aligned CNT films covering the entire chip, which is ideally suitable for device fabrication. The films are formed from pre-separated, 99% purely semiconducting CNTs and, as a result, the CNT-TFTs exhibit simultaneously high drive currents and large on/off current ratios. Moreover, they deliver strong photocurrents and are also both photo- and electroluminescent.

  10. 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.

  11. BAYESIAN PROTEIN STRUCTURE ALIGNMENT1

    PubMed Central

    RODRIGUEZ, ABEL; SCHMIDLER, SCOTT C.

    2015-01-01

    The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over evolutionary timescales. A key challenge is the identification and evaluation of structural similarity between proteins; such analysis can aid in understanding the role of newly discovered proteins and help elucidate evolutionary relationships between organisms. Computational biologists have developed many clever algorithmic techniques for comparing protein structures, however, all are based on heuristic optimization criteria, making statistical interpretation somewhat difficult. Here we present a fully probabilistic framework for pairwise structural alignment of proteins. Our approach has several advantages, including the ability to capture alignment uncertainty and to estimate key “gap” parameters which critically affect the quality of the alignment. We show that several existing alignment methods arise as maximum a posteriori estimates under specific choices of prior distributions and error models. Our probabilistic framework is also easily extended to incorporate additional information, which we demonstrate by including primary sequence information to generate simultaneous sequence–structure alignments that can resolve ambiguities obtained using structure alone. This combined model also provides a natural approach for the difficult task of estimating evolutionary distance based on structural alignments. The model is illustrated by comparison with well-established methods on several challenging protein alignment examples. PMID:26925188

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

    NASA Astrophysics Data System (ADS)

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

    2010-08-01

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

  13. Improving the Robustness of Local Network Alignment: Design and Extensive Assessment of a Markov Clustering-Based Approach.

    PubMed

    Mina, Marco; Guzzi, Pietro Hiram

    2014-01-01

    The analysis of protein behavior at the network level had been applied to elucidate the mechanisms of protein interaction that are similar in different species. Published network alignment algorithms proved to be able to recapitulate known conserved modules and protein complexes, and infer new conserved interactions confirmed by wet lab experiments. In the meantime, however, a plethora of continuously evolving protein-protein interaction (PPI) data sets have been developed, each featuring different levels of completeness and reliability. For instance, algorithms performance may vary significantly when changing the data set used in their assessment. Moreover, existing papers did not deeply investigate the robustness of alignment algorithms. For instance, some algorithms performances vary significantly when changing the data set used in their assessment. In this work, we design an extensive assessment of current algorithms discussing the robustness of the results on the basis of input networks. We also present AlignMCL, a local network alignment algorithm based on an improved model of alignment graph and Markov Clustering. AlignMCL performs better than other state-of-the-art local alignment algorithms over different updated data sets. In addition, AlignMCL features high levels of robustness, producing similar results regardless the selected data set.

  14. The effects of alignment error and alignment filtering on the sitewise detection of positive selection.

    PubMed

    Jordan, Gregory; Goldman, Nick

    2012-04-01

    When detecting positive selection in proteins, the prevalence of errors resulting from misalignment and the ability of alignment filters to mitigate such errors are not well understood, but filters are commonly applied to try to avoid false positive results. Focusing on the sitewise detection of positive selection across a wide range of divergence levels and indel rates, we performed simulation experiments to quantify the false positives and false negatives introduced by alignment error and the ability of alignment filters to improve performance. We found that some aligners led to many false positives, whereas others resulted in very few. False negatives were a problem for all aligners, increasing with sequence divergence. Of the aligners tested, PRANK's codon-based alignments consistently performed the best and ClustalW performed the worst. Of the filters tested, GUIDANCE performed the best and Gblocks performed the worst. Although some filters showed good ability to reduce the error rates from ClustalW and MAFFT alignments, none were found to substantially improve the performance of PRANK alignments under most conditions. Our results revealed distinct trends in error rates and power levels for aligners and filters within a biologically plausible parameter space. With the best aligner, a low false positive rate was maintained even with extremely divergent indel-prone sequences. Controls using the true alignment and an optimal filtering method suggested that performance improvements could be gained by improving aligners or filters to reduce the prevalence of false negatives, especially at higher divergence levels and indel rates.

  15. 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

  16. Self-aligned process for emitter- and base-regrowth GaN HBTs and BJTs

    NASA Astrophysics Data System (ADS)

    Lee, K. P.; Zhang, A. P.; Dang, G.; Ren, F.; Han, J.; Chu, S. N. G.; Hobson, W. S.; Lopata, J.; Abernathy, C. R.; Pearton, S. J.; Lee, J. W.

    2001-02-01

    The development of a self-aligned fabrication process for small emitter contact area ( 2×4 μm 2) GaN/AlGaN heterojunction bipolar transistors and GaN bipolar junction transistors is described. The process features dielectric-spacer sidewalls, low damage dry etching and selected-area regrowth of p-GaAs(C) on the base contact or n-GaN/AlGaN on the emitter contact. Series resistance effects are still found to influence the device performance.

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

    PubMed

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

    2007-08-01

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

  18. Alignment-free sequence comparison based on next-generation sequencing reads.

    PubMed

    Song, Kai; Ren, Jie; Zhai, Zhiyuan; Liu, Xuemei; Deng, Minghua; Sun, Fengzhu

    2013-02-01

    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, D(2), D(*)(2) and D(s)(2), 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 D(*)(2) and D(s)(2), outperform D(2) for detecting the relationship between two sequences based on NGS data. We then study the effects of length of the tuple, read length, coverage, and sequencing error on the power of D(*)(2) and D(s)(2). Finally, variations of these statistics, d(2), d(*)(2) and d(s)(2), respectively, are used to first cluster five mammalian species with known phylogenetic relationships, and then cluster 13 tree species whose complete genome sequences are not available using NGS shotgun reads. The clustering results using d(s)(2) are consistent with biological knowledge for the 5 mammalian and 13 tree species, respectively. Thus, the statistic d(s)(2) provides a powerful alignment-free comparison tool to study the relationships among different organisms based on NGS read data without assembly.

  19. Optical alignment of the Chromospheric Lyman-Alpha Spectro-Polarimeter using sophisticated methods to minimize activities under vacuum

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

    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 instrument main scientific goal is to achieve polarization measurement of the Lyman-α line at 121.56 nm emitted from the solar upper-chromosphere and transition region with an unprecedented 0.1% accuracy. 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-α profiles. A precise alignment of the optics is required to ensure the resolutions, but experiments under vacuum conditions are needed since Ly-α 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 explain these methods and present the results for the optical alignment of the CLASP telescope and spectrograph. We 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.

  20. 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.

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

    DOEpatents

    Ivanov, Ilia N [Knoxville, TN; Simpson, John T [Clinton, TN; Hendricks, Troy R [Knoxville, TN

    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.

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

    SciTech Connect

    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.

  3. 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…

  4. 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.

  5. A peptide-spectrum scoring system based on ion alignment, intensity, and pair probabilities.

    PubMed

    Risk, Brian A; Edwards, Nathan J; Giddings, Morgan C

    2013-09-06

    Peppy, the proteogenomic/proteomic search software, employs a novel method for assessing the match quality between an MS/MS spectrum and a theorized peptide sequence. The scoring system uses three score factors calculated with binomial probabilities: the probability that a fragment ion will randomly align with a peptide ion, the probability that the aligning ions will be selected from subsets of the most intense peaks, and the probability that the intensities of fragment ions identified as y-ions are greater than those of their counterpart b-ions. The scores produced by the method act as global confidence scores, which facilitate the accurate comparison of results and the estimation of false discovery rates. Peppy has been integrated into the meta-search engine PepArML to produce meaningful comparisons with Mascot, MSGF+, OMSSA, X!Tandem, k-Score and s-Score. For two of the four data sets examined with the PepArML analysis, Peppy exceeded the accuracy performance of the other scoring systems. Peppy is available for download at http://geneffects.com/peppy .

  6. System and method for detecting components of a mixture including tooth elements for alignment

    DOEpatents

    Sommer, Gregory Jon; Schaff, Ulrich Y.

    2016-11-22

    Examples are described including assay platforms having tooth elements. An impinging element may sequentially engage tooth elements on the assay platform to sequentially align corresponding detection regions with a detection unit. In this manner, multiple measurements may be made of detection regions on the assay platform without necessarily requiring the starting and stopping of a motor.

  7. 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.

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

    PubMed

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

    2015-06-01

    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.

  9. 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

  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. Retrieval, alignment, and clustering of computational models based on semantic annotations

    PubMed Central

    Schulz, Marvin; Krause, Falko; Le Novère, Nicolas; Klipp, Edda; Liebermeister, Wolfram

    2011-01-01

    The exploding number of computational models produced by Systems Biologists over the last years is an invitation to structure and exploit this new wealth of information. Researchers would like to trace models relevant to specific scientific questions, to explore their biological content, to align and combine them, and to match them with experimental data. To automate these processes, it is essential to consider semantic annotations, which describe their biological meaning. As a prerequisite for a wide range of computational methods, we propose general and flexible similarity measures for Systems Biology models computed from semantic annotations. By using these measures and a large extensible ontology, we implement a platform that can retrieve, cluster, and align Systems Biology models and experimental data sets. At present, its major application is the search for relevant models in the BioModels Database, starting from initial models, data sets, or lists of biological concepts. Beyond similarity searches, the representation of models by semantic feature vectors may pave the way for visualisation, exploration, and statistical analysis of large collections of models and corresponding data. PMID:21772260

  12. 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.

  13. Aligned Silk-Based 3D Architectures for Contact Guidance in Tissue Engineering

    PubMed Central

    Oliveira, A.L.; Sun, L.; Kim, H. J.; Hu, X.; Rice, W.; Kluge, J.; Reis, R. L.; Kaplan, D. L.

    2011-01-01

    An important challenge in the biomaterials field is to mimic the structure of functional tissues via cell and extracellular matrix (ECM) alignment and anisotropy. Toward this goal, silk-based scaffolds resembling bone lamellar structure were developed using a freeze-drying technique. The structure could be controlled directly by solute concentration and freezing parameters, resulting in lamellar scaffolds with regular morphology. Different post-treatments were investigated to induce water stability, such as methanol, water annealing and steam sterilization. The resulting structures exhibited significant differences in terms of morphological integrity, structure and mechanical properties. the lamellar thicknesses were around ~2,6 μm for the methanol treated scaffolds and ~5,8 μm for water-annealed. These values are in the range of the reported for human lamellar bone. Human bone marrow-derived mesenchymal stem cells (hMSCs) were seeded on these silk fibroin lamellar scaffolds and grown under osteogenic conditions to assess the effect of the microstructure on cell behaviour. Collagen in the newly deposited ECM, was found aligned along the lamellar architectures. In the case of methanol treated lamellar structures the hMSCs were able to migrate into the interior of the scaffolds producing a multilamellar hybrid construct. The present morphology constitutes a useful pattern onto which hMSCs cells attach and proliferate for guided formation of a highly oriented extracellular matrix. PMID:22202909

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

    PubMed

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

    2000-11-01

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

  16. 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.

  17. Optical Performance Evaluation and Aligning Method for Solid Immersion Lens Assembly with Wedge Plate Lateral Shearing Interferometer

    NASA Astrophysics Data System (ADS)

    Lee, Jin-Eui; Kim, Wan-Chin; Kim, Tae-Seob; Choi, Hyun; Yoon, Yong-Joong; Park, No-Cheol; Park, Young-Pil

    2007-08-01

    We present a simple and stable optical performance evaluation and aligning method for a solid immersion lens (SIL) assembly with a wedge plate lateral shearing interferometer (LSI). There are many advantages in the use of the wedge plate LSI compared with a current SIL measurement method using a Twyman-Green interferometer. We designed the thicknesses, wedge angles, materials, and reflectances of the first and second surfaces of the wedge plate to be 1 mm, 0.02°, fused silica and 21, and 30%, respectively. Simulation and experimental results are well matched in quantitative analyses at shear ratios of 10, 40, and 70%. On the basis of simulation results for an aberrated SIL assembly with many misaligned cases, we suggested the use of the aligning process with the wedge plate LSI.

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

    NASA Astrophysics Data System (ADS)

    Gajek, A.; Strzępek, P.

    2016-09-01

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

  19. 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.

  20. Protein Sequence Alignment Taking the Structure of Peptide Bond

    NASA Astrophysics Data System (ADS)

    Hara, Toshihide; Sato, Keiko; Ohya, Masanori

    2013-01-01

    In a previous paper1 we proposed a new method for performing pairwise alignment of protein sequences. The method, called MTRAP, achieves the highest performance compared with other alignment methods such as ClustalW22,3 on two benchmarks for alignment accuracy. In this paper, we introduce a new measure between two amino acids based on the formation of peptide bonds. The measure is implemented into MTRAP software to further improve alignment accuracy. Our alignment software is available at

  1. Fast growth of well-aligned ZnO nanowire arrays by a microwave heating method and their photocatalytic properties.

    PubMed

    Cao, Guangxia; Hong, Kunquan; Wang, Wenda; Liu, Liqing; Xu, Mingxiang

    2016-10-28

    The fast growth of aligned ZnO nanowire arrays with optimized structure is attractive for electrical and optical devices. In this paper, we report a controllable and rapid growth of ZnO nanowire arrays by a microwave-assisted hydrothermal method. When using different zinc salts as the precursors, the morphology of the samples changes a lot and the length growth rate is several times different. The growth mechanism is also investigated. It is found that the solution near neutral pH value is ideal for fast nanowire growth, in which the length of the nanowires increases linearly with growth time and the growth rate is over ten times faster than that in the traditional hydrothermal method. Therefore, aligned ZnO nanowire arrays can grow up to tens of microns in a few hours, while the density and sizes of these nanowires can be well controlled. The ZnO nanowire arrays used as photocatalysts present good photocatalytic performance to the degradation of methyl orange (MO) due to the large surface area. So this paper provides an effective method to obtain vertically aligned ZnO nanowire arrays for practical applications.

  2. Fast growth of well-aligned ZnO nanowire arrays by a microwave heating method and their photocatalytic properties

    NASA Astrophysics Data System (ADS)

    Cao, Guangxia; Hong, Kunquan; Wang, Wenda; Liu, Liqing; Xu, Mingxiang

    2016-10-01

    The fast growth of aligned ZnO nanowire arrays with optimized structure is attractive for electrical and optical devices. In this paper, we report a controllable and rapid growth of ZnO nanowire arrays by a microwave-assisted hydrothermal method. When using different zinc salts as the precursors, the morphology of the samples changes a lot and the length growth rate is several times different. The growth mechanism is also investigated. It is found that the solution near neutral pH value is ideal for fast nanowire growth, in which the length of the nanowires increases linearly with growth time and the growth rate is over ten times faster than that in the traditional hydrothermal method. Therefore, aligned ZnO nanowire arrays can grow up to tens of microns in a few hours, while the density and sizes of these nanowires can be well controlled. The ZnO nanowire arrays used as photocatalysts present good photocatalytic performance to the degradation of methyl orange (MO) due to the large surface area. So this paper provides an effective method to obtain vertically aligned ZnO nanowire arrays for practical applications.

  3. 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

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

    PubMed

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

    2014-02-01

    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.

  5. 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.

  6. 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).

  7. Alignment-free phylogenetics and population genetics.

    PubMed

    Haubold, Bernhard

    2014-05-01

    Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on comparative data, today usually DNA sequences. These have become so plentiful that alignment-free sequence comparison is of growing importance in the race between scientists and sequencing machines. In phylogenetics, efficient distance computation is the major contribution of alignment-free methods. A distance measure should reflect the number of substitutions per site, which underlies classical alignment-based phylogeny reconstruction. Alignment-free distance measures are either based on word counts or on match lengths, and I apply examples of both approaches to simulated and real data to assess their accuracy and efficiency. While phylogeny reconstruction is based on the number of substitutions, in population genetics, the distribution of mutations along a sequence is also considered. This distribution can be explored by match lengths, thus opening the prospect of alignment-free population genomics.

  8. Highly sensitive microfluidic flow sensor based on aligned piezoelectric poly(vinylidene fluoride-trifluoroethylene) nanofibers

    NASA Astrophysics Data System (ADS)

    Zhang, Lingling; Yu, Xiaolei; You, Sujian; Liu, Huiqin; Zhang, Cancan; Cai, Bo; Xiao, Liang; Liu, Wei; Guo, Shishang; Zhao, Xingzhong

    2015-12-01

    A microfluidic flow sensor based on aligned piezoelectric poly(vinylidene fluoride-trifluoroethylene) [P(VDF-TrFE)] nanofibers has been developed. The flow sensor is able to linearly measure low flow rates ranging from 13 μl/h to 301 μl/h with a sensitivity of 0.36 mV per 1 μl/h, and the highest voltage difference of 120 mV at a flow rate of 451 μl/h. Moreover, the viscosity of the ethylene glycol aqueous solution ranging from 1 mPa.s to 16.1 mPa.s at 25 °C can be detected in dynamic flow with a stable output. These findings highlight the potential of piezoelectric P(VDF-TrFE) nanofibers in multiferroic applications.

  9. 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.

  10. 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.

  11. Real-time observation of dynamic floor motion of the KEKB injector linac with a laser-based alignment system

    NASA Astrophysics Data System (ADS)

    Suwada, T.; Enomoto, Y.; Kakihara, K.; Mikawa, K.; Higo, T.

    2017-03-01

    A new remote-controllable sensing system for a laser-based alignment system is in development to measure slow dynamic displacements of the tunnel floor in real time at the KEKB injector linac. Although the injector linac had initially been aligned with a laser-based alignment system, we have found that, based on recent real-time observations, the transverse displacements of the tunnel floor to the laser axis caused by dynamic ground motion are not negligibly small compared with the required alignment tolerance, in terms of the straightness of the beam line. Based on spatial and temporal cross-correlation analyses performed using displacement vectors from data recorded during a nearly eight-month period, it was found that the tunnel floor moves coherently in space and time domains over the entire length of the linac on average over long periods of time, while the cross-correlation function varies irregularly and complexly over shorter periods of time. This report describes in detail the basic design, experimental results, and present status of the new remote-sensing system for real-time alignment observations at the KEKB injector linac.

  12. A method to align the coordinate system of accelerometers to the axes of a human body: The depitch algorithm.

    PubMed

    Gietzelt, Matthias; Schnabel, Stephan; Wolf, Klaus-Hendrik; Büsching, Felix; Song, Bianying; Rust, Stefan; Marschollek, Michael

    2012-05-01

    One of the key problems in accelerometry based gait analyses is that it may not be possible to attach an accelerometer to the lower trunk so that its axes are perfectly aligned to the axes of the subject. In this paper we will present an algorithm that was designed to virtually align the axes of the accelerometer to the axes of the subject during walking sections. This algorithm is based on a physically reasonable approach and built for measurements in unsupervised settings, where the test persons are applying the sensors by themselves. For evaluation purposes we conducted a study with 6 healthy subjects and measured their gait with a manually aligned and a skewed accelerometer attached to the subject's lower trunk. After applying the algorithm the intra-axis correlation of both sensors was on average 0.89±0.1 with a mean absolute error of 0.05g. We concluded that the algorithm was able to adjust the skewed sensor node virtually to the coordinate system of the subject.

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

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

    PubMed

    Nair, Pradeep S; John, Eugene B

    2007-01-01

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

  15. 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

  16. 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.

  17. 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

  18. Pulse-to-pulse alignment based on interference fringes and the second-order temporal coherence function of optical frequency combs for distance measurement.

    PubMed

    Zhu, Jigui; Cui, Pengfei; Guo, Yin; Yang, Linghui; Lin, Jiarui

    2015-05-18

    A pulse-to-pulse alignment method based on interference fringes and the second-order temporal coherence function of optical frequency combs is proposed for absolute distance measurement. The second-order temporal coherence function of the pulse train emitted from optical frequency combs is studied. A numerical model of the function is developed with an assumption of Gaussian pulse and has good agreement with experimental measurements taken by an ordinary Michelson interferometer. The experimental results show an improvement of standard deviation of peak finding results from 27.3 nm to 8.5 nm by the method in ordinary laboratory conditions. The absolute distance measurement with the pulse-to-pulse alignment method is also proposed and experimentally proved.

  19. 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…

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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.…

  5. 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.

  6. Design and reinforcement: vertically aligned carbon nanotube-based sandwich composites.

    PubMed

    Zeng, You; Ci, Lijie; Carey, Brent J; Vajtai, Robert; Ajayan, Pulickel M

    2010-11-23

    Carbon nanotube (CNT) reinforcement of polymer composites has not yielded optimum results in that the composite properties are typically compromised by poor dispersion and random orientation of CNTs in polymers. Given the short lengths available for nanotubes, opportunities lie in incorporating CNTs with other structural reinforcements such as carbon fibers (CFs) to achieve improvement over existing composite designs. Growth of vertically aligned CNTs (VACNTs) offers new avenues for designing high-performance composites by integrating CFs and nanotubes into layered 3D architectures. To obtain composites with high rigidity and damping, we have designed and fabricated VACNT-based sandwich composites from simply stacking the freestanding VACNTs and CF fabrics and infiltrating with epoxy matrix. Comparing with the CF/epoxy laminates, the VACNT-based sandwich composites exhibit higher flexural rigidity and damping, which is achieved due to the effective integration of the VACNTs as an interfacial layer between the CF stacks. Furthermore, the lighter weight of these VACNT-based sandwich composites offers advantages in aerospace and transportation applications.

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

    NASA Astrophysics Data System (ADS)

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

    2013-02-01

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

  8. A novel partial sequence alignment tool for finding large deletions.

    PubMed

    Aruk, Taner; Ustek, Duran; Kursun, Olcay

    2012-01-01

    Finding large deletions in genome sequences has become increasingly more useful in bioinformatics, such as in clinical research and diagnosis. Although there are a number of publically available next generation sequencing mapping and sequence alignment programs, these software packages do not correctly align fragments containing deletions larger than one kb. We present a fast alignment software package, BinaryPartialAlign, that can be used by wet lab scientists to find long structural variations in their experiments. For BinaryPartialAlign, we make use of the Smith-Waterman (SW) algorithm with a binary-search-based approach for alignment with large gaps that we called partial alignment. BinaryPartialAlign implementation is compared with other straight-forward applications of SW. Simulation results on mtDNA fragments demonstrate the effectiveness (runtime and accuracy) of the proposed method.

  9. 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.

  10. SQUARE--determining reliable regions in sequence alignments.

    PubMed

    Tress, Michael L; Graña, Osvaldo; Valencia, Alfonso

    2004-04-12

    The Server for Quick Alignment Reliability Evaluation (SQUARE) is a Web-based version of the method we developed to predict regions of reliably aligned residues in sequence alignments. Given an alignment between a query sequence and a sequence of known structure, SQUARE is able to predict which residues are reliably aligned. The server accesses a database of profiles of sequences of known three-dimensional structures in order to calculate the scores for each residue in the alignment. SQUARE produces a graphical output of the residue profile-derived alignment scores along with an indication of the reliability of the alignment. In addition, the scores can be compared against template secondary structure, conserved residues and important sites.

  11. 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

  12. Simulation of water impregnation through vertically aligned CNT forests using a molecular dynamics method

    NASA Astrophysics Data System (ADS)

    Tajiri, Tomohiro; Matsuzaki, Ryosuke; Shimamura, Yoshinobu

    2016-08-01

    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.

  13. 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

  14. Simulation of water impregnation through vertically aligned CNT forests using a molecular dynamics method.

    PubMed

    Tajiri, Tomohiro; Matsuzaki, Ryosuke; Shimamura, Yoshinobu

    2016-08-26

    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.

  15. 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.

  16. Assembly, Alignment, And Cold Focus Test Methods Utilized On Claes Optics

    NASA Astrophysics Data System (ADS)

    Dawson, Juan C.; Kauer, John F.; Reilly, Charles M.; Steakley, Bruce C.

    1988-04-01

    The CLAES Telescope and Spectrometer were aligned as separate units. The optical interface between the two units is at the intermediate Lyot stop, where close angular and centering tolerances are required, with control by the use of matched machined tooling. In the alignme-L. of the Spectrometer, all optical components were centered to the chief ray using centering targets to align the optical components. The initial assembly was made at room temperature, and tested at 20K. One key reason for this testing is that the refractive indices for ZnS and ZnSe are not known below 90K, and therefore the exact location of the image plane is not known. The tests at 20K established the location of the image plane. A beam of collimated carbon-dioxide laser power illuminates the cryogenically cooled Spectrometer or the CLAES Instrument along the optical axis. The collimation of the beam is adjustable in small increments; the beam is scanned over the edges of the individual detectors creating edge scans that were used to determine where the image plane is located. Given the offset from exact collimation of the input beam, the corrections required to locate the image at the detector plane are computed. To determine "best focus", the inverse of the slopes of the edge-traces are plotted. Data obtained on both sides of best focus is plotted; the curves look like parabolas with upward arms. The minimum of this curve is defined as the location of the image plane. Shims that compensate for the focus errors are cut to the correct thickness, and installed. In addition to setting focus, the cryogenic tests were used to determine stability of the optics over the specified environment, and blur size measurements were performed at operational temperatures.

  17. A novel method of aligning molecules by local surface shape similarity.

    PubMed

    Cosgrove, D A; Bayada, D M; Johnson, A P

    2000-08-01

    A novel shape-based method has been developed for overlaying a series of molecule surfaces into a common reference frame. The surfaces are represented by a set of circular patches of approximately constant curvature. Two molecules are overlaid using a clique-detection algorithm to find a set of patches in the two surfaces that correspond, and overlaying the molecules so that the similar patches on the two surfaces are coincident. The method is thus able to detect areas of local, rather than global, similarity. A consensus overlay for a group of molecules is performed by examining the scores of all pairwise overlays and performing a set of overlays with the highest scores. The utility of the method has been examined by comparing the overlaid and experimental configurations of 4 sets of molecules for which there are X-ray crystal structures of the molecules bound to a protein active site. Results for the overlays are generally encouraging. Of particular note is the correct prediction of the 'reverse orientation' for ligands binding to human rhinovirus coat protein HRV14.

  18. A novel method of aligning molecules by local surface shape similarity

    NASA Astrophysics Data System (ADS)

    Cosgrove, D. A.; Bayada, D. M.; Johnson, A. P.

    2000-08-01

    A novel shape-based method has been developed for overlaying a series of molecule surfaces into a common reference frame. The surfaces are represented by a set of circular patches of approximately constant curvature. Two molecules are overlaid using a clique-detection algorithm to find a set of patches in the two surfaces that correspond, and overlaying the molecules so that the similar patches on the two surfaces are coincident. The method is thus able to detect areas of local, rather than global, similarity. A consensus overlay for a group of molecules is performed by examining the scores of all pairwise overlays and performing a set of overlays with the highest scores. The utility of the method has been examined by comparing the overlaid and experimental configurations of 4 sets of molecules for which there are X-ray crystal structures of the molecules bound to a protein active site. Results for the overlays are generally encouraging. Of particular note is the correct prediction of the `reverse orientation' for ligands binding to human rhinovirus coat protein HRV14.

  19. 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

  20. 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.; Eichhorn, William L.; Gum, Jeffrey S.; Hadjimichael, Theodore J.; Hagopian, John G.; Hayden, Joseph E.; Hetherington, Samuel E.; Kubalak, David A.; McLean, Kyle F.; McMann, Joseph; Redman, Kevin W.; Sampler, Henry P.; Wenzel, Greg W.; Young, Jerrod L.

    2016-01-01

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

  1. 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.

  2. 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.

  3. Fine optical alignment correction of astronomical spectrographs via in-situ full-field moment-based wavefront sensing

    NASA Astrophysics Data System (ADS)

    Lee, Hanshin; Hill, Gary J.; Tuttle, Sarah E.; Vattiat, Brian L.

    2012-09-01

    The image moment-based wavefront sensing (IWFS) utilizes moments of focus-modulated focal plane images to determine modal wavefront aberrations. This permits fast, easy, and accurate measurement of wavefront error (WFE) on any available finite-sized isolated targets across the entire focal plane (FP) of an imaging system, thereby allowing not only in-situ full-field image quality assessment, but also deterministic fine alignment correction of the imaging system. We present an experimental demonstration where fine alignment correction of a fast camera system in a fiber-fed astronomical spectrograph, called VIRUS, is accomplished by using IWFS.

  4. 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).

  5. Thermoplastic-based conductive composites containing multi-wall carbon nanotubes aligned under the application of external electric fields

    NASA Astrophysics Data System (ADS)

    Osazuwa, Osayuki

    The objective of this thesis is to prepare thermoplastic/multi-wall carbon nanotubes (MWCNTs) and to apply external alternating current (AC) electric fields to achieve enhanced conductivity and dielectric properties. The first part of the thesis focuses on preparing polyolefin-based composites containing welldispersed MWCNTs. MWCNTs are functionalized with a hyperbranched polyethylene (HBPE) using a non-covalent, non-specific functionalization approach and melt compounded with an ethylene-octene copolymer (EOC) matrix. The improved filler dispersion in the functionalized EOC/MWCNT composite results in higher elongation at break compared to the non-functionalized composite. However, the electrical percolation threshold and the ultimate conductivity of the composites are not affected considerably, suggesting that this functionalization approach leaves the inherent properties of the nanotubes intact. EOC/HBPE-functionalized MWCNT composites are further subjected to external AC electric fields (35 -- 212 kV/m), which induce the formation of aligned columnar structures, as evidenced by Scanning Electron Microscopy. Experimentally acquired resistivity data are used to derive correlations between the characteristic insulator-to-conductor transition times of the composites and the electric field strength (E), polymer viscosity (eta) and MWCNT volume fraction (φ). A criterion for the selection of (eta, E, φ) conditions that enable MWCNT assembly under an electric field controlled regime (minimal Brownian motion-driven aggregation effects) is developed. The dielectric properties of the solidified aligned EOC/MWCNT composites are further studied using dielectric spectroscopy. Annealing of the composites at 160 °C results in the formation of interconnected structures, whereas electrification, using AC field of 71 and 212 kV/m induces the formation of aligned columnar structures. The electrified and annealed composites have increased real and imaginary permittivity compared

  6. 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.

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

    PubMed Central

    Zheng, Qi; Grice, Elizabeth A.

    2016-01-01

    Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present. Here we developed a generalized software toolkit "AlignerBoost", which utilizes a Bayesian-based framework to accurately estimate mapping quality of ambiguously mapped NGS reads. We tested AlignerBoost with both simulated and real DNA-seq and RNA-seq datasets at various thresholds. In most cases, but especially for reads falling within repetitive regions, AlignerBoost dramatically increases the mapping precision of modern NGS aligners without significantly compromising the sensitivity even without mapping quality filters. When using higher mapping quality cutoffs, AlignerBoost achieves a much lower false mapping rate while exhibiting comparable or higher sensitivity compared to the aligner default modes, therefore significantly boosting the detection power of NGS aligners even using extreme thresholds. AlignerBoost is also SNP-aware, and higher quality alignments can be achieved if provided with known SNPs. AlignerBoost’s algorithm is computationally efficient, and can process one million alignments within 30 seconds on a typical desktop computer. AlignerBoost is implemented as a uniform Java application and is freely available at https://github.com/Grice-Lab/AlignerBoost. PMID:27706155

  8. Impact of Self-Aligned Metal Capping Method on Submicron Copper Interconnections

    NASA Astrophysics Data System (ADS)

    Saito, Tatsuyuki; Noguchi, Junji; Kubo, Maki; Imai, Toshinori; Ito, Yuko

    2004-05-01

    Novel copper (Cu) interconnection technology using self-aligned metallic cap was developed to reduce effective dielectric constant (k-value) as well as to improve reliability. Tungsten (W) was preferentially deposited on Cu wiring by chemical vapor deposition (CVD) using tungsten hexa-fluoride (WF6) and hydrogen (H2). Though W selectivity loss occurred without additional cleaning because of Cu contamination on the dielectric film during the chemical mechanical polishing (CMP) process, this problem was solved by surface cleaning prior to W-CVD combined with lift-off process just after it, resulting in improved yield in the test element group (TEG) during a short check. Using these processes, we fabricated a large-scale integration (LSI) with 4-level Cu interconnections eliminating capping barrier dielectrics such as silicon nitride (SiN), which had a relatively high k-value, and confirmed that there was no degradation in LSI yield. We also confirmed effective k-value was reduced by comparing propagation delay in conventional and metal-capped interconnections.

  9. 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.

  10. 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.

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

    PubMed

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

    2012-09-01

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

  12. 3D QSAR models built on structure-based alignments of Abl tyrosine kinase inhibitors.

    PubMed

    Falchi, Federico; Manetti, Fabrizio; Carraro, Fabio; Naldini, Antonella; Maga, Giovanni; Crespan, Emmanuele; Schenone, Silvia; Bruno, Olga; Brullo, Chiara; Botta, Maurizio

    2009-06-01

    Quality QSAR: A combination of docking calculations and a statistical approach toward Abl inhibitors resulted in a 3D QSAR model, the analysis of which led to the identification of ligand portions important for affinity. New compounds designed on the basis of the model were found to have very good affinity for the target, providing further validation of the model itself.The X-ray crystallographic coordinates of the Abl tyrosine kinase domain in its active, inactive, and Src-like inactive conformations were used as targets to simulate the binding mode of a large series of pyrazolo[3,4-d]pyrimidines (known Abl inhibitors) by means of GOLD software. Receptor-based alignments provided by molecular docking calculations were submitted to a GRID-GOLPE protocol to generate 3D QSAR models. Analysis of the results showed that the models based on the inactive and Src-like inactive conformations had very poor statistical parameters, whereas the sole model based on the active conformation of Abl was characterized by significant internal and external predictive ability. Subsequent analysis of GOLPE PLS pseudo-coefficient contour plots of this model gave us a better understanding of the relationships between structure and affinity, providing suggestions for the next optimization process. On the basis of these results, new compounds were designed according to the hydrophobic and hydrogen bond donor and acceptor contours, and were found to have improved enzymatic and cellular activity with respect to parent compounds. Additional biological assays confirmed the important role of the selected compounds as inhibitors of cell proliferation in leukemia cells.

  13. 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.

  14. Tidal alignment of galaxies

    SciTech Connect

    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.

  15. Tidal alignment of galaxies

    SciTech Connect

    Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš E-mail: zvlah@stanford.edu

    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.

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

    NASA Astrophysics Data System (ADS)

    Cox, Marie E.; Dunand, David C.

    2013-07-01

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

  17. 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

  18. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  20. 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.

  1. 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…

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

    PubMed Central

    2011-01-01

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

  3. [100] or [110] aligned, semiconductor-based, large-area, flexible, electronic devices

    DOEpatents

    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.

  4. MP-Align: alignment of metabolic pathways

    PubMed Central

    2014-01-01

    Background Comparing the metabolic pathways of different species is useful for understanding metabolic functions and can help in studying diseases and engineering drugs. Several comparison techniques for metabolic pathways have been introduced in the literature as a first attempt in this direction. The approaches are based on some simplified representation of metabolic pathways and on a related definition of a similarity score (or distance measure) between two pathways. More recent comparative research focuses on alignment techniques that can identify similar parts between pathways. Results We propose a methodology for the pairwise comparison and alignment of metabolic pathways that aims at providing the largest conserved substructure of the pathways under consideration. The proposed methodology has been implemented in a tool called MP-Align, which has been used to perform several validation tests. The results showed that our similarity score makes it possible to discriminate between different domains and to reconstruct a meaningful phylogeny from metabolic data. The results further demonstrate that our alignment algorithm correctly identifies subpathways sharing a common biological function. Conclusion The results of the validation tests performed with MP-Align are encouraging. A comparison with another proposal in the literature showed that our alignment algorithm is particularly well-suited to finding the largest conserved subpathway of the pathways under examination. PMID:24886436

  5. 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

  6. 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.

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

    PubMed

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

    2017-01-01

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

  8. 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

  9. Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach

    PubMed Central

    Elemento, Olivier; Tavazoie, Saeed

    2005-01-01

    We describe a powerful new approach for discovering globally conserved regulatory elements between two genomes. The method is fast, simple and comprehensive, without requiring alignments. Its application to pairs of yeasts, worms, flies and mammals yields a large number of known and novel putative regulatory elements. Many of these are validated by independent biological observations, have spatial and/or orientation biases, are co-conserved with other elements and show surprising conservation across large phylogenetic distances. PMID:15693947

  10. High-Performance Ttransparent and Stretchable All-Solid Supercapacitors Based on Highly Aligned Carbon Nanotube Sheets

    DTIC Science & Technology

    2014-01-09

    the cured piece. A gel containing poly(vinyl alcohol) powder (10 g) and H3PO4 (10 g) in water (100 mL) was used as the solid electrolyte . The gel...High-performance transparent and stretchable all- solid supercapacitors based on highly aligned carbon nanotube sheets Tao Chen1, Huisheng Peng2...stretchable all- solid supercapacitors with a good stability were developed. A transmittance up to 75% at the wavelength of 550 nmwas achieved for a

  11. 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.

  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. DISCO: Distance and Spectrum Correlation Optimization Alignment for Two Dimensional Gas Chromatography Time-of-Flight Mass Spectrometry-based Metabolomics

    PubMed Central

    Wang, Bing; Fang, Aiqin; Heim, John; Bogdanov, Bogdan; Pugh, Scott; Libardoni, Mark; Zhang, Xiang

    2010-01-01

    A novel peak alignment algorithm using a distance and spectrum correlation optimization (DISCO) method has been developed for two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC/TOF-MS) based metabolomics. This algorithm uses the output of the instrument control software, ChromaTOF, as its input data. It detects and merges multiple peak entries of the same metabolite into one peak entry in each input peak list. After a z-score transformation of metabolite retention times, DISCO selects landmark peaks from all samples based on both two-dimensional retention times and mass spectrum similarity of fragment ions measured by Pearson’s correlation coefficient. A local linear fitting method is employed in the original two-dimensional retention time space to correct retention time shifts. A progressive retention time map searching method is used to align metabolite peaks in all samples together based on optimization of the Euclidean distance and mass spectrum similarity. The effectiveness of the DISCO algorithm is demonstrated using data sets acquired under different experiment conditions and a spiked-in experiment. PMID:20476746

  14. Common Core State Standards for Mathematics: How Well Do the Textbook and Instructional Methods Align?

    ERIC Educational Resources Information Center

    Rawding, Denise M.

    2016-01-01

    The Common Core Math Standards were written to address concerns that the math curriculum in the United States was not focused and coherent. Based on national and international assessments, the United States math scores have remained stagnant, while other countries have seen significant growth in their scores. This study, designed as an action…

  15. Method of Making Self-Aligned GAAS/ALGAAS FET’s.

    DTIC Science & Technology

    having a predetermined crystalline structure is obtained having a heavily doped top GaAs layer, having a heavily doped AlGaAs layer under the top layer...recess is wider at the base of the recess than at the top of the recess because of the predetermined crystalline structure and the orientation-dependent

  16. 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

  17. 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…

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

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

    SciTech Connect

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

    2016-04-01

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

  6. 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…

  7. Beam-Based Alignment of the NLC Main Linac, Part One: Single-Bunch Comparative Study of Three Algorithms(LCC-0013)

    SciTech Connect

    Tenenbaum, P

    2004-04-20

    We describe the results of a series of simulation studies of beam-based alignment of the NLC main linacs using the program LIAR. Three algorithms for alignment of quadrupoles and girders are considered: the algorithm used in the ZDR, the ZDR algorithm combined with a post-alignment MICADO operation, and an algorithm which requires no steering dipoles but requires twice as many alignment segments per linac as the ZDR algorithm. The third algorithm appears to be the most robust, based on convergence time, required quad mover step sizes, and variation in extracted beam emittance as a function of BNS profile. We also study the effect of structure BPM resolution and ATL misalignments during the alignment process.

  8. 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.

  9. Chemical solution deposition method of fabricating highly aligned MgO templates

    DOEpatents

    Paranthaman, Mariappan Parans [Knoxville, TN; Sathyamurthy, Srivatsan [Knoxville, TN; Aytug, Tolga [Knoxville, TN; Arendt, Paul N [Los Alamos, NM; Stan, Liliana [Los Alamos, NM; Foltyn, Stephen R [Los Alamos, NM

    2012-01-03

    A superconducting article includes a substrate having an untextured metal surface; an untextured barrier layer of La.sub.2Zr.sub.2O.sub.7 or Gd.sub.2Zr.sub.2O.sub.7 supported by and in contact with the surface of the substrate; a biaxially textured buffer layer supported by the untextured barrier layer; and a biaxially textured superconducting layer supported by the biaxially textured buffer layer. Moreover, a method of forming a buffer layer on a metal substrate includes the steps of: providing a substrate having an untextured metal surface; coating the surface of the substrate with a barrier layer precursor; converting the precursor to an untextured barrier layer; and depositing a biaxially textured buffer layer above and supported by the untextured barrier layer.

  10. 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.

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

    PubMed

    Afridi, Muhammad Ishaq

    2013-01-01

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

  12. Sequence alignments and pair hidden Markov models using evolutionary history.

    PubMed

    Knudsen, Bjarne; Miyamoto, Michael M

    2003-10-17

    This work presents a novel pairwise statistical alignment method based on an explicit evolutionary model of insertions and deletions (indels). Indel events of any length are possible according to a geometric distribution. The geometric distribution parameter, the indel rate, and the evolutionary time are all maximum likelihood estimated from the sequences being aligned. Probability calculations are done using a pair hidden Markov model (HMM) with transition probabilities calculated from the indel parameters. Equations for the transition probabilities make the pair HMM closely approximate the specified indel model. The method provides an optimal alignment, its likelihood, the likelihood of all possible alignments, and the reliability of individual alignment regions. Human alpha and beta-hemoglobin sequences are aligned, as an illustration of the potential utility of this pair HMM approach.

  13. An optimized and low-cost FPGA-based DNA sequence alignment--a step towards personal genomics.

    PubMed

    Shah, Hurmat Ali; Hasan, Laiq; Ahmad, Nasir

    2013-01-01

    DNA sequence alignment is a cardinal process in computational biology but also is much expensive computationally when performing through traditional computational platforms like CPU. Of many off the shelf platforms explored for speeding up the computation process, FPGA stands as the best candidate due to its performance per dollar spent and performance per watt. These two advantages make FPGA as the most appropriate choice for realizing the aim of personal genomics. The previous implementation of DNA sequence alignment did not take into consideration the price of the device on which optimization was performed. This paper presents optimization over previous FPGA implementation that increases the overall speed-up achieved as well as the price incurred by the platform that was optimized. The optimizations are (1) The array of processing elements is made to run on change in input value and not on clock, so eliminating the need for tight clock synchronization, (2) the implementation is unrestrained by the size of the sequences to be aligned, (3) the waiting time required for the sequences to load to FPGA is reduced to the minimum possible and (4) an efficient method is devised to store the output matrix that make possible to save the diagonal elements to be used in next pass, in parallel with the computation of output matrix. Implemented on Spartan3 FPGA, this implementation achieved 20 times performance improvement in terms of CUPS over GPP implementation.

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

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

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

    PubMed

    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.

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

    PubMed Central

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

    2017-01-01

    Supercapacitors, which store electrical energy through reversible ion on the surface of conductive electrodes have gained enormous attention for variously portable energy storage devices. Since the capacitive performance is mainly determined by the structural and electrochemical properties of electrodes, the electrodes become more crucial to higher performance. However, due to the disordered microstructure and low electrochemical activity of electrode for ion tortuous migration and accumulation, the supercapacitors present relatively low capacitance and energy density. Here we report a high-performance supercapacitor based on polyaniline/vertical-aligned carbon nanotubes (PANI/VA-CNTs) nanocomposite electrodes where the vertical-aligned-structure is formed by the electrochemical-induction (0.75 V). The supercapacitor displays large specific capacitance of 403.3 F g−1, which is 6 times higher than disordered CNTs in HClO4 electrolyte. Additionally, the supercapacitor can also present high specific capacitance (314.6 F g−1), excellent cycling stability (90.2% retention after 3000 cycles at 4 A g−1) and high energy density (98.1 Wh kg−1) in EMIBF4 organic electrolyte. The key to high-performance lies in the vertical-aligned-structure providing direct path channel for ion faster diffusion and high electrochemical capacitance of polyaniline for ion more accommodation. PMID:28272474

  17. 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

  18. 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

  19. 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.

  20. 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

  1. Fabrication of aligned poly(lactic acid)-chitosan nanofibers by novel parallel blade collector method for skin tissue engineering.

    PubMed

    Shalumon, K T; Sathish, D; Nair, S V; Chennazhi, K P; Tamura, H; Jayakumar, R

    2012-06-01

    Poly(lactic acid) (PLA) was blended with chitosan (CS) to fabricate electrospun aligned PLA-CS nanofibers. These prepared nanofibers were aligned using a novel collector made of parallel blades which is designed to increase the transversal electric field across the gap. SEM images show that the fiber diameter mostly ranges between 150 +/- 60 nm and Fourier Transform infrared Spectroscopy (FTIR) analysis confirm the presence of PLA and CS. X-Ray Diffraction (XRD) studies explains the amorphous nature of electrospun PLA-CS nanofibers, suitable for faster degradation. Degradation studies confirmed that PLA-CS nanofiber has enhanced degradation than the pure PLA fibers. Cell studies with human dermal fibroblasts (HDF) show the orientation of cells along the direction of fiber alignment. The results indicate that the prepared PLA-CS aligned nanofibers are promising material for skin tissue engineering.

  2. Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints

    PubMed Central

    Dowell, Robin D; Eddy, Sean R

    2006-01-01

    Background We are interested in the problem of predicting secondary structure for small sets of homologous RNAs, by incorporating limited comparative sequence information into an RNA folding model. The Sankoff algorithm for simultaneous RNA folding and alignment is a basis for approaches to this problem. There are two open problems in applying a Sankoff algorithm: development of a good unified scoring system for alignment and folding and development of practical heuristics for dealing with the computational complexity of the algorithm. Results We use probabilistic models (pair stochastic context-free grammars, pairSCFGs) as a unifying framework for scoring pairwise alignment and folding. A constrained version of the pairSCFG structural alignment algorithm was developed which assumes knowledge of a few confidently aligned positions (pins). These pins are selected based on the posterior probabilities of a probabilistic pairwise sequence alignment. Conclusion Pairwise RNA structural alignment improves on structure prediction accuracy relative to single sequence folding. Constraining on alignment is a straightforward method of reducing the runtime and memory requirements of the algorithm. Five practical implementations of the pairwise Sankoff algorithm – this work (Consan), David Mathews' Dynalign, Ian Holmes' Stemloc, Ivo Hofacker's PMcomp, and Jan Gorodkin's FOLDALIGN – have comparable overall performance with different strengths and weaknesses. PMID:16952317

  3. 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.

  4. 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.

  5. 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.

  6. 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

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

    PubMed

    Freedman, Benjamin R; Sheehan, Frances T

    2013-03-01

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

  8. Constructing sequence alignments from a Markov decision model with estimated parameter values.

    PubMed

    Hunt, Fern Y; Kearsley, Anthony J; O'Gallagher, Agnes

    2004-01-01

    Current methods for aligning biological sequences are based on dynamic programming algorithms. If large numbers of sequences or a number of long sequences are to be aligned, the required computations are expensive in memory and central processing unit (CPU) time. In an attempt to bring the tools of large-scale linear programming (LP) methods to bear on this problem, we formulate the alignment process as a controlled Markov chain and construct a suggested alignment based on policies that minimise the expected total cost of the alignment. We discuss the LP associated with the total expected discounted cost and show the results of a solution of the problem based on a primal-dual interior point method. Model parameters, estimated from aligned sequences, along with cost function parameters are used to construct the objective and constraint conditions of the LP problem. This article concludes with a discussion of some alignments obtained from the LP solutions of problems with various cost function parameter values.

  9. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2008-07-01

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

  11. 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.

  12. Dynamic programming algorithms for comparing multineuronal spike trains via cost-based metrics and alignments.

    PubMed

    Victor, Jonathan D; Goldberg, David H; Gardner, Daniel

    2007-04-15

    Cost-based metrics formalize notions of distance, or dissimilarity, between two spike trains, and are applicable to single- and multineuronal responses. As such, these metrics have been used to characterize neural variability and neural coding. By examining the structure of an efficient algorithm [Aronov D, 2003. Fast algorithm for the metric-space analysis of simultaneous responses of multiple single neurons. J Neurosci Methods 124(2), 175-79] implementing a metric for multineuronal responses, we determine criteria for its generalization, and identify additional efficiencies that are applicable when related dissimilarity measures are computed in parallel. The generalized algorithm provides the means to test a wide range of coding hypotheses.

  13. 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.

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

    PubMed

    Soon, Villu; Saarma, Urmas

    2011-07-01

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

  15. 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.

  16. 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.

  17. DALIX: optimal DALI protein structure alignment.

    PubMed

    Wohlers, Inken; Andonov, Rumen; Klau, Gunnar W

    2013-01-01

    We present a mathematical model and exact algorithm for optimally aligning protein structures using the DALI scoring model. This scoring model is based on comparing the interresidue distance matrices of proteins and is used in the popular DALI software tool, a heuristic method for protein structure alignment. Our model and algorithm extend an integer linear programming approach that has been previously applied for the related, but simpler, contact map overlap problem. To this end, we introduce a novel type of constraint that handles negative score values and relax it in a Lagrangian fashion. The new algorithm, which we call DALIX, is applicable to any distance matrix-based scoring scheme. We also review options that allow to consider fewer pairs of interresidue distances explicitly because their large number hinders the optimization process. Using four known data sets of varying structural similarity, we compute many provably score-optimal DALI alignments. This allowed, for the first time, to evaluate the DALI heuristic in sound mathematical terms. The results indicate that DALI usually computes optimal or close to optimal alignments. However, we detect a subset of small proteins for which DALI fails to generate any significant alignment, although such alignments do exist.

  18. Cell Alignment Driven by Mechanically Induced Collagen Fiber Alignment in Collagen/Alginate Coatings

    PubMed Central

    Chaubaroux, Christophe; Perrin-Schmitt, Fabienne; Senger, Bernard; Vidal, Loïc; Voegel, Jean-Claude; Schaaf, Pierre; Haikel, Youssef; Boulmedais, Fouzia; Lavalle, Philippe

    2015-01-01

    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

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

    PubMed

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

    2013-09-01

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

  20. Metabolic network alignment in large scale by network compression.

    PubMed

    Ay, Ferhat; Dang, Michael; Kahveci, Tamer

    2012-03-21

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

  1. Investigating the structural bases of voltage-gating model channels by using perfectly aligned multilayer samples

    NASA Astrophysics Data System (ADS)

    Huang, Huey W.

    1988-09-01

    One dimensional quasi crystals of perfect multilayers, in which ion channels are uniformly oriented within parallel membranes, can be used to study the structural base of channel conductivities. We have developed 1) the techniques for preparing such multilayer samples and 2) the spectroscopic methods (circular dichroism and x-ray diffraction) for extracting structural information from these samples. The sample variables include electric field, water content, ion concentrations, etc. We have observed conformation changes of alamethicin with water content, a result in favor of the barrel model (rather than the flip-flop model) for the channel. Our goal is to probe the conformation changes of the channels as we vary the sample variables, in order to elucidate the molecular mechanisms of voltage gating.

  2. Value-Based Health Care for Chronic Care: Aligning Outcomes Measurement with the Patient Perspective

    PubMed Central

    Forsberg, Helena Hvitfeldt; Essén, Anna; Ernestam, Sofia

    2016-01-01

    Background: Value-based health care is increasingly used for developing health care services by relating patient outcomes to costs. A hierarchical value scorecard for creating outcome measurements has been suggested: the 3-tier model. The objective of this study was to test the model against the patient's view of value in a chronic care setting. Methods: Semistructured interviews with 22 persons with rheumatoid arthritis were conducted, transcribed, and analyzed using qualitative content analysis. Themes were extracted, and the model was critically applied and revised. Results: The study validates existing dimensions in the model but suggests adding information, social health, predictability, and continuity to make it more useful and representative of patients' preferences. Conclusion: Although the model aims to focus on outcomes relevant to patients, it lacks dimensions important to individuals with rheumatoid arthritis. The data illustrate difficulties in finding patients' preferred outcomes and imply tactics for arriving at meaningful measurements. PMID:27749717

  3. Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments

    PubMed Central

    2010-01-01

    generate novel alignments by using the probabilities in lieu of a scoring matrix. These alignments are typically better than the optimal sequence alignment, and include novel correct structural edges. We find that the probA alignments sample a larger variety of alignments than the Zuker set, which more frequently results in alignments that are closer to the structural alignments, but that using the probA alignments as input to the regression model does not increase performance. Conclusions The pool of suboptimal pairwise protein sequence alignments substantially overlaps structure-based alignments for pairs with statistically significant similarity, and a regression model based on information contained in this alignment pool improves the accuracy of pairwise alignments with respect to structure-based alignments. PMID:20307279

  4. 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

  5. SGP-1: Prediction and Validation of Homologous Genes Based on Sequence Alignments

    PubMed Central

    Wiehe, Thomas; Gebauer-Jung, Steffi; Mitchell-Olds, Thomas; Guigó, Roderic

    2001-01-01

    Conventional methods of gene prediction rely on the recognition of DNA-sequence signals, the coding potential or the comparison of a genomic sequence with a cDNA, EST, or protein database. Reasons for limited accuracy in many circumstances are species-specific training and the incompleteness of reference databases. Lately, comparative genome analysis has attracted increasing attention. Several analysis tools that are based on human/mouse comparisons are already available. Here, we present a program for the prediction of protein-coding genes, termed SGP-1 (Syntenic Gene Prediction), which is based on the similarity of homologous genomic sequences. In contrast to most existing tools, the accuracy of SGP-1 depends little on species-specific properties such as codon usage or the nucleotide distribution. SGP-1 may therefore be applied to nonstandard model organisms in vertebrates as well as in plants, without the need for extensive parameter training. In addition to predicting genes in large-scale genomic sequences, the program may be useful to validate gene structure annotations from databases. To this end, SGP-1 output also contains comparisons between predicted and annotated gene structures in HTML format. The program can be accessed via a Web server at http://soft.ice.mpg.de/sgp-1. The source code, written in ANSI C, is available on request from the authors. PMID:11544202

  6. Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer

    PubMed Central

    Zhang, Qian; Jun, Se-Ran; Leuze, Michael; Ussery, David; Nookaew, Intawat

    2017-01-01

    The development of rapid, economical genome sequencing has shed new light on the classification of viruses. As of October 2016, the National Center for Biotechnology Information (NCBI) database contained >2 million viral genome sequences and a reference set of ~4000 viral genome sequences that cover a wide range of known viral families. Whole-genome sequences can be used to improve viral classification and provide insight into the viral “tree of life”. However, due to the lack of evolutionary conservation amongst diverse viruses, it is not feasible to build a viral tree of life using traditional phylogenetic methods based on conserved proteins. In this study, we used an alignment-free method that uses k-mers as genomic features for a large-scale comparison of complete viral genomes available in RefSeq. To determine the optimal feature length, k (an essential step in constructing a meaningful dendrogram), we designed a comprehensive strategy that combines three approaches: (1) cumulative relative entropy, (2) average number of common features among genomes, and (3) the Shannon diversity index. This strategy was used to determine k for all 3,905 complete viral genomes in RefSeq. The resulting dendrogram shows consistency with the viral taxonomy of the ICTV and the Baltimore classification of viruses. PMID:28102365

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

    PubMed

    Vullings, R; Mischi, M

    2013-01-01

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

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

    PubMed

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

  10. Learning about and from others' prudence, impatience or laziness: The computational bases of attitude alignment

    PubMed Central

    Devaine, Marie

    2017-01-01

    Peoples' subjective attitude towards costs such as, e.g., risk, delay or effort are key determinants of inter-individual differences in goal-directed behaviour. Thus, the ability to learn about others' prudent, impatient or lazy attitudes is likely to be critical for social interactions. Conversely, how adaptive such attitudes are in a given environment is highly uncertain. Thus, the brain may be tuned to garner information about how such costs ought to be arbitrated. In particular, observing others' attitude may change one's uncertain belief about how to best behave in related difficult decision contexts. In turn, learning from others' attitudes is determined by one's ability to learn about others' attitudes. We first derive, from basic optimality principles, the computational properties of such a learning mechanism. In particular, we predict two apparent cognitive biases that would arise when individuals are learning about others’ attitudes: (i) people should overestimate the degree to which they resemble others (false-consensus bias), and (ii) they should align their own attitudes with others’ (social influence bias). We show how these two biases non-trivially interact with each other. We then validate these predictions experimentally by profiling people's attitudes both before and after guessing a series of cost-benefit arbitrages performed by calibrated artificial agents (which are impersonating human individuals). PMID:28358869

  11. Integrated routing and fill for self-aligned double patterning (SADP) using grid-based design

    NASA Astrophysics Data System (ADS)

    Song, Youngsoo; Lee, Jeemyung; Lee, Seongmin; Shin, Youngsoo

    2016-03-01

    Self-aligned double patterning (SADP) has been proposed as an alternative patterning solution for sub-10nm technology because of delay of advanced lithography beyond 193nm ArF. In conventional SADP, line and space style of dummy metal fills are inserted once main design is complete. A large buffer distance is required around the main design because no further verification of main design (in presence of fills) is performed. This causes irregular pattern density, which becomes a source of process variations. We propose integrated-fill, in which main design and dummy fill insertion are performed together. This requires a change in overall design flow, which we discuss. Integrated-fill is demonstrated in M2 layer of SADP process; M2 density increases by 15.7% with 2.3% reduction in standard deviation of density distribution; metal thickness variation is also reduced by 24%. More dummy fills cause increased coupling capacitance, which however is shown to be insignificant.

  12. Two Hybrid Algorithms for Multiple Sequence Alignment

    NASA Astrophysics Data System (ADS)

    Naznin, Farhana; Sarker, Ruhul; Essam, Daryl

    2010-01-01

    In order to design life saving drugs, such as cancer drugs, the design of Protein or DNA structures has to be accurate. These structures depend on Multiple Sequence Alignment (MSA). MSA is used to find the accurate structure of Protein and DNA sequences from existing approximately correct sequences. To overcome the overly greedy nature of the well known global progressive alignment method for multiple sequence alignment, we have proposed two different algorithms in this paper; one is using an iterative approach with a progressive alignment method (PAMIM) and the second one is using a genetic algorithm with a progressive alignment method (PAMGA). Both of our methods started with a "kmer" distance table to generate single guide-tree. In the iterative approach, we have introduced two new techniques: the first technique is to generate Guide-trees with randomly selected sequences and the second is of shuffling the sequences inside that tree. The output of the tree is a multiple sequence alignment which has been evaluated by the Sum of Pairs Method (SPM) considering the real value data from PAM250. In our second GA approach, these two techniques are used to generate an initial population and also two different approaches of genetic operators are implemented in crossovers and mutation. To test the performance of our two algorithms, we have compared these with the existing well known methods: T-Coffee, MUSCEL, MAFFT and Probcon, using BAliBase benchmarks. The experimental results show that the first algorithm works well for some situations, where other existing methods face difficulties in obtaining better solutions. The proposed second method works well compared to the existing methods for all situations and it shows better performance over the first one.

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

    PubMed

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

    2013-08-01

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

  14. 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.

  15. 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

  16. The alignment strategy of HADES

    NASA Astrophysics Data System (ADS)

    Pechenova, O.; Pechenov, V.; Galatyuk, T.; Hennino, T.; Holzmann, R.; Kornakov, G.; Markert, J.; Müntz, C.; Salabura, P.; Schmah, A.; Schwab, E.; Stroth, J.

    2015-06-01

    The global as well as intrinsic alignment of any spectrometer impacts directly on its performance and the quality of the achievable physics results. An overview of the current alignment procedure of the DiElectron Spectrometer HADES is presented with an emphasis on its main features and its accuracy. The sequence of all steps and procedures is given, including details on photogrammetric and track-based alignment.

  17. An introduction to the Lagan alignment toolkit.

    PubMed

    Brudno, Michael

    2007-01-01

    The Lagan Toolkit is a software package for comparison of genomic sequences. It includes the CHAOS local alignment program, LAGAN global alignment program for two, or more sequences and Shuffle-LAGAN, a "glocal" alignment method that handles genomic rearrangements in a global alignment framework. The alignment programs included in the Lagan Toolkit have been widely used to compare genomes of many organisms, from bacteria to large mammalian genomes. This chapter provides an overview of the algorithms used by the LAGAN programs to construct genomic alignments, explains how to build alignments using either the standalone program or the web server, and discusses some of the common pitfalls users encounter when using the toolkit.

  18. PILOT optical alignment

    NASA Astrophysics Data System (ADS)

    Longval, Y.; Mot, B.; Ade, P.; André, Y.; Aumont, J.; Baustista, L.; Bernard, J.-Ph.; Bray, N.; de Bernardis, P.; Boulade, O.; Bousquet, F.; Bouzit, M.; Buttice, V.; Caillat, A.; Charra, M.; Chaigneau, M.; Crane, B.; Crussaire, J.-P.; Douchin, F.; Doumayrou, E.; Dubois, J.-P.; Engel, C.; Etcheto, P.; Gélot, P.; Griffin, M.; Foenard, G.; Grabarnik, S.; Hargrave, P..; Hughes, A.; Laureijs, R.; Lepennec, Y.; Leriche, B.; Maestre, S.; Maffei, B.; Martignac, J.; Marty, C.; Marty, W.; Masi, S.; Mirc, F.; Misawa, R.; Montel, J.; Montier, L.; Narbonne, J.; Nicot, J.-M.; Pajot, F.; Parot, G.; Pérot, E.; Pimentao, J.; Pisano, G.; Ponthieu, N.; Ristorcelli, I.; Rodriguez, L.; Roudil, G.; Salatino, M.; Savini, G.; Simonella, O.; Saccoccio, M.; Tapie, P.; Tauber, J.; Torre, J.-P.; Tucker, C.

    2016-07-01

    PILOT is a balloon-borne astronomy experiment designed to study the polarization of dust emission in the diffuse interstellar medium in our Galaxy at wavelengths 240 μm with an angular resolution about two arcminutes. Pilot optics is composed an off-axis Gregorian type telescope and a refractive re-imager system. All optical elements, except the primary mirror, are in a cryostat cooled to 3K. We combined the optical, 3D dimensional measurement methods and thermo-elastic modeling to perform the optical alignment. The talk describes the system analysis, the alignment procedure, and finally the performances obtained during the first flight in September 2015.

  19. 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.

  20. A MEMS-based device used for alignment and manipulation of MLL x-ray focusing optics

    NASA Astrophysics Data System (ADS)

    Xu, Weihe; Lauer, Kenneth; Yan, Hui; Millanovic, Veljko; Nazaretski, Evgeny; Brookhaven Natl Lab Team; Mirrorcle Technologies, Inc. Team

    2015-03-01

    Multilayer Laue lenses (MLLs) X-ray microscopy is a powerful tool used for materials research. To push the spatial resolution of x-ray microscopy studies below 10 nm the system needs to be compact and rigid. Applications of MEMS based tip-tilt stages used for alignment and manipulation of nanofocusing optics is a promising route to achieve high stability. In this work, we report characterization and stability testing of a MEMS device suitable for manipulation of nanofocusing optics. We developed two closed-loop circuits implemented in a MEMS tip-tilt device utilizing capacitive and laser interferometry techniques. Test results demonstrate better than 10 mille-degree resolution when using capacitive sensors and better than 0.8 mille-degree resolution when using interferometry sensing respectively.

  1. Magnetically Aligned Supramolecular Hydrogels

    PubMed Central

    Wallace, Matthew; Cardoso, Andre Zamith; Frith, William J; Iggo, Jonathan A; Adams, Dave J

    2014-01-01

    The magnetic-field-induced alignment of the fibrillar structures present in an aqueous solution of a dipeptide gelator, and the subsequent retention of this alignment upon transformation to a hydrogel upon the addition of CaCl2 or upon a reduction in solution pH is reported. Utilising the switchable nature of the magnetic field coupled with the slow diffusion of CaCl2, it is possible to precisely control the extent of anisotropy across a hydrogel, something that is generally very difficult to do using alternative methods. The approach is readily extended to other compounds that form viscous solutions at high pH. It is expected that this work will greatly expand the utility of such low-molecular-weight gelators (LMWG) in areas where alignment is key. PMID:25345918

  2. 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.

  3. 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.

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

    SciTech Connect

    Komatsoulis, G.A.; Waterman, M.S.

    1997-12-01

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

  5. 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.

  6. Vortex-aligned fullerene nanowhiskers as a scaffold for orienting cell growth.

    PubMed

    Krishnan, Venkata; Kasuya, Yuki; Ji, Qingmin; Sathish, Marappan; Shrestha, Lok Kumar; Ishihara, Shinsuke; Minami, Kosuke; Morita, Hiromi; Yamazaki, Tomohiko; Hanagata, Nobutaka; Miyazawa, Kun'ichi; Acharya, Somobrata; Nakanishi, Waka; Hill, Jonathan P; Ariga, Katsuhiko

    2015-07-22

    A versatile method for the rapid fabrication of aligned fullerene C60 nanowhiskers (C60NWs) at the air-water interface is presented. This method is based on the vortex motion of a subphase (water), which directs floating C60NWs to align on the water surface according to the direction of rotational flow. Aligned C60NWs could be transferred onto many different flat substrates, and, in this case, aligned C60NWs on glass substrates were employed as a scaffold for cell culture. Bone forming human osteoblast MG63 cells adhered well to the C60NWs, and their growth was found to be oriented with the axis of the aligned C60NWs. Cells grown on aligned C60NWs were more highly oriented with the axis of alignment than when grown on randomly oriented nanowhiskers. A study of cell proliferation on the C60NWs revealed their low toxicity, indicating their potential for use in biomedical applications.

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

    PubMed

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

    2017-01-01

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

  8. 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.

  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. Time-varying gyrocompass alignment for fiber-optic-gyro inertial navigation system with large misalignment angle

    NASA Astrophysics Data System (ADS)

    Ben, Yueyang; Li, Qian; Zhang, Yi; Huo, Liang

    2014-09-01

    Conventional strapdown gyrocompass alignment methods are based on the assumption that the fiber-optic-gyro inertial navigation system has a small azimuth misalignment angle. A large azimuth misalignment angle would lead to an extension of the alignment duration. A time-varying gyrocompass alignment method to solve this problem is provided. An appropriate parameter setting is given for the gyrocompass alignment with a large misalignment angle. Also, a proper protocol for a parametric switch is derived. Simulation and trail results show that the proposed method has better alignment performance than conventional ones, as the system has large misalignment angles.

  12. 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.

  13. Synthesis of high-density, large-diameter, and aligned single-walled carbon nanotubes by multiple-cycle growth methods.

    PubMed

    Zhou, Weiwei; Ding, Lei; Yang, Sungwoo; Liu, Jie

    2011-05-24

    A dense array of parallel single-walled carbon nanotubes (SWNTs) as the device channel can carry higher current, be more robust, and have smaller device-to-device variation, thus is more desirable for and compatible with applications in future highly integrated circuits when compared with single-tube devices. The density of the parallel SWNT arrays and the diameter of SWNTs both are key factors in the determination of the device performance. In this paper, we present a new multiple-cycle chemical vapor deposition (CVD) method to synthesize horizontally aligned arrays of SWNTs with densities of 20-40 SWNT/μm over large area and a diameter distribution of 2.4 ± 0.5 nm on the quartz surface based on a methanol/ethanol CVD method. The high nucleation efficiency of catalyst particles in multiple-cycle CVD processes has been demonstrated to be the main reason for the improvements in the density of SWNT arrays. More interestingly, we confirmed the existence of an etching effect, which strongly affects the final products in the multiple-cycle growth. This etching effect is likely the reason that only large-diameter SWNTs were obtained in the multiple-cycle CVD growth. Using these high-density and large-diameter nanotube arrays, two-terminal devices with back-gates were fabricated. The performances of these devices have been greatly improved in overall resistance and on-state current, which indicates these SWNT arrays have high potential for applications such as interconnects, high-frequency devices, and high-current transistors in future micro- or nanoelectronics.

  14. ALIGN_MTX--an optimal pairwise textual sequence alignment program, adapted for using in sequence-structure alignment.

    PubMed

    Vishnepolsky, Boris; Pirtskhalava, Malak

    2009-06-01

    The presented program ALIGN_MTX makes alignment of two textual sequences with an opportunity to use any several characters for the designation of sequence elements and arbitrary user substitution matrices. It can be used not only for the alignment of amino acid and nucleotide sequences but also for sequence-structure alignment used in threading, amino acid sequence alignment, using preliminary known PSSM matrix, and in other cases when alignment of biological or non-biological textual sequences is required. This distinguishes it from the majority of similar alignment programs that make, as a rule, alignment only of amino acid or nucleotide sequences represented as a sequence of single alphabetic characters. ALIGN_MTX is presented as downloadable zip archive at http://www.imbbp.org/software/ALIGN_MTX/ and available for free use. As application of using the program, the results of comparison of different types of substitution matrix for alignment quality in distantly related protein pair sets were presented. Threading matrix SORDIS, based on side-chain orientation in relation to hydrophobic core centers with evolutionary change-based substitution matrix BLOSUM and using multiple sequence alignment information position-specific score matrices (PSSM) were taken for test alignment accuracy. The best performance shows PSSM matrix, but in the reduced set with lower sequence similarity threading matrix SORDIS shows the same performance and it was shown that combined potential with SORDIS and PSSM can improve alignment quality in evolutionary distantly related protein pairs.

  15. Accurate multiple network alignment through context-sensitive random walk

    PubMed Central

    2015-01-01

    Background Comparative network analysis can provide an effective means of analyzing large-scale biological networks and gaining novel insights into their structure and organization. Global network alignment aims to predict the best overall mapping between a given set of biological networks, thereby identifying important similarities as well as differences among the networks. It has been shown that network alignment methods can be used to detect pathways or network modules that are conserved across different networks. Until now, a number of network alignment algorithms have been proposed based on different formulations and approaches, many of them focusing on pairwise alignment. Results In this work, we propose a novel multiple network alignment algorithm based on a context-sensitive random walk model. The random walker employed in the proposed algorithm switches between two different modes, namely, an individual walk on a single network and a simultaneous walk on two networks. The switching decision is made in a context-sensitive manner by examining the current neighborhood, which is effective for quantitatively estimating the degree of correspondence between nodes that belong to different networks, in a manner that sensibly integrates node similarity and topological similarity. The resulting node correspondence scores are then used to predict the maximum expected accuracy (MEA) alignment of the given networks. Conclusions Performance evaluation based on synthetic networks as well as real protein-protein interaction networks shows that the proposed algorithm can construct more accurate multiple network alignments compared to other leading methods. PMID:25707987

  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. Multiscale white matter fiber tract coregistration: a new feature-based approach to align diffusion tensor data.

    PubMed

    Leemans, A; Sijbers, J; De Backer, S; Vandervliet, E; Parizel, P

    2006-06-01

    In this paper an automatic multiscale feature-based rigid-body coregistration technique for diffusion tensor imaging (DTI) based on the local curvature kappa and torsion tau of the white matter (WM) fiber pathways is presented. As a similarity measure, the mean squared difference (MSD) of corresponding fiber pathways in (kappa, tau)-space is chosen. After the MSD is minimized along the arc length of the curve, principal component analysis is applied to calculate the transformation parameters. In addition, a scale-space representation of the space curves is incorporated, resulting in a multiscale robust coregistration technique. This fully automatic technique inherently allows one to apply region of interest (ROI) coregistration, and is adequate for performing both global and local transformations. Simulations were performed on synthetic DT data to evaluate the coregistration accuracy and precision. An in vivo coregistration example is presented and compared with a voxel-based coregistration approach, demonstrating the feasibility and advantages of the proposed technique to align DT data of the human brain.

  18. 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…

  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 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)…

  1. 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.

  2. 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.

  3. Determination of Energy Band Alignment in Ultrathin Hf-based Oxide/Pt System

    NASA Astrophysics Data System (ADS)

    Ohta, A.; Murakami, H.; Higashi, S.; Miyazaki, S.

    2013-03-01

    Effect of incorporating a third element into HfO2 on the electronic structures has been studied by high resolution x-ray photoelectron spectroscopy (XPS). Hf-IIIa (La, Y, Gd, and Dy) oxide and Hf-Ti oxide films were deposited on a Pt layer by metal organic chemical vapor deposition (MOCVD) and co-sputtering and followed by post-deposition annealing in O2 ambience at 500°C. The energy bandgap (Eg) of these Hf-based oxide films was determined by analyzing the energy loss spectra of O 1s photoelectrons in consideration of the overlap with Hf 4s core-line signals. From analyses of the valence band signals and the cut-off energy for photoelectrons, the valence band offset between the Hf based-oxide, and the Pt electrode and the work function value of the Pt layer were evaluated. By combining the oxide bandgap values, the valence band line-ups, and the Pt work function value, the energy band profile of the Hf-based oxide/Pt has been determined.

  4. Efficient registration of multitemporal and multisensor aerial images based on alignment of nonparametric edge features

    NASA Astrophysics Data System (ADS)

    Makrogiannis, Sokratis; Bourbakis, Nikolaos G.

    2010-01-01

    The topic of aerial image registration attracts considerable interest within the imaging research community due to its significance for several applications, including change detection, sensor fusion, and topographic mapping. Our interest is focused on finding the optimal transformation between two aerial images that depict the same visual scene in the presence of pronounced spatial, temporal, and sensor variations. We first introduce a stochastic edge estimation process suitable for geometric shape-based registration, which we also compare to intensity-based registration. Furthermore, we propose an objective function that weights the L2 distances of the edge estimates by the feature points' energy, which we denote by sum of normalized squared differences and compare to standard objective functions, such as mutual information and the sum of absolute centered differences. In the optimization stage, we employ a genetic algorithm scheme in a multiscale image representation scheme to enhance the registration accuracy and reduce the computational load. Our experimental tests, measuring registration accuracy, rate of convergence, and statistical properties of registration errors, suggest that the proposed edge-based representation and objective function in conjunction with genetic algorithm optimization are capable of addressing several forms of imaging variations and producing encouraging registration results.

  5. A Robust Method for Determining the Magnitude of the Fully Asymmetric Alignment Tensor of Oriented Macromolecules in the Absence of Structural Information

    NASA Astrophysics Data System (ADS)

    Clore, G. Marius; Gronenborn, Angela M.; Bax, Ad

    1998-07-01

    It has recently been shown that the degree of alignment of macromolecules in an aqueous dilute liquid crystalline medium of bicelles is sufficient to permit accurate values of residual15N-1H,13C-1H, and13Cα-C‧ dipolar couplings to be obtained on a routine basis, thereby providing potentially unique long-range structural information. To make use of this information in macromolecular structure determination, the magnitude of the axial and rhombic components of the molecular alignment tensor must be determined. This can be achieved by taking advantage of the fact that different, fixed-distance internuclear vector types are differently distributed relative to the alignment tensor. A histogram of the ensemble of normalized residual dipolar couplings for several such vector types approximates a powder pattern from which the magnitude of the axial and rhombic components are readily extracted in the absence of any prior structural information. The applicability of this method is demonstrated using synthetic data derived from four proteins representative of different sizes, topologies, and secondary structures, and experimental data measured on the small protein ubiquitin.

  6. Multiobjective optimization of cartilage stress for non-invasive, patient-specific recommendations of high tibial osteotomy correction angle - a novel method to investigate alignment correction.

    PubMed

    Zheng, Keke; Scholes, Corey J; Chen, Junning; Parker, David; Li, Qing

    2017-04-01

    Medial opening wedge high tibial osteotomy (MOWHTO) is a surgical procedure to treat knee osteoarthritis associated with varus deformity. However, the ideal final alignment of the Hip-Knee-Ankle (HKA) angle in the frontal plane, that maximizes procedural success and post-operative knee function, remains controversial. Therefore, the purpose of this study was to introduce a subject-specific modeling procedure in determining the biomechanical effects of MOWHTO alignment on tibiofemoral cartilage stress distribution. A 3D finite element knee model derived from magnetic resonance imaging of a healthy participant was manipulated in-silico to simulate a range of final HKA angles (i.e. 0.2°, 2.7°, 3.9° and 6.6° valgus). Loading and boundary conditions were assigned based on subject-specific kinematic and kinetic data from gait analysis. Multiobjective optimization was used to identify the final alignment that balanced compressive and shear forces between medial and lateral knee compartments. Peak stresses decreased in the medial and increased in the lateral compartment as the HKA was shifted into valgus, with balanced loading occurring at angles of 4.3° and 2.9° valgus for the femoral and tibial cartilage respectively. The concept introduced here provides a platform for non-invasive, patient-specific preoperative planning of the osteotomy for medial compartment knee osteoarthritis.

  7. 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.

  8. Laser-optic instruments improve machinery alignment

    SciTech Connect

    Bloch, H.P.

    1987-10-12

    Laser-optic alignment systems are fast becoming cost-effective devices that improve the accuracy and speed of machinery shaft alignment. Because of the difficulty, if not impossibility, of aligning operating machinery, cold alignment specifications must be determined to compensate for thermal growth so that the shaft alignment remains within tolerances when the machine reaches normal operating temperature. Some methods for accomplishing this are reviewed here. Three years' field experience with laser-optic alignment systems shows that many of these limitations can be eliminated, resulting in a more accurate alignment in less time. Some actual field alignments are given as examples of the improvement achieved by the use of laser equipment, and a procedure is given that shows how the laser-optic system may be used to determine running alignment changes caused by thermal growth.

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

    PubMed

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

    2013-01-01

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

  10. Progressive alignment of genomic signals by multiple dynamic time warping.

    PubMed

    Skutkova, Helena; Vitek, Martin; Sedlar, Karel; Provaznik, Ivo

    2015-11-21

    This paper presents the utilization of progressive alignment principle for positional adjustment of a set of genomic signals with different lengths. The new method of multiple alignment of signals based on dynamic time warping is tested for the purpose of evaluating the similarity of different length genes in phylogenetic studies. Two sets of phylogenetic markers were used to demonstrate the effectiveness of the evaluation of intraspecies and interspecies genetic variability. The part of the proposed method is modification of pairwise alignment of two signals by dynamic time warping with using correlation in a sliding window. The correlation based dynamic time warping allows more accurate alignment dependent on local homologies in sequences without the need of scoring matrix or evolutionary models, because mutual similarities of residues are included in the numerical code of signals.

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

    EPA Science Inventory

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

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

    PubMed

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

    2015-06-17

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

  13. 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

  14. Aligning graphs and finding substructures by a cavity approach

    NASA Astrophysics Data System (ADS)

    Bradde, S.; Braunstein, A.; Mahmoudi, H.; Tria, F.; Weigt, M.; Zecchina, R.

    2010-02-01

    We introduce a new distributed algorithm for aligning graphs or finding substructures within a given graph. It is based on the cavity method and is used to study the maximum-clique and the graph-alignment problems in random graphs. The algorithm allows to analyze large graphs and may find applications in fields such as computational biology. As a proof of concept we use our algorithm to align the similarity graphs of two interacting protein families involved in bacterial signal transduction, and to predict actually interacting protein partners between these families.

  15. Alignment of leading-edge and peak-picking time of arrival methods to obtain accurate source locations

    SciTech Connect

    Roussel-Dupre, R.; Symbalisty, E.; Fox, C.; and Vanderlinde, O.

    2009-08-01

    The location of a radiating source can be determined by time-tagging the arrival of the radiated signal at a network of spatially distributed sensors. The accuracy of this approach depends strongly on the particular time-tagging algorithm employed at each of the sensors. If different techniques are used across the network, then the time tags must be referenced to a common fiducial for maximum location accuracy. In this report we derive the time corrections needed to temporally align leading-edge, time-tagging techniques with peak-picking algorithms. We focus on broadband radio frequency (RF) sources, an ionospheric propagation channel, and narrowband receivers, but the final results can be generalized to apply to any source, propagation environment, and sensor. Our analytic results are checked against numerical simulations for a number of representative cases and agree with the specific leading-edge algorithm studied independently by Kim and Eng (1995) and Pongratz (2005 and 2007).

  16. Multiple sequence alignment in HTML: colored, possibly hyperlinked, compact representations.

    PubMed

    Campagne, F; Maigret, B

    1998-02-01

    Protein sequence alignments are widely used in protein structure prediction, protein engineering, modeling of proteins, etc. This type of representation is useful at different stages of scientific activity: looking at previous results, working on a research project, and presenting the results. There is a need to make it available through a network (intranet or WWW), in a way that allows biologists, chemists, and noncomputer specialists to look at the data and carry on research--possibly in a collaborative research. Previous methods (text-based, Java-based) are reported and their advantages are discussed. We have developed two novel approaches to represent the alignments as colored, hyper-linked HTML pages. The first method creates an HTML page that uses efficiently the image cache mechanism of a WWW browser, thereby allowing the user to browse different alignments without waiting for the images to be loaded through the network, but only for the first viewed alignment. The generated pages can be browsed with any HTML2.0-compliant browser. The second method that we propose uses W3C-CSS1-style sheets to render alignments. This new method generates pages that require recent browsers to be viewed. We implemented these methods in the Viseur program and made a WWW service available that allows a user to convert an MSF alignment file in HTML for WWW publishing. The latter service is available at http:@www.lctn.u-nancy.fr/viseur/services.htm l.

  17. Recursive dynamic programming for adaptive sequence and structure alignment

    SciTech Connect

    Thiele, R.; Zimmer, R.; Lengauer, T.

    1995-12-31

    We propose a new alignment procedure that is capable of aligning protein sequences and structures in a unified manner. Recursive dynamic programming (RDP) is a hierarchical method which, on each level of the hierarchy, identifies locally optimal solutions and assembles them into partial alignments of sequences and/or structures. In contrast to classical dynamic programming, RDP can also handle alignment problems that use objective functions not obeying the principle of prefix optimality, e.g. scoring schemes derived from energy potentials of mean force. For such alignment problems, RDP aims at computing solutions that are near-optimal with respect to the involved cost function and biologically meaningful at the same time. Towards this goal, RDP maintains a dynamic balance between different factors governing alignment fitness such as evolutionary relationships and structural preferences. As in the RDP method gaps are not scored explicitly, the problematic assignment of gap cost parameters is circumvented. In order to evaluate the RDP approach we analyse whether known and accepted multiple alignments based on structural information can be reproduced with the RDP method.

  18. Multiple protein structure alignment.

    PubMed Central

    Taylor, W. R.; Flores, T. P.; Orengo, C. A.

    1994-01-01

    A method was developed to compare protein structures and to combine them into a multiple structure consensus. Previous methods of multiple structure comparison have only concatenated pairwise alignments or produced a consensus structure by averaging coordinate sets. The current method is a fusion of the fast structure comparison program SSAP and the multiple sequence alignment program MULTAL. As in MULTAL, structures are progressively combined, producing intermediate consensus structures that are compared directly to each other and all remaining single structures. This leads to a hierarchic "condensation," continually evaluated in the light of the emerging conserved core regions. Following the SSAP approach, all interatomic vectors were retained with well-conserved regions distinguished by coherent vector bundles (the structural equivalent of a conserved sequence position). Each bundle of vectors is summarized by a resultant, whereas vector coherence is captured in an error term, which is the only distinction between conserved and variable positions. Resultant vectors are used directly in the comparison, which is weighted by their error values, giving greater importance to the matching of conserved positions. The resultant vectors and their errors can also be used directly in molecular modeling. Applications of the method were assessed by the quality of the resulting sequence alignments, phylogenetic tree construction, and databank scanning with the consensus. Visual assessment of the structural superpositions and consensus structure for various well-characterized families confirmed that the consensus had identified a reasonable core. PMID:7849601

  19. Progressive multiple sequence alignments from triplets

    PubMed Central

    Kruspe, Matthias; Stadler, Peter F

    2007-01-01

    Background The quality of progressive sequence alignments strongly depends on the accuracy of the individual pairwise alignment steps since gaps that are introduced at one step cannot be removed at later aggregation steps. Adjacent insertions and deletions necessarily appear in arbitrary order in pairwise alignments and hence form an unavoidable source of errors. Research Here we present a modified variant of progressive sequence alignments that addresses both issues. Instead of pairwise alignments we use exact dynamic programming to align sequence or profile triples. This avoids a large fractions of the ambiguities arising in pairwise alignments. In the subsequent aggregation steps we follow the logic of the Neighbor-Net algorithm, which constructs a phylogenetic network by step-wisely replacing triples by pairs instead of combining pairs to singletons. To this end the three-way alignments are subdivided into two partial alignments, at which stage all-gap columns are naturally removed. This alleviates the "once a gap, always a gap" problem of progressive alignment procedures. Conclusion The three-way Neighbor-Net based alignment program aln3nn is shown to compare favorably on both protein sequences and nucleic acids sequences to other progressive alignment tools. In the latter case one easily can include scoring terms that consider secondary structure features. Overall, the quality of resulting alignments in general exceeds that of clustalw or other multiple alignments tools even though our software does not included heuristics for context dependent (mis)match scores. PMID:17631683

  20. Making Macroscopic Assemblies of Aligned Carbon Nanotubes

    NASA Technical Reports Server (NTRS)

    Smalley, Richard E.; Colbert, Daniel T.; Smith, Ken A.; Walters, Deron A.; Casavant, Michael J.; Qin, Xiaochuan; Yakobson, Boris; Hauge, Robert H.; Saini, Rajesh Kumar; Chiung, Wan-Ting; Huffman, Charles B.

    2005-01-01

    of the method (see figure) includes a reservoir containing SWNTs dispersed in a suspending agent (for example, dimethylformamide) and a reservoir containing a suitable solvent (for example, water mixed with a surfactant). By use of either pressurized gas supplied from upstream or suction from downstream, the suspension of SWNTs and the solvent are forced to mix and flow into a tank. A filter inside the tank contains pores small enough to prevent the passage of most SWNTs, but large enough to allow the passage of molecules of the solvent and suspending agent. The filter is oriented perpendicular to the flow path. A magnetic field parallel to the plane of the filter is applied. The success of the method is based on the tendency of SWNTs to become aligned with their longitudinal axes parallel to an applied magnetic field. The alignment energy of an SWNT increases with the length of the SWNT and the magnetic-field strength. In order to obtain an acceptably small degree of statistical deviation of SWNTs of a given length from alignment with a magnetic field, one must make the field strong enough so that the thermal energy associated with rotation of an SWNT away from alignment is less than the alignment energy.

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

    PubMed

    Zhao, Lin; Guan, Dongxue; Cheng, Jianhua; Xu, Xiaomin; Fei, Zaihui

    2016-10-15

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

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

    PubMed Central

    Zhao, Lin; Guan, Dongxue; Cheng, Jianhua; Xu, Xiaomin; Fei, Zaihui

    2016-01-01

    A ship experiences the random motion of sea waves during its travels. Hence, the coarse alignment of the marine strapdown Inertial Navigation System (INS) suffers from rocking disturbances such as pitch and roll. In this paper, a novel approach of marine coarse alignment was proposed for avoiding the resulting loss of accuracy from rocking disturbances. Unlike several current techniques, our alignment scheme is intuitional and concise. Moreover, the coarse alignment can be implemented without any external information. The gravity vector and its derivative expressed within the inertial frame can describe the attitude matrix between an inertial frame and the local geographic frame. We address the challenge of calculating the gravity derivative by the least-squares fitting of the trajectory of the gravity movement in the inertial frame. Meanwhile, the integration of angular rates measured by gyroscopes allows one to compute the attitude matrix between the inertial frame and the body frame. The coarse alignment can be thus accomplished by the combination of the above two attitude matrices. The experimental results show that the coarse alignment is effective with high accuracy and stability for demanding marine applications. PMID:27754457

  3. Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution.

    PubMed

    Jun, Se-Ran; Sims, Gregory E; Wu, Guohong A; Kim, Sung-Hou

    2010-01-05

    We present a whole-proteome phylogeny of prokaryotes constructed by comparing feature frequency profiles (FFPs) of whole proteomes. Features are l-mers of amino acids, and each organism is represented by a profile of frequencies of all features. The selection of feature length is critical in the FFP method, and we have developed a procedure for identifying the optimal feature lengths for inferring the phylogeny of prokaryotes, strictly speaking, a proteome phylogeny. Our FFP trees are constructed with whole proteomes of 884 prokaryotes, 16 unicellular eukaryotes, and 2 random sequences. To highlight the branching order of major groups, we present a simplified proteome FFP tree of monophyletic class or phylum with branch support. In our whole-proteome FFP trees (i) Archaea, Bacteria, Eukaryota, and a random sequence outgroup are clearly separated; (ii) Archaea and Bacteria form a sister group when rooted with random sequences; (iii) Planctomycetes, which possesses an intracellular membrane compartment, is placed at the basal position of the Bacteria domain; (iv) almost all groups are monophyletic in prokaryotes at most taxonomic levels, but many differences in the branching order of major groups are observed between our proteome FFP tree and trees built with other methods; and (v) previously "unclassified" genomes may be assigned to the most likely taxa. We describe notable similarities and differences between our FFP trees and those based on other methods in grouping and phylogeny of prokaryotes.

  4. CATO: The Clone Alignment Tool.

    PubMed

    Henstock, Peter V; LaPan, Peter

    2016-01-01

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

  5. CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy.

    PubMed

    Zuo, Guanghong; Hao, Bailin

    2015-10-01

    A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. We now provide one solution in the latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster of 64 cores and is equipped with an interactive, collapsible, and expandable tree display. It is capable of comparing the tree branching order with prokaryotic classification at all taxonomic ranks from domains down to species and strains. CVTree3 allows for inquiry by taxon names and trial on lineage modifications. In addition, it reports a summary of monophyletic and non-monophyletic taxa at all ranks as well as produces print-quality subtree figures. After giving an overview of retrospective verification of the CVTree approach, the power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes. A few discrepancies between CVTree and 16S rRNA analyses are also summarized with regard to possible taxonomic revisions. CVTree3 is freely accessible to all users at http://tlife.fudan.edu.cn/cvtree3/ without login requirements.

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

    PubMed

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

    2009-01-01

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

  7. Effect of gamma irradiation on Schottky-contacted vertically aligned ZnO nanorod-based hydrogen sensor

    NASA Astrophysics Data System (ADS)

    Ranwa, Sapana; Singh Barala, Surendra; Fanetti, Mattia; Kumar, Mahesh

    2016-08-01

    We report the impact of gamma irradiation on the performance of a gold Schottky-contacted ZnO nanorod-based hydrogen sensor. RF-sputtered vertically aligned highly c-axis-oriented ZnO NRs were grown on Si(100) substrate. X-ray diffraction shows no significant change in crystal structure at low gamma doses from 1 to 5 kGy. As gamma irradiation doses increase to 10 kGy, the single crystalline ZnO structure converts to polycrystalline. The photoluminescence spectra also shows suppression of the near-band emission peak and the huge wide-band spectrum indicates the generation of structural defects at high gamma doses. At 1 kGy, the hydrogen sensor response was enhanced from 67% to 77% for 1% hydrogen in pure argon at a 150 °C operating temperature. However, at 10 kGy, the relative response decreases to 33.5%. High gamma irradiation causes displacement damage and defects in ZnO NRs, and as a result, degrades the sensor’s performance as a result. Low gamma irradiation doses activate the ZnO NR surface through ionization, which enhances the sensor performance. The relative response of the hydrogen sensor was enhanced by ∼14.9% with respect to pristine ZnO using 1 kGy gamma ray treatment.

  8. CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy

    PubMed Central

    Zuo, Guanghong; Hao, Bailin

    2015-01-01

    A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. We now provide one solution in the latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster of 64 cores and is equipped with an interactive, collapsible, and expandable tree display. It is capable of comparing the tree branching order with prokaryotic classification at all taxonomic ranks from domains down to species and strains. CVTree3 allows for inquiry by taxon names and trial on lineage modifications. In addition, it reports a summary of monophyletic and non-monophyletic taxa at all ranks as well as produces print-quality subtree figures. After giving an overview of retrospective verification of the CVTree approach, the power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes. A few discrepancies between CVTree and 16S rRNA analyses are also summarized with regard to possible taxonomic revisions. CVTree3 is freely accessible to all users at http://tlife.fudan.edu.cn/cvtree3/ without login requirements. PMID:26563468

  9. Vertically aligned nanostructure scanning probe microscope tips

    DOEpatents

    Guillorn, Michael A.; Ilic, Bojan; Melechko, Anatoli V.; Merkulov, Vladimir I.; Lowndes, Douglas H.; Simpson, Michael L.

    2006-12-19

    Methods and apparatus are described for cantilever structures that include a vertically aligned nanostructure, especially vertically aligned carbon nanofiber scanning probe microscope tips. An apparatus includes a cantilever structure including a substrate including a cantilever body, that optionally includes a doped layer, and a vertically aligned nanostructure coupled to the cantilever body.

  10. Automatic slice-alignment method in cardiac magnetic resonance imaging for evaluation of the right ventricle in patients with pulmonary hypertension

    NASA Astrophysics Data System (ADS)

    Yokoyama, Kenichi; Nitta, Shuhei; Kuhara, Shigehide; Ishimura, Rieko; Kariyasu, Toshiya; Imai, Masamichi; Nitatori, Toshiaki; Takeguchi, Tomoyuki; Shiodera, Taichiro

    2015-09-01

    We propose a new automatic slice-alignment method, which enables right ventricular scan planning in addition to the left ventricular scan planning developed in our previous work, to simplify right ventricular cardiac scan planning and assess its accuracy and the clinical acceptability of the acquired imaging planes in the evaluation of patients with pulmonary hypertension. Steady-state free precession (SSFP) sequences covering the whole heart in the end-diastolic phase with ECG gating were used to acquire 2D axial multislice images. To realize right ventricular scan planning, two morphological feature points are added to be detected and a total of eight morphological features of the heart were extracted from these series of images, and six left ventricular planes and four right ventricular planes were calculated simultaneously based on the extracted features. The subjects were 33 patients (25 with chronic thromboembolic pulmonary hypertension and 8 with idiopathic pulmonary arterial hypertension). The four right ventricular reference planes including right ventricular short-axis, 4-chamber, 2-chamber, and 3-chamber images were evaluated. The acceptability of the acquired imaging planes was visually evaluated using a 4-point scale, and the angular differences between the results obtained by this method and by conventional manual annotation were measured for each view. The average visual scores were 3.9±0.4 for short-axis images, 3.8±0.4 for 4-chamber images, 3.8±0.4 for 2-chamber images, and 3.5±0.6 for 3-chamber images. The average angular differences were 8.7±5.3, 8.3±4.9, 8.1±4.8, and 7.9±5.3 degrees, respectively. The processing time was less than 2.5 seconds in all subjects. The proposed method, which enables right ventricular scan planning in addition to the left ventricular scan planning developed in our previous work, can provide clinically acceptable planes in a short time and is useful because special proficiency in performing cardiac MR for

  11. Dynamic Alignment at SLS

    SciTech Connect

    Ruland, Robert E.

    2003-04-23

    The relative alignment of components in the storage ring of the Swiss Light Source (SLS) is guaranteed by mechanical means. The magnets are rigidly fixed to 48 girders by means of alignment rails with tolerances of less than {+-}15 {micro}m. The bending magnets, supported by 3 point ball bearings, overlap adjacent girders and thus establish virtual train links between the girders, located near the bending magnet centres. Keeping the distortion of the storage ring geometry within a tolerance of {+-}100 {micro}m in order to guarantee sufficient dynamic apertures, requires continuous monitoring and correction of the girder locations. Two monitoring systems for the horizontal and the vertical direction will be installed to measure displacements of the train link between girders, which are due to ground settings and temperature effects: The hydrostatic levelling system (HLS) gives an absolute vertical reference, while the horizontal positioning system (HPS), which employs low cost linear encoders with sub-micron resolution, measures relative horizontal movements. The girder mover system based on five DC motors per girder allows a dynamic realignment of the storage ring within a working window of more than {+-}1 mm for girder translations and {+-}1 mrad for rotations. We will describe both monitoring systems (HLS and HPS) as well as the applied correction scheme based on the girder movers. We also show simulations indicating that beam based girder alignment takes care of most of the static closed orbit correction.

  12. High sensitivity Schottky junction diode based on monolithically grown aligned polypyrrole nanofibers: Broad range detection of m-dihydroxybenzene.

    PubMed

    Ameen, Sadia; Akhtar, M Shaheer; Seo, Hyung-Kee; Shin, Hyung Shik

    2015-07-30

    Aligned p-type polypyrrole (PPy) nanofibers (NFs) thin film was grown on n-type silicon (100) substrate by an electrochemical technique to fabricate Schottky junction diode for the efficient detection of m-dihydroxybenzene chemical. The highly dense and well aligned PPy NFs with the average diameter (∼150-200 nm) were grown on n-type Si substrate. The formation of aligned PPy NFs was confirmed by elucidating the structural, compositional and the optical properties. The electrochemical behavior of the fabricated Pt/p-aligned PPy NFs/n-silicon Schottky junction diode was evaluated by cyclovoltametry (CV) and current (I)-voltage (V) measurements with the variation of m-dihydroxybenzene concentration in the phosphate buffer solution (PBS). The fabricated Pt/p-aligned PPy NFs/n-silicon Schottky junction diode exhibited the rectifying behavior of I-V curve with the addition of m-dihydroxybenzene chemical, while a weak rectifying I-V behavior was observed without m-dihydroxybenzene chemical. This non-linear I-V behavior suggested the formation of Schottky barrier at the interface of Pt layer and p-aligned PPy NFs/n-silicon thin film layer. By analyzing the I-V characteristics, the fabricated Pt/p-aligned PPy NFs/n-silicon Schottky junction diode displayed reasonably high sensitivity ∼23.67 μAmM(-1)cm(-2), good detection limit of ∼1.51 mM with correlation coefficient (R) of ∼0.9966 and short response time (10 s).

  13. Anti-drift and auto-alignment mechanism for an astigmatic atomic force microscope system based on a digital versatile disk optical head.

    PubMed

    Hwu, E-T; Illers, H; Wang, W-M; Hwang, I-S; Jusko, L; Danzebrink, H-U

    2012-01-01

    In this work, an anti-drift and auto-alignment mechanism is applied to an astigmatic detection system (ADS)-based atomic force microscope (AFM) for drift compensation and cantilever alignment. The optical path of the ADS adopts a commercial digital versatile disc (DVD) optical head using the astigmatic focus error signal. The ADS-based astigmatic AFM is lightweight, compact size, low priced, and easy to use. Furthermore, the optical head is capable of measuring sub-atomic displacements of high-frequency AFM probes with a sub-micron laser spot (~570 nm, FWHM) and a high-working bandwidth (80 MHz). Nevertheless, conventional DVD optical heads suffer from signal drift problems. In a previous setup, signal drifts of even thousands of nanometers had been measured. With the anti-drift and auto-alignment mechanism, the signal drift is compensated by actuating a voice coil motor of the DVD optical head. A nearly zero signal drift was achieved. Additional benefits of this mechanism are automatic cantilever alignment and simplified design.

  14. Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees

    PubMed Central

    2010-01-01

    Background Methods of alignment masking, which refers to the technique of excluding alignment blocks prior to tree reconstructions, have been successful in improving the signal-to-noise ratio in sequence alignments. However, the lack of formally well defined methods to identify randomness in sequence alignments has prevented a routine application of alignment masking. In this study, we compared the effects on tree reconstructions of the most commonly used profiling method (GBLOCKS) which uses a predefined set of rules in combination with alignment masking, with a new profiling approach (ALISCORE) based on Monte Carlo resampling within a sliding window, using different data sets and alignment methods. While the GBLOCKS approach excludes variable sections above a certain threshold which choice is left arbitrary, the ALISCORE algorithm is free of a priori rating of parameter space and therefore more objective. Results ALISCORE was successfully extended to amino acids using a proportional model and empirical substitution matrices to score randomness in multiple sequence alignments. A complex bootstrap resampling leads to an even distribution of scores of randomly similar sequences to assess randomness of the observed sequence similarity. Testing performance on real data, both masking methods, GBLOCKS and ALISCORE, helped to improve tree resolution. The sliding window approach was less sensitive to different alignments of identical data sets and performed equally well on all data sets. Concurrently, ALISCORE is capable of dealing with different substitution patterns and heterogeneous base composition. ALISCORE and the most relaxed GBLOCKS gap parameter setting performed best on all data sets. Correspondingly, Neighbor-Net analyses showed the most decrease in conflict. Conclusions Alignment masking improves signal-to-noise ratio in multiple sequence alignments prior to phylogenetic reconstruction. Given the robust performance of alignment profiling, alignment masking

  15. Consensus-based course design and implementation of constructive alignment theory in a power system analysis course

    NASA Astrophysics Data System (ADS)

    Vanfretti, Luigi; Farrokhabadi, Mostafa

    2015-03-01

    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 different perceptions. The considerations required to implement this approach are described in detail. To examine the effect of this approach, three different course evaluations were conducted by querying the students during different stages of the course. These evaluations show that most of the students find a benefit for their learning in the implementation of CAT within the new course design. These observations are supported by a comparison of the students' performance in the new course and the previous one. Finally, the revised two-factor study process questionnaire (R-SPQ-2F) is utilised to identify the students' learning approach towards the course. The aim is to correlate the students' approach with their final grade to assess if students adopting a deep learning approach are rewarded with higher marks and vice versa, that is, to check if the CAT implementation was successful. Meanwhile, some of the R-SPQ-2F limitations, which affect the quality of the results, are identified and discussed. Additionally, to facilitate the practical usage of R-SPQ-2F, an algorithm was developed by the authors to rank the students' approach towards the course. The results of the new ranking algorithm demonstrate positive correlation with the students' final grade, which is an indication of the effective CAT implementation.

  16. Structure and method for controlling band offset and alignme