Optimized mirror shape tuning using beam weightings based on distance, angle of incidence, reflectivity, and power.

PubMed

Goldberg, Kenneth A; Yashchuk, Valeriy V

2016-05-01

For glancing-incidence optical systems, such as short-wavelength optics used for nano-focusing, incorporating physical factors in the calculations used for shape optimization can improve performance. Wavefront metrology, including the measurement of a mirror's shape or slope, is routinely used as input for mirror figure optimization on mirrors that can be bent, actuated, positioned, or aligned. Modeling shows that when the incident power distribution, distance from focus, angle of incidence, and the spatially varying reflectivity are included in the optimization, higher Strehl ratios can be achieved. Following the works of Maréchal and Mahajan, optimization of the Strehl ratio (for peak intensity with a coherently illuminated system) occurs when the expectation value of the phase error's variance is minimized. We describe an optimization procedure based on regression analysis that incorporates these physical parameters. This approach is suitable for coherently illuminated systems of nearly diffraction-limited quality. Mathematically, this work is an enhancement of the methods commonly applied for ex situ alignment based on uniform weighting of all points on the surface (or a sub-region of the surface). It follows a similar approach to the optimization of apodized and non-uniformly illuminated optical systems. Significantly, it reaches a different conclusion than a more recent approach based on minimization of focal plane ray errors.

Improved alignment evaluation and optimization : final report.

DOT National Transportation Integrated Search

2007-09-11

This report outlines the development of an enhanced highway alignment evaluation and optimization : model. A GIS-based software tool is prepared for alignment optimization that uses genetic algorithms for : optimal search. The software is capable of ...

Finite Element Vibration Modeling and Experimental Validation for an Aircraft Engine Casing

NASA Astrophysics Data System (ADS)

Rabbitt, Christopher

This thesis presents a procedure for the development and validation of a theoretical vibration model, applies this procedure to a pair of aircraft engine casings, and compares select parameters from experimental testing of those casings to those from a theoretical model using the Modal Assurance Criterion (MAC) and linear regression coefficients. A novel method of determining the optimal MAC between axisymmetric results is developed and employed. It is concluded that the dynamic finite element models developed as part of this research are fully capable of modelling the modal parameters within the frequency range of interest. Confidence intervals calculated in this research for correlation coefficients provide important information regarding the reliability of predictions, and it is recommended that these intervals be calculated for all comparable coefficients. The procedure outlined for aligning mode shapes around an axis of symmetry proved useful, and the results are promising for the development of further optimization techniques.

Search-based optimization

NASA Technical Reports Server (NTRS)

Wheeler, Ward C.

2003-01-01

The problem of determining the minimum cost hypothetical ancestral sequences for a given cladogram is known to be NP-complete (Wang and Jiang, 1994). Traditionally, point estimations of hypothetical ancestral sequences have been used to gain heuristic, upper bounds on cladogram cost. These include procedures with such diverse approaches as non-additive optimization of multiple sequence alignment, direct optimization (Wheeler, 1996), and fixed-state character optimization (Wheeler, 1999). A method is proposed here which, by extending fixed-state character optimization, replaces the estimation process with a search. This form of optimization examines a diversity of potential state solutions for cost-efficient hypothetical ancestral sequences and can result in greatly more parsimonious cladograms. Additionally, such an approach can be applied to other NP-complete phylogenetic optimization problems such as genomic break-point analysis. c2003 The Willi Hennig Society. Published by Elsevier Science (USA). All rights reserved.

An Efficient Referencing And Sample Positioning System To Investigate Heterogeneous Substances With Combined Microfocused Synchrotron X-ray Techniques

DOE Office of Scientific and Technical Information (OSTI.GOV)

Spangenberg, Thomas; Goettlicher, Joerg; Steininger, Ralph

2009-01-29

A referencing and sample positioning system has been developed to transfer object positions measured with an offline microscope to a synchrotron experimental station. The accuracy should be sufficient to deal with heterogeneous samples on micrometer scale. Together with an online fluorescence mapping visualisation the optical alignment helps to optimize measuring procedures for combined microfocused X-ray techniques.

Estimation of optimal pivot point for remote center of motion alignment in surgery.

PubMed

Rosa, Benoît; Gruijthuijsen, Caspar; Van Cleynenbreugel, Ben; Sloten, Jos Vander; Reynaerts, Dominiek; Poorten, Emmanuel Vander

2015-02-01

The determination of an optimal pivot point ([Formula: see text]) is important for instrument manipulation in minimally invasive surgery. Such knowledge is of particular importance for robotic-assisted surgery where robots need to rotate precisely around a specific point in space in order to minimize trauma to the body wall while maintaining position control. Remote center of motion (RCM) mechanisms are commonly used, where the RCM point is manually and visually aligned. If not positioned appropriately, this misalignment might lead to intolerably high forces on the body wall with increased risk of postoperative complications or instrument damage. An automated method to align the RCM with the [Formula: see text] was developed and tested. Computer vision and a lightweight calibration procedure are used to estimate the optimal pivot point. One or two pre-calibrated cameras viewing the surgical scene are employed. The surgeon is asked to make short pivoting movements, applying as little torque as possible, with an instrument of choice passing through the insertion point while camera images are being recorded. The physical properties of an instrument rotating around a pivot point are exploited in a random sample consensus scheme to robustly estimate the ideal position of the RCM in the image planes. Triangulation is used to estimate the RCM position in 3D. Experiments were performed on a specially designed mockup to test the method. The position of the pivot point is estimated with an average error less than 1.85 mm using two webcams placed from approximately 30 cm to 1 m away from the scene. The entire procedure was completed in a few seconds. In automated method to estimate the ideal position of the RCM was shown to be reliable. The method can be implemented within a visual servoing approach to automatically place the RCM point, or the results can be displayed on a screen to provide guidance to the surgeon. Further work includes the development of an image-guided alignment method and validation with in vivo experiments.

Iterative refinement of structure-based sequence alignments by Seed Extension

PubMed Central

Kim, Changhoon; Tai, Chin-Hsien; Lee, Byungkook

2009-01-01

Background Accurate sequence alignment is required in many bioinformatics applications but, when sequence similarity is low, it is difficult to obtain accurate alignments based on sequence similarity alone. The accuracy improves when the structures are available, but current structure-based sequence alignment procedures still mis-align substantial numbers of residues. In order to correct such errors, we previously explored the possibility of replacing the residue-based dynamic programming algorithm in structure alignment procedures with the Seed Extension algorithm, which does not use a gap penalty. Here, we describe a new procedure called RSE (Refinement with Seed Extension) that iteratively refines a structure-based sequence alignment. Results RSE uses SE (Seed Extension) in its core, which is an algorithm that we reported recently for obtaining a sequence alignment from two superimposed structures. The RSE procedure was evaluated by comparing the correctly aligned fractions of residues before and after the refinement of the structure-based sequence alignments produced by popular programs. CE, DaliLite, FAST, LOCK2, MATRAS, MATT, TM-align, SHEBA and VAST were included in this analysis and the NCBI's CDD root node set was used as the reference alignments. RSE improved the average accuracy of sequence alignments for all programs tested when no shift error was allowed. The amount of improvement varied depending on the program. The average improvements were small for DaliLite and MATRAS but about 5% for CE and VAST. More substantial improvements have been seen in many individual cases. The additional computation times required for the refinements were negligible compared to the times taken by the structure alignment programs. Conclusion RSE is a computationally inexpensive way of improving the accuracy of a structure-based sequence alignment. It can be used as a standalone procedure following a regular structure-based sequence alignment or to replace the traditional iterative refinement procedures based on residue-level dynamic programming algorithm in many structure alignment programs. PMID:19589133

Direct current injection and thermocapillary flow for purification of aligned arrays of single-walled carbon nanotubes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, Xu; Islam, Ahmad E.; Seabron, Eric

2015-04-07

Aligned arrays of semiconducting single-walled carbon nanotubes (s-SWNTs) represent ideal configurations for use of this class of material in high performance electronics. Development of means for removing the metallic SWNTs (m-SWNTs) in as-grown arrays represents an essential challenge. Here, we introduce a simple scheme that achieves this type of purification using direct, selective current injection through interdigitated electrodes into the m-SWNTs, to allow their complete removal using processes of thermocapillarity and dry etching. Experiments and numerical simulations establish the fundamental aspects that lead to selectivity in this process, thereby setting design rules for optimization. Single-step purification of arrays that includemore » thousands of SWNTs demonstrates the effectiveness and simplicity of the procedures. The result is a practical route to large-area aligned arrays of purely s-SWNTs with low-cost experimental setups.« less

Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization.

PubMed

Bauer, Markus; Klau, Gunnar W; Reinert, Knut

2007-07-27

The discovery of functional non-coding RNA sequences has led to an increasing interest in algorithms related to RNA analysis. Traditional sequence alignment algorithms, however, fail at computing reliable alignments of low-homology RNA sequences. The spatial conformation of RNA sequences largely determines their function, and therefore RNA alignment algorithms have to take structural information into account. We present a graph-based representation for sequence-structure alignments, which we model as an integer linear program (ILP). We sketch how we compute an optimal or near-optimal solution to the ILP using methods from combinatorial optimization, and present results on a recently published benchmark set for RNA alignments. The implementation of our algorithm yields better alignments in terms of two published scores than the other programs that we tested: This is especially the case with an increasing number of input sequences. Our program LARA is freely available for academic purposes from http://www.planet-lisa.net.

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 single and multi-domain comparisons. The CAB-align software is freely available to academic users as stand-alone software at http://www.pharm.kitasato-u.ac.jp/bmd/bmd/Publications.html.

A Mathematical Optimization Problem in Bioinformatics

ERIC Educational Resources Information Center

Heyer, Laurie J.

2008-01-01

This article describes the sequence alignment problem in bioinformatics. Through examples, we formulate sequence alignment as an optimization problem and show how to compute the optimal alignment with dynamic programming. The examples and sample exercises have been used by the author in a specialized course in bioinformatics, but could be adapted…

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…

Attenuation-emission alignment in cardiac PET∕CT based on consistency conditions

PubMed Central

Alessio, Adam M.; Kinahan, Paul E.; Champley, Kyle M.; Caldwell, James H.

2010-01-01

Purpose: In cardiac PET and PET∕CT imaging, misaligned transmission and emission images are a common problem due to respiratory and cardiac motion. This misalignment leads to erroneous attenuation correction and can cause errors in perfusion mapping and quantification. This study develops and tests a method for automated alignment of attenuation and emission data. Methods: The CT-based attenuation map is iteratively transformed until the attenuation corrected emission data minimize an objective function based on the Radon consistency conditions. The alignment process is derived from previous work by Welch et al. [“Attenuation correction in PET using consistency information,” IEEE Trans. Nucl. Sci. 45, 3134–3141 (1998)] for stand-alone PET imaging. The process was evaluated with the simulated data and measured patient data from multiple cardiac ammonia PET∕CT exams. The alignment procedure was applied to simulations of five different noise levels with three different initial attenuation maps. For the measured patient data, the alignment procedure was applied to eight attenuation-emission combinations with initially acceptable alignment and eight combinations with unacceptable alignment. The initially acceptable alignment studies were forced out of alignment a known amount and quantitatively evaluated for alignment and perfusion accuracy. The initially unacceptable studies were compared to the proposed aligned images in a blinded side-by-side review. Results: The proposed automatic alignment procedure reduced errors in the simulated data and iteratively approaches global minimum solutions with the patient data. In simulations, the alignment procedure reduced the root mean square error to less than 5 mm and reduces the axial translation error to less than 1 mm. In patient studies, the procedure reduced the translation error by >50% and resolved perfusion artifacts after a known misalignment for the eight initially acceptable patient combinations. The side-by-side review of the proposed aligned attenuation-emission maps and initially misaligned attenuation-emission maps revealed that reviewers preferred the proposed aligned maps in all cases, except one inconclusive case. Conclusions: The proposed alignment procedure offers an automatic method to reduce attenuation correction artifacts in cardiac PET∕CT and provides a viable supplement to subjective manual realignment tools. PMID:20384256

Alignment of Tractograms As Graph Matching.

PubMed

Olivetti, Emanuele; Sharmin, Nusrat; Avesani, Paolo

2016-01-01

The white matter pathways of the brain can be reconstructed as 3D polylines, called streamlines, through the analysis of diffusion magnetic resonance imaging (dMRI) data. The whole set of streamlines is called tractogram and represents the structural connectome of the brain. In multiple applications, like group-analysis, segmentation, or atlasing, tractograms of different subjects need to be aligned. Typically, this is done with registration methods, that transform the tractograms in order to increase their similarity. In contrast with transformation-based registration methods, in this work we propose the concept of tractogram correspondence, whose aim is to find which streamline of one tractogram corresponds to which streamline in another tractogram, i.e., a map from one tractogram to another. As a further contribution, we propose to use the relational information of each streamline, i.e., its distances from the other streamlines in its own tractogram, as the building block to define the optimal correspondence. We provide an operational procedure to find the optimal correspondence through a combinatorial optimization problem and we discuss its similarity to the graph matching problem. In this work, we propose to represent tractograms as graphs and we adopt a recent inexact sub-graph matching algorithm to approximate the solution of the tractogram correspondence problem. On tractograms generated from the Human Connectome Project dataset, we report experimental evidence that tractogram correspondence, implemented as graph matching, provides much better alignment than affine registration and comparable if not better results than non-linear registration of volumes.

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

PubMed

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

2010-06-01

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

Wavefront sensor and wavefront corrector matching in adaptive optics

PubMed Central

Dubra, Alfredo

2016-01-01

Matching wavefront correctors and wavefront sensors by minimizing the condition number and mean wavefront variance is proposed. The particular cases of two continuous-sheet deformable mirrors and a Shack-Hartmann wavefront sensor with square packing geometry are studied in the presence of photon noise, background noise and electronics noise. Optimal number of lenslets across each actuator are obtained for both deformable mirrors, and a simple experimental procedure for optimal alignment is described. The results show that high-performance adaptive optics can be achieved even with low cost off-the-shelf Shack-Hartmann arrays with lenslet spacing that do not necessarily match those of the wavefront correcting elements. PMID:19532513

Wavefront sensor and wavefront corrector matching in adaptive optics.

PubMed

Dubra, Alfredo

2007-03-19

Matching wavefront correctors and wavefront sensors by minimizing the condition number and mean wavefront variance is proposed. The particular cases of two continuous-sheet deformable mirrors and a Shack-Hartmann wavefront sensor with square packing geometry are studied in the presence of photon noise, background noise and electronics noise. Optimal number of lenslets across each actuator are obtained for both deformable mirrors, and a simple experimental procedure for optimal alignment is described. The results show that high-performance adaptive optics can be achieved even with low cost off-the-shelf Shack-Hartmann arrays with lenslet spacing that do not necessarily match those of the wavefront correcting elements.

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

PubMed

de Groot, Marius; Vernooij, Meike W; Klein, Stefan; Ikram, M Arfan; Vos, Frans M; Smith, Stephen M; Niessen, Wiro J; Andersson, Jesper L R

2013-08-01

Anatomical alignment in neuroimaging studies is of such importance that considerable effort is put into improving the registration used to establish spatial correspondence. Tract-based spatial statistics (TBSS) is a popular method for comparing diffusion characteristics across subjects. TBSS establishes spatial correspondence using a combination of nonlinear registration and a "skeleton projection" that may break topological consistency of the transformed brain images. We therefore investigated feasibility of replacing the two-stage registration-projection procedure in TBSS with a single, regularized, high-dimensional registration. To optimize registration parameters and to evaluate registration performance in diffusion MRI, we designed an evaluation framework that uses native space probabilistic tractography for 23 white matter tracts, and quantifies tract similarity across subjects in standard space. We optimized parameters for two registration algorithms on two diffusion datasets of different quality. We investigated reproducibility of the evaluation framework, and of the optimized registration algorithms. Next, we compared registration performance of the regularized registration methods and TBSS. Finally, feasibility and effect of incorporating the improved registration in TBSS were evaluated in an example study. The evaluation framework was highly reproducible for both algorithms (R(2) 0.993; 0.931). The optimal registration parameters depended on the quality of the dataset in a graded and predictable manner. At optimal parameters, both algorithms outperformed the registration of TBSS, showing feasibility of adopting such approaches in TBSS. This was further confirmed in the example experiment. Copyright © 2013 Elsevier Inc. All rights reserved.

Developmental long trace profiler using optimally aligned mirror based pentaprism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barber, Samuel K; Morrison, Gregory Y.; Yashchuk, Valeriy V.

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 basedmore » 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.« less

Finite element design procedure for correcting the coining die profiles

NASA Astrophysics Data System (ADS)

Alexandrino, Paulo; Leitão, Paulo J.; Alves, Luis M.; Martins, Paulo A. F.

2018-05-01

This paper presents a new finite element based design procedure for correcting the coining die profiles in order to optimize the distribution of pressure and the alignment of the resultant vertical force at the end of the die stroke. The procedure avoids time consuming and costly try-outs, does not interfere with the creative process of the sculptors and extends the service life of the coining dies by significantly decreasing the applied pressure and bending moments. The numerical simulations were carried out in a computer program based on the finite element flow formulation that is currently being developed by the authors in collaboration with the Portuguese Mint. A new experimental procedure based on the stack compression test is also proposed for determining the stress-strain curve of the materials directly from the coin blanks.

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. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Template based protein structure modeling by global optimization in CASP11.

PubMed

Joo, Keehyoung; Joung, InSuk; Lee, Sun Young; Kim, Jong Yun; Cheng, Qianyi; Manavalan, Balachandran; Joung, Jong Young; Heo, Seungryong; Lee, Juyong; Nam, Mikyung; Lee, In-Ho; Lee, Sung Jong; Lee, Jooyoung

2016-09-01

For the template-based modeling (TBM) of CASP11 targets, we have developed three new protein modeling protocols (nns for server prediction and LEE and LEER for human prediction) by improving upon our previous CASP protocols (CASP7 through CASP10). We applied the powerful global optimization method of conformational space annealing to three stages of optimization, including multiple sequence-structure alignment, three-dimensional (3D) chain building, and side-chain remodeling. For more successful fold recognition, a new alignment method called CRFalign was developed. It can incorporate sensitive positional and environmental dependence in alignment scores as well as strong nonlinear correlations among various features. Modifications and adjustments were made to the form of the energy function and weight parameters pertaining to the chain building procedure. For the side-chain remodeling step, residue-type dependence was introduced to the cutoff value that determines the entry of a rotamer to the side-chain modeling library. The improved performance of the nns server method is attributed to successful fold recognition achieved by combining several methods including CRFalign and to the current modeling formulation that can incorporate native-like structural aspects present in multiple templates. The LEE protocol is identical to the nns one except that CASP11-released server models are used as templates. The success of LEE in utilizing CASP11 server models indicates that proper template screening and template clustering assisted by appropriate cluster ranking promises a new direction to enhance protein 3D modeling. Proteins 2016; 84(Suppl 1):221-232. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

United States Air Force Summer Research Program 1991. Graduate Student Research Program (GSRP) Reports. Volume 9. Wright Laboratory

DTIC Science & Technology

1992-01-09

Materials 22 Deply of Laminated Panels with Perforation due to Impact John Lair 23 Actuator Location and Optimal Control Design for Flexible Structures...procedure is the focusing and alignment of the UV souce. Though the output of a vapor lamp is nonuniform ., intensity peaks can be smoothed by expanding the...surface, localized surface heatig may occur. Secondly, the output of a mercury vapor lame is nonuniform , requiring diffusion tc obtain a more- uniform

Spatial filters for high-peak-power multistage laser amplifiers.

PubMed

Potemkin, A K; Barmashova, T V; Kirsanov, A V; Martyanov, M A; Khazanov, E A; Shaykin, A A

2007-07-10

We describe spatial filters used in a Nd:glass laser with an output pulse energy up to 300 J and a pulse duration of 1 ns. This laser is designed for pumping of a chirped-pulse optical parametric amplifier. We present data required to choose the shape and diameter of a spatial filter lens, taking into account aberrations caused by spherical surfaces. Calculation of the optimal pinhole diameter is presented. Design features of the spatial filters and the procedure of their alignment are discussed in detail.

Unsupervised parameter optimization for automated retention time alignment of severely shifted gas chromatographic data using the piecework alignment algorithm.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pierce, Karisa M.; Wright, Bob W.; Synovec, Robert E.

2007-02-02

First, simulated chromatographic separations with declining retention time precision were used to study the performance of the piecewise retention time alignment algorithm and to demonstrate an unsupervised parameter optimization method. The average correlation coefficient between the first chromatogram and every other chromatogram in the data set was used to optimize the alignment parameters. This correlation method does not require a training set, so it is unsupervised and automated. This frees the user from needing to provide class information and makes the alignment algorithm more generally applicable to classifying completely unknown data sets. For a data set of simulated chromatograms wheremore » the average chromatographic peak was shifted past two neighboring peaks between runs, the average correlation coefficient of the raw data was 0.46 ± 0.25. After automated, optimized piecewise alignment, the average correlation coefficient was 0.93 ± 0.02. Additionally, a relative shift metric and principal component analysis (PCA) were used to independently quantify and categorize the alignment performance, respectively. The relative shift metric was defined as four times the standard deviation of a given peak’s retention time in all of the chromatograms, divided by the peak-width-at-base. The raw simulated data sets that were studied contained peaks with average relative shifts ranging between 0.3 and 3.0. Second, a “real” data set of gasoline separations was gathered using three different GC methods to induce severe retention time shifting. In these gasoline separations, retention time precision improved ~8 fold following alignment. Finally, piecewise alignment and the unsupervised correlation optimization method were applied to severely shifted GC separations of reformate distillation fractions. The effect of piecewise alignment on peak heights and peak areas is also reported. Piecewise alignment either did not change the peak height, or caused it to slightly decrease. The average relative difference in peak height after piecewise alignment was –0.20%. Piecewise alignment caused the peak areas to either stay the same, slightly increase, or slightly decrease. The average absolute relative difference in area after piecewise alignment was 0.15%.« less

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

PubMed

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

2006-12-15

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

Evaluating Content Alignment in Computerized Adaptive Testing

ERIC Educational Resources Information Center

Wise, Steven L.; Kingsbury, G. Gage; Webb, Norman L.

2015-01-01

The alignment between a test and the content domain it measures represents key evidence for the validation of test score inferences. Although procedures have been developed for evaluating the content alignment of linear tests, these procedures are not readily applicable to computerized adaptive tests (CATs), which require large item pools and do…

Diagnostic procedures for non-small-cell lung cancer (NSCLC): recommendations of the European Expert Group

PubMed Central

Dietel, Manfred; Bubendorf, Lukas; Dingemans, Anne-Marie C; Dooms, Christophe; Elmberger, Göran; García, Rosa Calero; Kerr, Keith M; Lim, Eric; López-Ríos, Fernando; Thunnissen, Erik; Van Schil, Paul E; von Laffert, Maximilian

2016-01-01

Background There is currently no Europe-wide consensus on the appropriate preanalytical measures and workflow to optimise procedures for tissue-based molecular testing of non-small-cell lung cancer (NSCLC). To address this, a group of lung cancer experts (see list of authors) convened to discuss and propose standard operating procedures (SOPs) for NSCLC. Methods Based on earlier meetings and scientific expertise on lung cancer, a multidisciplinary group meeting was aligned. The aim was to include all relevant aspects concerning NSCLC diagnosis. After careful consideration, the following topics were selected and each was reviewed by the experts: surgical resection and sampling; biopsy procedures for analysis; preanalytical and other variables affecting quality of tissue; tissue conservation; testing procedures for epidermal growth factor receptor, anaplastic lymphoma kinase and ROS proto-oncogene 1, receptor tyrosine kinase (ROS1) in lung tissue and cytological specimens; as well as standardised reporting and quality control (QC). Finally, an optimal workflow was described. Results Suggested optimal procedures and workflows are discussed in detail. The broad consensus was that the complex workflow presented can only be executed effectively by an interdisciplinary approach using a well-trained team. Conclusions To optimise diagnosis and treatment of patients with NSCLC, it is essential to establish SOPs that are adaptable to the local situation. In addition, a continuous QC system and a local multidisciplinary tumour-type-oriented board are essential. PMID:26530085

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

PubMed

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

2012-01-01

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

Robust alignment of chromatograms by statistically analyzing the shifts matrix generated by moving window fast Fourier transform cross-correlation.

PubMed

Zhang, Mingjing; Wen, Ming; Zhang, Zhi-Min; Lu, Hongmei; Liang, Yizeng; Zhan, Dejian

2015-03-01

Retention time shift is one of the most challenging problems during the preprocessing of massive chromatographic datasets. Here, an improved version of the moving window fast Fourier transform cross-correlation algorithm is presented to perform nonlinear and robust alignment of chromatograms by analyzing the shifts matrix generated by moving window procedure. The shifts matrix in retention time can be estimated by fast Fourier transform cross-correlation with a moving window procedure. The refined shift of each scan point can be obtained by calculating the mode of corresponding column of the shifts matrix. This version is simple, but more effective and robust than the previously published moving window fast Fourier transform cross-correlation method. It can handle nonlinear retention time shift robustly if proper window size has been selected. The window size is the only one parameter needed to adjust and optimize. The properties of the proposed method are investigated by comparison with the previous moving window fast Fourier transform cross-correlation and recursive alignment by fast Fourier transform using chromatographic datasets. The pattern recognition results of a gas chromatography mass spectrometry dataset of metabolic syndrome can be improved significantly after preprocessing by this method. Furthermore, the proposed method is available as an open source package at https://github.com/zmzhang/MWFFT2. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A quick and reliable procedure for assessing foot alignment in athletes.

PubMed

De Michelis Mendonça, Luciana; Bittencourt, Natália Franco Netto; Amaral, Giovanna Mendes; Diniz, Lívia Santos; Souza, Thales Rezende; da Fonseca, Sérgio Teixeira

2013-01-01

Quick procedures with proper psychometric properties that can capture the combined alignment of the foot-ankle complex in a position that may be more representative of the status of the lower limb during ground contact are essential for assessing a large group of athletes. The assessed lower limb was positioned with the calcaneus surface facing upward in a way that all of the marks could be seen at the center of the camera display. After guaranteeing maintenance of the foot at 90° of dorsiflexion actively sustained by the athlete, the examiner took the picture of the foot-ankle alignment. Intraclass correlation coefficients ranging from 0.82 to 0.93 demonstrated excellent intratester and intertester reliability for the proposed measurements of forefoot, rearfoot, and shank-forefoot alignments. The intraclass correlation coefficient between the shank-forefoot measures and the sum of the rearfoot and forefoot measures was 0.98, suggesting that the shank-forefoot alignment measures can represent the combined rearfoot and forefoot alignments. This study describes a reliable and practical measurement procedure for rearfoot, forefoot, and shank-forefoot alignments that can be applied to clinical and research situations as a screening procedure for risk factors for lower-limb injuries in athletes.

A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation

PubMed Central

Eddy, Sean R.

2008-01-01

Sequence database searches require accurate estimation of the statistical significance of scores. Optimal local sequence alignment scores follow Gumbel distributions, but determining an important parameter of the distribution (λ) requires time-consuming computational simulation. Moreover, optimal alignment scores are less powerful than probabilistic scores that integrate over alignment uncertainty (“Forward” scores), but the expected distribution of Forward scores remains unknown. Here, I conjecture that both expected score distributions have simple, predictable forms when full probabilistic modeling methods are used. For a probabilistic model of local sequence alignment, optimal alignment bit scores (“Viterbi” scores) are Gumbel-distributed with constant λ = log 2, and the high scoring tail of Forward scores is exponential with the same constant λ. Simulation studies support these conjectures over a wide range of profile/sequence comparisons, using 9,318 profile-hidden Markov models from the Pfam database. This enables efficient and accurate determination of expectation values (E-values) for both Viterbi and Forward scores for probabilistic local alignments. PMID:18516236

Modular and configurable optimal sequence alignment software: Cola.

PubMed

Zamani, Neda; Sundström, Görel; Höppner, Marc P; Grabherr, Manfred G

2014-01-01

The fundamental challenge in optimally aligning homologous sequences is to define a scoring scheme that best reflects the underlying biological processes. Maximising the overall number of matches in the alignment does not always reflect the patterns by which nucleotides mutate. Efficiently implemented algorithms that can be parameterised to accommodate more complex non-linear scoring schemes are thus desirable. We present Cola, alignment software that implements different optimal alignment algorithms, also allowing for scoring contiguous matches of nucleotides in a nonlinear manner. The latter places more emphasis on short, highly conserved motifs, and less on the surrounding nucleotides, which can be more diverged. To illustrate the differences, we report results from aligning 14,100 sequences from 3' untranslated regions of human genes to 25 of their mammalian counterparts, where we found that a nonlinear scoring scheme is more consistent than a linear scheme in detecting short, conserved motifs. Cola is freely available under LPGL from https://github.com/nedaz/cola.

IUS prerelease alignment

NASA Technical Reports Server (NTRS)

Evans, F. A.

1978-01-01

Space shuttle orbiter/IUS alignment transfer was evaluated. Although the orbiter alignment accuracy was originally believed to be the major contributor to the overall alignment transfer error, it was shown that orbiter alignment accuracy is not a factor affecting IUS alignment accuracy, if certain procedures are followed. Results are reported of alignment transfer accuracy analysis.

HIRES the high-resolution spectrograph for the E-ELT: dynamics and control of the repositioning mechanism for the E-ELT HIRES polarimeter

NASA Astrophysics Data System (ADS)

Di Varano, I.; Strassmeier, K. G.; Woche, M.

2016-08-01

A full Stokes dual channel polarimeter for the E-ELT HIRES spectrograph has been envisioned for the intermediate focus f/4.4, operating within a spectral range of 0.4-1.6 μ. It will feed the EELT- HIRES instrument located on the Nasmyth platform via two pairs of dedicated fibers: one fibre pair optimized for the BVRI, the other one optimized for the JH band or any other feasible combination. The instrument must be retractable within a workspace in fulfillment with the ESO requirements on the allocated volume and the dynamic response of the AO tower. For such purpose a swinging arm has been designed with a rotation provided by 5 revolute joints and a jackscrew. Moreover repeatability in repositioning has to be guaranteed by a parallel manipulator, performing an alignment procedure mainly along 5 axes. Dynamics and control criteria with a feed forward chain to compensate for vibration forces and feedback chain for tracking procedure are hereafter presented.

Introduction of a computer-based method for automated planning of reduction paths under consideration of simulated muscular forces.

PubMed

Buschbaum, Jan; Fremd, Rainer; Pohlemann, Tim; Kristen, Alexander

2017-08-01

Reduction is a crucial step in the surgical treatment of bone fractures. Finding an optimal path for restoring anatomical alignment is considered technically demanding because collisions as well as high forces caused by surrounding soft tissues can avoid desired reduction movements. The repetition of reduction movements leads to a trial-and-error process which causes a prolonged duration of surgery. By planning an appropriate reduction path-an optimal sequence of target-directed movements-these problems should be overcome. For this purpose, a computer-based method has been developed. Using the example of simple femoral shaft fractures, 3D models are generated out of CT images. A reposition algorithm aligns both fragments by reconstructing their broken edges. According to the criteria of a deduced planning strategy, a modified A*-algorithm searches collision-free route of minimal force from the dislocated into the computed target position. Muscular forces are considered using a musculoskeletal reduction model (OpenSim model), and bone collisions are detected by an appropriate method. Five femoral SYNBONE models were broken into different fracture classification types and were automatically reduced from ten randomly selected displaced positions. Highest mean translational and rotational error for achieving target alignment is [Formula: see text] and [Formula: see text]. Mean value and standard deviation of occurring forces are [Formula: see text] for M. tensor fasciae latae and [Formula: see text] for M. semitendinosus over all trials. These pathways are precise, collision-free, required forces are minimized, and thus regarded as optimal paths. A novel method for planning reduction paths under consideration of collisions and muscular forces is introduced. The results deliver additional knowledge for an appropriate tactical reduction procedure and can provide a basis for further navigated or robotic-assisted developments.

Distance-near disparity esotropia: can we shrink the gap?

PubMed

Burke, J P

2015-02-01

Distance-near disparity esotropias are a group of heterogenous usually acquired strabismus disorders, where the angle of misalignment at near exceeds that at distance by 10 prism diopters or more, where the accurate correction of refractive errors and ambylopia are important early objectives. These aetiologically diverse entities respond non-uniformally to strabismus surgery and bifocals. The management challenge is one of 'shrinking' the disparity so that the affected individuals can develop and comfortably maintain binocular single vision and/or optimal alignment. Surgical procedures have continued to evolve but none of the current operative procedures are superior for all patients. Subclassifying this strabismus and highlighting publication data from more homogenous clinical series may assist with the optimisation of future management and treatment outcomes.

Parallax-Robust Surveillance Video Stitching

PubMed Central

He, Botao; Yu, Shaohua

2015-01-01

This paper presents a parallax-robust video stitching technique for timely synchronized surveillance video. An efficient two-stage video stitching procedure is proposed in this paper to build wide Field-of-View (FOV) videos for surveillance applications. In the stitching model calculation stage, we develop a layered warping algorithm to align the background scenes, which is location-dependent and turned out to be more robust to parallax than the traditional global projective warping methods. On the selective seam updating stage, we propose a change-detection based optimal seam selection approach to avert ghosting and artifacts caused by moving foregrounds. Experimental results demonstrate that our procedure can efficiently stitch multi-view videos into a wide FOV video output without ghosting and noticeable seams. PMID:26712756

Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria.

PubMed

Padial, José M; Grant, Taran; Frost, Darrel R

2014-06-26

Brachycephaloidea is a monophyletic group of frogs with more than 1000 species distributed throughout the New World tropics, subtropics, and Andean regions. Recently, the group has been the target of multiple molecular phylogenetic analyses, resulting in extensive changes in its taxonomy. Here, we test previous hypotheses of phylogenetic relationships for the group by combining available molecular evidence (sequences of 22 genes representing 431 ingroup and 25 outgroup terminals) and performing a tree-alignment analysis under the parsimony optimality criterion using the program POY. To elucidate the effects of alignment and optimality criterion on phylogenetic inferences, we also used the program MAFFT to obtain a similarity-alignment for analysis under both parsimony and maximum likelihood using the programs TNT and GARLI, respectively. Although all three analytical approaches agreed on numerous points, there was also extensive disagreement. Tree-alignment under parsimony supported the monophyly of the ingroup and the sister group relationship of the monophyletic marsupial frogs (Hemiphractidae), while maximum likelihood and parsimony analyses of the MAFFT similarity-alignment did not. All three methods differed with respect to the position of Ceuthomantis smaragdinus (Ceuthomantidae), with tree-alignment using parsimony recovering this species as the sister of Pristimantis + Yunganastes. All analyses rejected the monophyly of Strabomantidae and Strabomantinae as originally defined, and the tree-alignment analysis under parsimony further rejected the recently redefined Craugastoridae and Pristimantinae. Despite the greater emphasis in the systematics literature placed on the choice of optimality criterion for evaluating trees than on the choice of method for aligning DNA sequences, we found that the topological differences attributable to the alignment method were as great as those caused by the optimality criterion. Further, the optimal tree-alignment indicates that insertions and deletions occurred in twice as many aligned positions as implied by the optimal similarity-alignment, confirming previous findings that sequence turnover through insertion and deletion events plays a greater role in molecular evolution than indicated by similarity-alignments. Our results also provide a clear empirical demonstration of the different effects of wildcard taxa produced by missing data in parsimony and maximum likelihood analyses. Specifically, maximum likelihood analyses consistently (81% bootstrap frequency) provided spurious resolution despite a lack of evidence, whereas parsimony correctly depicted the ambiguity due to missing data by collapsing unsupported nodes. We provide a new taxonomy for the group that retains previously recognized Linnaean taxa except for Ceuthomantidae, Strabomantidae, and Strabomantinae. A phenotypically diagnosable superfamily is recognized formally as Brachycephaloidea, with the informal, unranked name terrarana retained as the standard common name for these frogs. We recognize three families within Brachycephaloidea that are currently diagnosable solely on molecular grounds (Brachycephalidae, Craugastoridae, and Eleutherodactylidae), as well as five subfamilies (Craugastorinae, Eleutherodactylinae, Holoadeninae, Phyzelaphryninae, and Pristimantinae) corresponding in large part to previous families and subfamilies. Our analyses upheld the monophyly of all tested genera, but we found numerous subgeneric taxa to be non-monophyletic and modified the taxonomy accordingly.

Strategy for alignment of electron beam trajectory in LEReC cooling section

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seletskiy, S.; Blaskiewicz, M.; Fedotov, A.

2016-09-23

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

A short note on dynamic programming in a band.

PubMed

Gibrat, Jean-François

2018-06-15

Third generation sequencing technologies generate long reads that exhibit high error rates, in particular for insertions and deletions which are usually the most difficult errors to cope with. The only exact algorithm capable of aligning sequences with insertions and deletions is a dynamic programming algorithm. In this note, for the sake of efficiency, we consider dynamic programming in a band. We show how to choose the band width in function of the long reads' error rates, thus obtaining an [Formula: see text] algorithm in space and time. We also propose a procedure to decide whether this algorithm, when applied to semi-global alignments, provides the optimal score. We suggest that dynamic programming in a band is well suited to the problem of aligning long reads between themselves and can be used as a core component of methods for obtaining a consensus sequence from the long reads alone. The function implementing the dynamic programming algorithm in a band is available, as a standalone program, at: https://forgemia.inra.fr/jean-francois.gibrat/BAND_DYN_PROG.git.

In vivo dosimetry and shielding disk alignment verification by EBT3 GAFCHROMIC film in breast IOERT treatment.

PubMed

Severgnini, Mara; de Denaro, Mario; Bortul, Marina; Vidali, Cristiana; Beorchia, Aulo

2014-01-08

Intraoperative electron radiation therapy (IOERT) cannot usually benefit, as conventional external radiotherapy, from software systems of treatment planning based on computed tomography and from common dose verify procedures. For this reason, in vivo film dosimetry (IVFD) proves to be an effective methodology to evaluate the actual radiation dose delivered to the target. A practical method for IVFD during breast IOERT was carried out to improve information on the dose actually delivered to the tumor target and on the alignment of the shielding disk with respect to the electron beam. Two EBT3 GAFCHROMIC films have been positioned on the two sides of the shielding disk in order to obtain the dose maps at the target and beyond the disk. Moreover the postprocessing analysis of the dose distribution measured on the films provides a quantitative estimate of the misalignment between the collimator and the disk. EBT3 radiochromic films have been demonstrated to be suitable dosimeters for IVD due to their linear dose-optical density response in a narrow range around the prescribed dose, as well as their capability to be fixed to the shielding disk without giving any distortion in the dose distribution. Off-line analysis of the radiochromic film allowed absolute dose measurements and this is indeed a very important verification of the correct exposure to the target organ, as well as an estimate of the dose to the healthy tissue underlying the shielding. These dose maps allow surgeons and radiation oncologists to take advantage of qualitative and quantitative feedback for setting more accurate treatment strategies and further optimized procedures. The proper alignment using elastic bands has improved the absolute dose accuracy and the collimator disk alignment by more than 50%.

In vivo dosimetry and shielding disk alignment verification by EBT3 GAFCHROMIC film in breast IOERT treatment

PubMed Central

de Denaro, Mario; Bortul, Marina; Vidali, Cristiana; Beorchia, Aulo

2014-01-01

Intraoperative electron radiation therapy (IOERT) cannot usually benefit, as conventional external radiotherapy, from software systems of treatment planning based on computed tomography and from common dose verify procedures. For this reason, in vivo film dosimetry (IVFD) proves to be an effective methodology to evaluate the actual radiation dose delivered to the target. A practical method for IVFD during breast IOERT was carried out to improve information on the dose actually delivered to the tumor target and on the alignment of the shielding disk with respect to the electron beam. Two EBT3 GAFCHROMIC films have been positioned on the two sides of the shielding disk in order to obtain the dose maps at the target and beyond the disk. Moreover the postprocessing analysis of the dose distribution measured on the films provides a quantitative estimate of the misalignment between the collimator and the disk. EBT3 radiochromic films have been demonstrated to be suitable dosimeters for IVD due to their linear dose‐optical density response in a narrow range around the prescribed dose, as well as their capability to be fixed to the shielding disk without giving any distortion in the dose distribution. Off‐line analysis of the radiochromic film allowed absolute dose measurements and this is indeed a very important verification of the correct exposure to the target organ, as well as an estimate of the dose to the healthy tissue underlying the shielding. These dose maps allow surgeons and radiation oncologists to take advantage of qualitative and quantitative feedback for setting more accurate treatment strategies and further optimized procedures. The proper alignment using elastic bands has improved the absolute dose accuracy and the collimator disk alignment by more than 50%. PACS number: 87.55.kh

[Diagnostic imaging of urolithiais. Current recommendations and new developments].

PubMed

Thalgott, M; Kurtz, F; Gschwend, J E; Straub, M

2015-07-01

Prevalence of urolithiasis is increasing in industrialized countries--in both adults and children, representing a unique diagnostic and therapeutic challenge. Risk-adapted diagnostic imaging currently means assessment with maximized sensitivity and specificity together with minimal radiation exposure. In clinical routine, imaging is performed by sonography, unenhanced computed tomography (NCCT) or intravenous urography (IVU) as well as plain kidney-ureter-bladder (KUB) radiographs. The aim of the present review is a critical guideline-based and therapy-aligned presentation of diagnostic imaging procedures for optimized treatment of urolithiasis considering the specifics in children and pregnant women.

QUASAR--scoring and ranking of sequence-structure alignments.

PubMed

Birzele, Fabian; Gewehr, Jan E; Zimmer, Ralf

2005-12-15

Sequence-structure alignments are a common means for protein structure prediction in the fields of fold recognition and homology modeling, and there is a broad variety of programs that provide such alignments based on sequence similarity, secondary structure or contact potentials. Nevertheless, finding the best sequence-structure alignment in a pool of alignments remains a difficult problem. QUASAR (quality of sequence-structure alignments ranking) provides a unifying framework for scoring sequence-structure alignments that aids finding well-performing combinations of well-known and custom-made scoring schemes. Those scoring functions can be benchmarked against widely accepted quality scores like MaxSub, TMScore, Touch and APDB, thus enabling users to test their own alignment scores against 'standard-of-truth' structure-based scores. Furthermore, individual score combinations can be optimized with respect to benchmark sets based on known structural relationships using QUASAR's in-built optimization routines.

An atomistic fingerprint algorithm for learning ab initio molecular force fields

NASA Astrophysics Data System (ADS)

Tang, Yu-Hang; Zhang, Dongkun; Karniadakis, George Em

2018-01-01

Molecular fingerprints, i.e., feature vectors describing atomistic neighborhood configurations, is an important abstraction and a key ingredient for data-driven modeling of potential energy surface and interatomic force. In this paper, we present the density-encoded canonically aligned fingerprint algorithm, which is robust and efficient, for fitting per-atom scalar and vector quantities. The fingerprint is essentially a continuous density field formed through the superimposition of smoothing kernels centered on the atoms. Rotational invariance of the fingerprint is achieved by aligning, for each fingerprint instance, the neighboring atoms onto a local canonical coordinate frame computed from a kernel minisum optimization procedure. We show that this approach is superior over principal components analysis-based methods especially when the atomistic neighborhood is sparse and/or contains symmetry. We propose that the "distance" between the density fields be measured using a volume integral of their pointwise difference. This can be efficiently computed using optimal quadrature rules, which only require discrete sampling at a small number of grid points. We also experiment on the choice of weight functions for constructing the density fields and characterize their performance for fitting interatomic potentials. The applicability of the fingerprint is demonstrated through a set of benchmark problems.

Automated registration of multispectral MR vessel wall images of the carotid artery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klooster, R. van 't; Staring, M.; Reiber, J. H. C.

2013-12-15

Purpose: Atherosclerosis is the primary cause of heart disease and stroke. The detailed assessment of atherosclerosis of the carotid artery requires high resolution imaging of the vessel wall using multiple MR sequences with different contrast weightings. These images allow manual or automated classification of plaque components inside the vessel wall. Automated classification requires all sequences to be in alignment, which is hampered by patient motion. In clinical practice, correction of this motion is performed manually. Previous studies applied automated image registration to correct for motion using only nondeformable transformation models and did not perform a detailed quantitative validation. The purposemore » of this study is to develop an automated accurate 3D registration method, and to extensively validate this method on a large set of patient data. In addition, the authors quantified patient motion during scanning to investigate the need for correction. Methods: MR imaging studies (1.5T, dedicated carotid surface coil, Philips) from 55 TIA/stroke patients with ipsilateral <70% carotid artery stenosis were randomly selected from a larger cohort. Five MR pulse sequences were acquired around the carotid bifurcation, each containing nine transverse slices: T1-weighted turbo field echo, time of flight, T2-weighted turbo spin-echo, and pre- and postcontrast T1-weighted turbo spin-echo images (T1W TSE). The images were manually segmented by delineating the lumen contour in each vessel wall sequence and were manually aligned by applying throughplane and inplane translations to the images. To find the optimal automatic image registration method, different masks, choice of the fixed image, different types of the mutual information image similarity metric, and transformation models including 3D deformable transformation models, were evaluated. Evaluation of the automatic registration results was performed by comparing the lumen segmentations of the fixed image and moving image after registration. Results: The average required manual translation per image slice was 1.33 mm. Translations were larger as the patient was longer inside the scanner. Manual alignment took 187.5 s per patient resulting in a mean surface distance of 0.271 ± 0.127 mm. After minimal user interaction to generate the mask in the fixed image, the remaining sequences are automatically registered with a computation time of 52.0 s per patient. The optimal registration strategy used a circular mask with a diameter of 10 mm, a 3D B-spline transformation model with a control point spacing of 15 mm, mutual information as image similarity metric, and the precontrast T1W TSE as fixed image. A mean surface distance of 0.288 ± 0.128 mm was obtained with these settings, which is very close to the accuracy of the manual alignment procedure. The exact registration parameters and software were made publicly available. Conclusions: An automated registration method was developed and optimized, only needing two mouse clicks to mark the start and end point of the artery. Validation on a large group of patients showed that automated image registration has similar accuracy as the manual alignment procedure, substantially reducing the amount of user interactions needed, and is multiple times faster. In conclusion, the authors believe that the proposed automated method can replace the current manual procedure, thereby reducing the time to analyze the images.« less

Protein structure modeling for CASP10 by multiple layers of global optimization.

PubMed

Joo, Keehyoung; Lee, Juyong; Sim, Sangjin; Lee, Sun Young; Lee, Kiho; Heo, Seungryong; Lee, In-Ho; Lee, Sung Jong; Lee, Jooyoung

2014-02-01

In the template-based modeling (TBM) category of CASP10 experiment, we introduced a new protocol called protein modeling system (PMS) to generate accurate protein structures in terms of side-chains as well as backbone trace. In the new protocol, a global optimization algorithm, called conformational space annealing (CSA), is applied to the three layers of TBM procedure: multiple sequence-structure alignment, 3D chain building, and side-chain re-modeling. For 3D chain building, we developed a new energy function which includes new distance restraint terms of Lorentzian type (derived from multiple templates), and new energy terms that combine (physical) energy terms such as dynamic fragment assembly (DFA) energy, DFIRE statistical potential energy, hydrogen bonding term, etc. These physical energy terms are expected to guide the structure modeling especially for loop regions where no template structures are available. In addition, we developed a new quality assessment method based on random forest machine learning algorithm to screen templates, multiple alignments, and final models. For TBM targets of CASP10, we find that, due to the combination of three stages of CSA global optimizations and quality assessment, the modeling accuracy of PMS improves at each additional stage of the protocol. It is especially noteworthy that the side-chains of the final PMS models are far more accurate than the models in the intermediate steps. Copyright © 2013 Wiley Periodicals, Inc.

Content Analysis of Vomit and Diarrhea Cleanup Procedures To Prevent Norovirus Infections in Retail and Food Service Operations.

PubMed

Chao, Morgan G; Dubé, Anne-Julie; Leone, Cortney M; Moore, Christina M; Fraser, Angela M

2016-11-01

Human noroviruses are the leading cause of foodborne disease in the United States, sickening 19 to 21 million Americans each year. Vomit and diarrhea are both highly concentrated sources of norovirus particles. For this reason, establishing appropriate cleanup procedures for these two substances is critical. Food service establishments in states that have adopted the 2009 or 2013 U.S. Food and Drug Administration Food Code are required to have a program detailing specific cleanup procedures. The aim of our study was to determine the alignment of existing vomit and diarrhea cleanup procedures with the 11 elements recommended in Annex 3 of the 2011 Supplement to the 2009 Food Code and to determine their readability and clarity of presentation. In July 2015, we located vomit and diarrhea cleanup procedures by asking Norovirus Collaborative for Outreach, Research, and Education stakeholders for procedures used by their constituency groups and by conducting a Google Advanced Search of the World Wide Web. We performed content analysis to determine alignment with the recommendations in Annex 3. Readability and clarity of presentation were also assessed. A total of 38 artifacts were analyzed. The mean alignment score was 7.0 ± 1.7 of 11 points; the mean clarity score was 6.7 ± 2.5 of 17 points. Only nine artifacts were classified as high clarity, high alignment. Vomit and diarrhea cleanup procedures should align with Annex 3 in the Food Code and should, as well, be clearly presented; yet, none of the artifacts completely met both conditions. To reduce the spread of norovirus infections in food service establishments, editable guidelines are needed that are aligned with Annex 3 and are clearly written, into which authors could insert their facility-specific information.

Optimized smith waterman processor design for breast cancer early diagnosis

NASA Astrophysics Data System (ADS)

Nurdin, D. S.; Isa, M. N.; Ismail, R. C.; Ahmad, M. I.

2017-09-01

This paper presents an optimized design of Processing Element (PE) of Systolic Array (SA) which implements affine gap penalty Smith Waterman (SW) algorithm on the Xilinx Virtex-6 XC6VLX75T Field Programmable Gate Array (FPGA) for Deoxyribonucleic Acid (DNA) sequence alignment. The PE optimization aims to reduce PE logic resources to increase number of PEs in FPGA for higher degree of parallelism during alignment matrix computations. This is useful for aligning long DNA-based disease sequence such as Breast Cancer (BC) for early diagnosis. The optimized PE architecture has the smallest PE area with 15 slices in a PE and 776 PEs implemented in the Virtex - 6 FPGA.

Fast 3-T MR-guided transrectal prostate biopsy using an in-room tablet device for needle guide alignment: a feasibility study.

PubMed

Overduin, Christiaan G; Heidkamp, Jan; Rothgang, Eva; Barentsz, Jelle O; de Lange, Frank; Fütterer, Jurgen J

2018-05-22

To assess the feasibility of adding a tablet device inside the scanner room to assist needle-guide alignment during magnetic resonance (MR)-guided transrectal prostate biopsy. Twenty patients with one cancer-suspicious region (CSR) with PI-RADS score ≥ 4 on diagnostic multiparametric MRI were prospectively enrolled. Two orthogonal scan planes of an MR fluoroscopy sequence (~3 images/s) were aligned to the CSR and needle-guide pivoting point. Targeting was achieved by manipulating the needle-guide under MR fluoroscopy feedback on the in-room tablet device. Technical feasibility and targeting success were assessed. Complications and biopsy procedure times were also recorded. Needle-guide alignment with the in-room tablet device was technically successful in all patients and allowed sampling after a single alignment step in 19/20 (95%) CSRs (median size 14 mm, range: 4-45). Biopsy cores contained cancer in 18/20 patients. There were no per-procedural or post-biopsy complications. Using the tablet device, the mean time to first biopsy was 5.8 ± 1.0 min and the mean total procedure time was 23.7 ± 4.1 min. Use of an in-room tablet device to assist needle-guide alignment was feasible and safe during MR-guided transrectal prostate biopsy. Initial experience indicates potential for procedure time reduction. • Performing MR-guided prostate biopsy using an in-room tablet device is feasible. • CSRs could be sampled after a single alignment step in 19/20 patients. • The mean procedure time for biopsy with the tablet device was 23.7 min.

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

PubMed

Kuziemko, Andrew; Honig, Barry; Petrey, Donald

2011-10-01

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

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

PubMed

Ibarra, Ignacio L; Melo, Francisco

2010-07-01

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

Optimization of bicelle lipid composition and temperature for EPR spectroscopy of aligned membranes.

PubMed

McCaffrey, Jesse E; James, Zachary M; Thomas, David D

2015-01-01

We have optimized the magnetic alignment of phospholipid bilayered micelles (bicelles) for EPR spectroscopy, by varying lipid composition and temperature. Bicelles have been extensively used in NMR spectroscopy for several decades, in order to obtain aligned samples in a near-native membrane environment and take advantage of the intrinsic sensitivity of magnetic resonance to molecular orientation. Recently, bicelles have also seen increasing use in EPR, which offers superior sensitivity and orientational resolution. However, the low magnetic field strength (less than 1 T) of most conventional EPR spectrometers results in homogeneously oriented bicelles only at a temperature well above physiological. To optimize bicelle composition for magnetic alignment at reduced temperature, we prepared bicelles containing varying ratios of saturated (DMPC) and unsaturated (POPC) phospholipids, using EPR spectra of a spin-labeled fatty acid to assess alignment as a function of lipid composition and temperature. Spectral analysis showed that bicelles containing an equimolar mixture of DMPC and POPC homogeneously align at 298 K, 20 K lower than conventional DMPC-only bicelles. It is now possible to perform EPR studies of membrane protein structure and dynamics in well-aligned bicelles at physiological temperatures and below. Copyright © 2014 Elsevier Inc. All rights reserved.

3D highway alignment optimization for Brookeville Bypass : final report.

DOT National Transportation Integrated Search

2005-06-01

This study applies the previously developed Highway Alignment Optimization (HAO) : model to the MD 97 Bypass project in Brookeville, Maryland. The objective of this study is to : demonstrate the applicability of the HAO model to a real highway projec...

Automatic alignment of pre- and post-interventional liver CT images for assessment of radiofrequency ablation

NASA Astrophysics Data System (ADS)

Rieder, Christian; Wirtz, Stefan; Strehlow, Jan; Zidowitz, Stephan; Bruners, Philipp; Isfort, Peter; Mahnken, Andreas H.; Peitgen, Heinz-Otto

2012-02-01

Image-guided radiofrequency ablation (RFA) is becoming a standard procedure for minimally invasive tumor treatment in clinical practice. To verify the treatment success of the therapy, reliable post-interventional assessment of the ablation zone (coagulation) is essential. Typically, pre- and post-interventional CT images have to be aligned to compare the shape, size, and position of tumor and coagulation zone. In this work, we present an automatic workflow for masking liver tissue, enabling a rigid registration algorithm to perform at least as accurate as experienced medical experts. To minimize the effect of global liver deformations, the registration is computed in a local region of interest around the pre-interventional lesion and post-interventional coagulation necrosis. A registration mask excluding lesions and neighboring organs is calculated to prevent the registration algorithm from matching both lesion shapes instead of the surrounding liver anatomy. As an initial registration step, the centers of gravity from both lesions are aligned automatically. The subsequent rigid registration method is based on the Local Cross Correlation (LCC) similarity measure and Newton-type optimization. To assess the accuracy of our method, 41 RFA cases are registered and compared with the manually aligned cases from four medical experts. Furthermore, the registration results are compared with ground truth transformations based on averaged anatomical landmark pairs. In the evaluation, we show that our method allows to automatic alignment of the data sets with equal accuracy as medical experts, but requiring significancy less time consumption and variability.

Alternative alignments development and evaluation for the US 220 project in Maryland.

DOT National Transportation Integrated Search

2011-06-01

This project aims to find the preferred alternative alignments for the Maryland section of existing US 220, using the highway : alignment optimization (HAO) model. The model was used to explore alternative alignments within a 4,000 foot-wide buffer o...

An optimal beam alignment method for large-scale distributed space surveillance radar system

NASA Astrophysics Data System (ADS)

Huang, Jian; Wang, Dongya; Xia, Shuangzhi

2018-06-01

Large-scale distributed space surveillance radar is a very important ground-based equipment to maintain a complete catalogue for Low Earth Orbit (LEO) space debris. However, due to the thousands of kilometers distance between each sites of the distributed radar system, how to optimally implement the Transmitting/Receiving (T/R) beams alignment in a great space using the narrow beam, which proposed a special and considerable technical challenge in the space surveillance area. According to the common coordinate transformation model and the radar beam space model, we presented a two dimensional projection algorithm for T/R beam using the direction angles, which could visually describe and assess the beam alignment performance. Subsequently, the optimal mathematical models for the orientation angle of the antenna array, the site location and the T/R beam coverage are constructed, and also the beam alignment parameters are precisely solved. At last, we conducted the optimal beam alignment experiments base on the site parameters of Air Force Space Surveillance System (AFSSS). The simulation results demonstrate the correctness and effectiveness of our novel method, which can significantly stimulate the construction for the LEO space debris surveillance equipment.

Optimizing Mechanical Alignment With Modular Stems in Revision TKA.

PubMed

Fleischman, Andrew N; Azboy, Ibrahim; Restrepo, Camilo; Maltenfort, Mitchell G; Parvizi, Javad

2017-09-01

Although mechanical alignment is critical for optimal function and long-term implant durability, the role of modular stems in achieving ideal alignment is unclear. We identified 319 revision total knee arthroplasty from 2003-2013, for which stem length, stem diameter, and stem fixation method were recorded prospectively. Three-dimensional canal-filling ratio, the product of canal-filling ratio at the stem tip in both the anteroposterior and lateral planes, and alignment were measured radiographically. Ideal alignment of the femur was considered to be 95° in the anteroposterior (AP) plane and from 1° of extension to 4° of flexion in the lateral plane, and ideal tibial alignment was considered to be 90° in the AP plane. Even after accounting for difference in stem size and canal-fill, ideal AP alignment was more reliably achieved with press-fit stems. Furthermore, increased engagement of the diaphysis and its anatomical axis with canal-filling stems facilitates accurate alignment. Copyright © 2017 Elsevier Inc. All rights reserved.

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

PubMed

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

2014-08-01

Evaluation of prostate imaging tests against whole-mount histology specimens requires accurate alignment between radiologic and histologic data sets. Misalignment results in false-positive and -negative zones as assessed by imaging. We describe a workflow for three-dimensional alignment of prostate imaging data against whole-mount prostatectomy reference specimens and assess its performance against a standard workflow. Ethical approval was granted. Patients underwent motorized transrectal ultrasound (Prostate Histoscanning) to generate a three-dimensional image of the prostate before radical prostatectomy. The test workflow incorporated steps for axial alignment between imaging and histology, size adjustments following formalin fixation, and use of custom-made parallel cutters and digital caliper instruments. The control workflow comprised freehand cutting and assumed homogeneous block thicknesses at the same relative angles between pathology and imaging sections. Thirty radical prostatectomy specimens were histologically and radiologically processed, either by an alignment-optimized workflow (n = 20) or a control workflow (n = 10). The optimized workflow generated tissue blocks of heterogeneous thicknesses but with no significant drifting in the cutting plane. The control workflow resulted in significantly nonparallel blocks, accurately matching only one out of four histology blocks to their respective imaging data. The image-to-histology alignment accuracy was 20% greater in the optimized workflow (P < .0001), with higher sensitivity (85% vs. 69%) and specificity (94% vs. 73%) for margin prediction in a 5 × 5-mm grid analysis. A significantly better alignment was observed in the optimized workflow. Evaluation of prostate imaging biomarkers using whole-mount histology references should include a test-to-reference spatial alignment workflow. Copyright © 2014 AUR. Published by Elsevier Inc. All rights reserved.

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

PubMed

Toews, Matthew; Wells, William M

2013-04-01

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

Efficient and Robust Model-to-Image Alignment using 3D Scale-Invariant Features

PubMed Central

Toews, Matthew; Wells, William M.

2013-01-01

This paper presents feature-based alignment (FBA), a general method for efficient and robust model-to-image alignment. Volumetric images, e.g. CT scans of the human body, are modeled probabilistically as a collage of 3D scale-invariant image features within a normalized reference space. Features are incorporated as a latent random variable and marginalized out in computing a maximum a-posteriori alignment solution. The model is learned from features extracted in pre-aligned training images, then fit to features extracted from a new image to identify a globally optimal locally linear alignment solution. Novel techniques are presented for determining local feature orientation and efficiently encoding feature intensity in 3D. Experiments involving difficult magnetic resonance (MR) images of the human brain demonstrate FBA achieves alignment accuracy similar to widely-used registration methods, while requiring a fraction of the memory and computation resources and offering a more robust, globally optimal solution. Experiments on CT human body scans demonstrate FBA as an effective system for automatic human body alignment where other alignment methods break down. PMID:23265799

Matt: local flexibility aids protein multiple structure alignment.

PubMed

Menke, Matthew; Berger, Bonnie; Cowen, Lenore

2008-01-01

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

Two Simple and Efficient Algorithms to Compute the SP-Score Objective Function of a Multiple Sequence Alignment.

PubMed

Ranwez, Vincent

2016-01-01

Multiple sequence alignment (MSA) is a crucial step in many molecular analyses and many MSA tools have been developed. Most of them use a greedy approach to construct a first alignment that is then refined by optimizing the sum of pair score (SP-score). The SP-score estimation is thus a bottleneck for most MSA tools since it is repeatedly required and is time consuming. Given an alignment of n sequences and L sites, I introduce here optimized solutions reaching O(nL) time complexity for affine gap cost, instead of O(n2L), which are easy to implement.

Optimizing alignment and growth of low-loss YAG single crystal fibers using laser heated pedestal growth technique.

PubMed

Bera, Subhabrata; Nie, Craig D; Soskind, Michael G; Harrington, James A

2017-12-10

The effect of misalignments of different optical components in the laser heated pedestal growth apparatus have been modeled using Zemax optical design software. By isolating the misalignments causing the non-uniformity in the melt zone, the alignment of the components was fine-tuned. Using this optimized alignment, low-loss YAG single crystal fibers of 120 μm diameter were grown, with total attenuation loss as low as 0.5 dB/m at 1064 nm.

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

PubMed

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

2015-07-29

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

Quantifying selective alignment of ensemble nitrogen-vacancy centers in (111) diamond

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tahara, Kosuke; Ozawa, Hayato; Iwasaki, Takayuki

2015-11-09

Selective alignment of nitrogen-vacancy (NV) centers in diamond is an important technique towards its applications. Quantification of the alignment ratio is necessary to design the optimized diamond samples. However, this is not a straightforward problem for dense ensemble of the NV centers. We estimate the alignment ratio of ensemble NV centers along the [111] direction in (111) diamond by optically detected magnetic resonance measurements. Diamond films deposited by N{sub 2} doped chemical vapor deposition have NV center densities over 1 × 10{sup 15 }cm{sup −3} and alignment ratios over 75%. Although spin coherence time (T{sub 2}) is limited to a few μs bymore » electron spins of nitrogen impurities, the combination of the selective alignment and the high density can be a possible way to optimize NV-containing diamond samples for the sensing applications.« less

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.

Capabilities and challenges in transferring the wavefront-based alignment approach to small aperture multi-element optical systems

NASA Astrophysics Data System (ADS)

Krappig, Reik; Schmitt, Robert

2017-02-01

Present alignment methods already have an accuracy of some microns, allowing in general the fairly precise assembly of multi element optical systems. Nevertheless, they suffer decisive drawbacks, such as the necessity of an iterative process, stepping through all optical surfaces of the system when using autocollimation telescopes. In contrast to these limitations, the wavefront based alignment offers an elegant approach to potentially reach sub-µm accuracy in the alignment within a highly efficient process, that simultaneously acquires and evaluates the best optical solution possible. However, the practical use of these capabilities in corresponding alignment devices needs to take real sensor behavior into account. This publication will especially elaborate on the influence of the sensor properties in relation to the alignment process. The first dominant requirement is a highly stable measurement, since tiny perturbations in the optical system will have an also tiny influence on the wavefront. Secondly, the lateral sampling of the measured wavefront is supposed to be as high as possible, in order to be able to extract higher order Zernike coefficients reliable. The resulting necessity of using the largest sensor area possible conflicts with the requirement to allow a certain lateral displacement of the measured spot, indicating a perturbation. A movement of the sensor with suitable stages in turn leads to additional uncertainties connected to the actuators. Further factors include the SNR-ratio of the sensor as well as multiple measurements, in order to improve data repeatability. This publication will present a procedure of dealing with these relevant influence factors. Depending on the optical system and its properties the optimal adjustment of these parameters is derived.

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

PubMed

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

2013-09-01

Multiple sequence alignments (MSAs) are widely used approaches in bioinformatics to carry out other tasks such as structure predictions, biological function analyses or phylogenetic modeling. However, current tools usually provide partially optimal alignments, as each one is focused on specific biological features. Thus, the same set of sequences can produce different alignments, above all when sequences are less similar. Consequently, researchers and biologists do not agree about which is the most suitable way to evaluate MSAs. Recent evaluations tend to use more complex scores including further biological features. Among them, 3D structures are increasingly being used to evaluate alignments. Because structures are more conserved in proteins than sequences, scores with structural information are better suited to evaluate more distant relationships between sequences. The proposed multiobjective algorithm, based on the non-dominated sorting genetic algorithm, aims to jointly optimize three objectives: STRIKE score, non-gaps percentage and totally conserved columns. It was significantly assessed on the BAliBASE benchmark according to the Kruskal-Wallis test (P < 0.01). This algorithm also outperforms other aligners, such as ClustalW, Multiple Sequence Alignment Genetic Algorithm (MSA-GA), PRRP, DIALIGN, Hidden Markov Model Training (HMMT), Pattern-Induced Multi-sequence Alignment (PIMA), MULTIALIGN, Sequence Alignment Genetic Algorithm (SAGA), PILEUP, Rubber Band Technique Genetic Algorithm (RBT-GA) and Vertical Decomposition Genetic Algorithm (VDGA), according to the Wilcoxon signed-rank test (P < 0.05), whereas it shows results not significantly different to 3D-COFFEE (P > 0.05) with the advantage of being able to use less structures. Structural information is included within the objective function to evaluate more accurately the obtained alignments. The source code is available at http://www.ugr.es/~fortuno/MOSAStrE/MO-SAStrE.zip.

A distributed system for fast alignment of next-generation sequencing data.

PubMed

Srimani, Jaydeep K; Wu, Po-Yen; Phan, John H; Wang, May D

2010-12-01

We developed a scalable distributed computing system using the Berkeley Open Interface for Network Computing (BOINC) to align next-generation sequencing (NGS) data quickly and accurately. NGS technology is emerging as a promising platform for gene expression analysis due to its high sensitivity compared to traditional genomic microarray technology. However, despite the benefits, NGS datasets can be prohibitively large, requiring significant computing resources to obtain sequence alignment results. Moreover, as the data and alignment algorithms become more prevalent, it will become necessary to examine the effect of the multitude of alignment parameters on various NGS systems. We validate the distributed software system by (1) computing simple timing results to show the speed-up gained by using multiple computers, (2) optimizing alignment parameters using simulated NGS data, and (3) computing NGS expression levels for a single biological sample using optimal parameters and comparing these expression levels to that of a microarray sample. Results indicate that the distributed alignment system achieves approximately a linear speed-up and correctly distributes sequence data to and gathers alignment results from multiple compute clients.

Optimal Parameter Design of Coarse Alignment for Fiber Optic Gyro Inertial Navigation System.

PubMed

Lu, Baofeng; Wang, Qiuying; Yu, Chunmei; Gao, Wei

2015-06-25

Two different coarse alignment algorithms for Fiber Optic Gyro (FOG) Inertial Navigation System (INS) based on inertial reference frame are discussed in this paper. Both of them are based on gravity vector integration, therefore, the performance of these algorithms is determined by integration time. In previous works, integration time is selected by experience. In order to give a criterion for the selection process, and make the selection of the integration time more accurate, optimal parameter design of these algorithms for FOG INS is performed in this paper. The design process is accomplished based on the analysis of the error characteristics of these two coarse alignment algorithms. Moreover, this analysis and optimal parameter design allow us to make an adequate selection of the most accurate algorithm for FOG INS according to the actual operational conditions. The analysis and simulation results show that the parameter provided by this work is the optimal value, and indicate that in different operational conditions, the coarse alignment algorithms adopted for FOG INS are different in order to achieve better performance. Lastly, the experiment results validate the effectiveness of the proposed algorithm.

VI. Uterine fibroid embolization: developing a clinical service.

PubMed

Chrisman, Howard B; Smith, Steven J; Sterling, Keith M; Vogelzang, Robert; Bonn, Joseph; Andrews, Robert T; Worthington-Kirsch, Robert L; Goodwin, Scott C; Lipman, John C; Siskin, Gary P; Hovsepian, David M

2002-03-01

Building a uterine fibroid embolization (UFE) practice can be a complex process. Choices must be made regarding whether to align oneself with a gynecologist or to accept direct referrals. For the interventional radiologist, the responsibilities of evaluation and patient care pose unique and time-consuming administrative and clinical challenges. Physician extenders, either nurse practitioners or physician's assistants, play key roles as clinical coordinators by guiding the patient through the medical system and making certain that she is cleared for the procedure medically and logistically. In some settings, they may also assist in many of the technical aspects of the procedure and postoperative care. Interventional radiologists must be prepared for battles with insurance companies and be willing to go through the appeals process. Business officers must also be trained to properly code for the procedures to insure optimal reimbursement. The success of building a UFE practice may also be bolstered by directly marketing to patients and by providing them with access via the Internet. Copyright 2002, Elsevier Science (USA). All rights reserved.

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

PubMed

Faust, Gregory G; Hall, Ira M

2012-10-01

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

Effect of alignment perturbations in a trans-tibial prosthesis user: A pilot study.

PubMed

Courtney, Anna; Orendurff, Michael S; Buis, Arjan

2016-04-01

A recurring complication in trans-tibial prosthetic limb users is "poor socket fit" with painful residuum-socket interfaces, a consequence of excess pressure. This is due to both poor socket fit and poor socket alignment; however, the interaction of these factors has not been quantified. Through evaluation of kinetic data this study aimed to articulate an interaction uniting socket design, alignment and interface pressures. The results will help to refine future studies and will hopefully help determine whether sockets can be designed, fitted and aligned to maximize mobility whilst minimizing injurious forces. Interface pressures were recorded throughout ambulation in one user with "optimal (reference) alignment" followed by 5 malalignments in a patellar tendon-bearing and a hydrocast socket. Marked differences in pressure distribution were discovered when equating the patellar tendon-bearing against the hydrocast socket and when comparing interface pressures from reference with offset alignment. Patellar tendon-bearing sockets were found to be more sensitive to alignment perturbations than hydrocast sockets. A complex interaction was found, with the most prominent finding demonstrating the requisite for attainment of optimal alignment: a translational alignment error of 10 mm can increase maximum peak pressures by 227% (mean 17.5%). Refinements for future trials are described and the necessity for future research into socket design, alignment and interface pressures has been estabilished.

MaxAlign: maximizing usable data in an alignment.

PubMed

Gouveia-Oliveira, Rodrigo; Sackett, Peter W; Pedersen, Anders G

2007-08-28

The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic and other analyses, for instance, gapped columns are often discarded entirely from the alignment. MaxAlign is a program that optimizes the alignment prior to such analyses. Specifically, it maximizes the number of nucleotide (or amino acid) symbols that are present in gap-free columns - the alignment area - by selecting the optimal subset of sequences to exclude from the alignment. MaxAlign can be used prior to phylogenetic and bioinformatical analyses as well as in other situations where this form of alignment improvement is useful. In this work we test MaxAlign's performance in these tasks and compare the accuracy of phylogenetic estimates including and excluding gapped columns from the analysis, with and without processing with MaxAlign. In this paper we also introduce a new simple measure of tree similarity, Normalized Symmetric Similarity (NSS) that we consider useful for comparing tree topologies. We demonstrate how MaxAlign is helpful in detecting misaligned or defective sequences without requiring manual inspection. We also show that it is not advisable to exclude gapped columns from phylogenetic analyses unless MaxAlign is used first. Finally, we find that the sequences removed by MaxAlign from an alignment tend to be those that would otherwise be associated with low phylogenetic accuracy, and that the presence of gaps in any given sequence does not seem to disturb the phylogenetic estimates of other sequences. The MaxAlign web-server is freely available online at http://www.cbs.dtu.dk/services/MaxAlign where supplementary information can also be found. The program is also freely available as a Perl stand-alone package.

Optimal control of the orientation and alignment of an asymmetric-top molecule with terahertz and laser pulses

NASA Astrophysics Data System (ADS)

Coudert, L. H.

2018-03-01

Quantum optimal control theory is applied to determine numerically the terahertz and nonresonant laser pulses leading, respectively, to the highest degree of orientation and alignment of the asymmetric-top H2S molecule. The optimized terahertz pulses retrieved for temperatures of zero and 50 K lead after 50 ps to an orientation with ⟨ΦZx⟩ = 0.959 73 and ⟨⟨ΦZx⟩⟩ = 0.742 30, respectively. For the zero temperature, the orientation is close to its maximum theoretical value; for the higher temperature, it is below the maximum theoretical value. The mechanism by which the terahertz pulse populates high lying rotational levels is elucidated. The 5 ps long optimized laser pulse calculated for a zero temperature leads to an alignment with ⟨ΦZy 2 ⟩ =0.944 16 and consists of several kick pulses with a duration of ≈0.1 ps. It is found that the timing of these kick pulses is such that it leads to an increase of the rotational energy of the molecule. The optimized laser pulse retrieved for a temperature of 20 K is 6 ps long and yields a lower alignment with ⟨⟨ΦZy 2 ⟩ ⟩ =0.717 20 .

PSO-based methods for medical image registration and change assessment of pigmented skin

NASA Astrophysics Data System (ADS)

Kacenjar, Steve; Zook, Matthew; Balint, Michael

2011-03-01

There are various scientific and technological areas in which it is imperative to rapidly detect and quantify changes in imagery over time. In fields such as earth remote sensing, aerospace systems, and medical imaging, searching for timedependent, regional changes across deformable topographies is complicated by varying camera acquisition geometries, lighting environments, background clutter conditions, and occlusion. Under these constantly-fluctuating conditions, the use of standard, rigid-body registration approaches often fail to provide sufficient fidelity to overlay image scenes together. This is problematic because incorrect assessments of the underlying changes of high-level topography can result in systematic errors in the quantification and classification of interested areas. For example, in the current naked-eye detection strategies of melanoma, a dermatologist often uses static morphological attributes to identify suspicious skin lesions for biopsy. This approach does not incorporate temporal changes which suggest malignant degeneration. By performing the co-registration of time-separated skin imagery, a dermatologist may more effectively detect and identify early morphological changes in pigmented lesions; enabling the physician to detect cancers at an earlier stage resulting in decreased morbidity and mortality. This paper describes an image processing system which will be used to detect changes in the characteristics of skin lesions over time. The proposed system consists of three main functional elements: 1.) coarse alignment of timesequenced imagery, 2.) refined alignment of local skin topographies, and 3.) assessment of local changes in lesion size. During the coarse alignment process, various approaches can be used to obtain a rough alignment, including: 1.) a manual landmark/intensity-based registration method1, and 2.) several flavors of autonomous optical matched filter methods2. These procedures result in the rough alignment of a patient's back topography. Since the skin is a deformable membrane, this process only provides an initial condition for subsequent refinements in aligning the localized topography of the skin. To achieve a refined enhancement, a Particle Swarm Optimizer (PSO) is used to optimally determine the local camera models associated with a generalized geometric transform. Here the optimization process is driven using the minimization of entropy between the multiple time-separated images. Once the camera models are corrected for local skin deformations, the images are compared using both pixel-based and regional-based methods. Limits on the detectability of change are established by the fidelity to which the algorithm corrects for local skin deformation and background alterations. These limits provide essential information in establishing early-warning thresholds for Melanoma detection. Key to this work is the development of a PSO alignment algorithm to perform the refined alignment in local skin topography between the time sequenced imagery (TSI). Test and validation of this alignment process is achieved using a forward model producing known geometric artifacts in the images and afterwards using a PSO algorithm to demonstrate the ability to identify and correct for these artifacts. Specifically, the forward model introduces local translational, rotational, and magnification changes within the image. These geometric modifiers are expected during TSI acquisition because of logistical issues to precisely align the patient to the image recording geometry and is therefore of paramount importance to any viable image registration system. This paper shows that the PSO alignment algorithm is effective in autonomously determining and mitigating these geometric modifiers. The degree of efficacy is measured by several statistically and morphologically based pre-image filtering operations applied to the TSI imagery before applying the PSO alignment algorithm. These trade studies show that global image threshold binarization provides rapid and superior convergence characteristics relative to that of morphologically based methods.

Alignment method for parabolic trough solar concentrators

DOEpatents

Diver, Richard B [Albuquerque, NM

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.

Joint pricing and production management: a geometric programming approach with consideration of cubic production cost function

NASA Astrophysics Data System (ADS)

Sadjadi, Seyed Jafar; Hamidi Hesarsorkh, Aghil; Mohammadi, Mehdi; Bonyadi Naeini, Ali

2015-06-01

Coordination and harmony between different departments of a company can be an important factor in achieving competitive advantage if the company corrects alignment between strategies of different departments. This paper presents an integrated decision model based on recent advances of geometric programming technique. The demand of a product considers as a power function of factors such as product's price, marketing expenditures, and consumer service expenditures. Furthermore, production cost considers as a cubic power function of outputs. The model will be solved by recent advances in convex optimization tools. Finally, the solution procedure is illustrated by numerical example.

Optimal configuration of microstructure in ferroelectric materials by stochastic optimization

NASA Astrophysics Data System (ADS)

Jayachandran, K. P.; Guedes, J. M.; Rodrigues, H. C.

2010-07-01

An optimization procedure determining the ideal configuration at the microstructural level of ferroelectric (FE) materials is applied to maximize piezoelectricity. Piezoelectricity in ceramic FEs differs significantly from that of single crystals because of the presence of crystallites (grains) possessing crystallographic axes aligned imperfectly. The piezoelectric properties of a polycrystalline (ceramic) FE is inextricably related to the grain orientation distribution (texture). The set of combination of variables, known as solution space, which dictates the texture of a ceramic is unlimited and hence the choice of the optimal solution which maximizes the piezoelectricity is complicated. Thus, a stochastic global optimization combined with homogenization is employed for the identification of the optimal granular configuration of the FE ceramic microstructure with optimum piezoelectric properties. The macroscopic equilibrium piezoelectric properties of polycrystalline FE is calculated using mathematical homogenization at each iteration step. The configuration of grains characterized by its orientations at each iteration is generated using a randomly selected set of orientation distribution parameters. The optimization procedure applied to the single crystalline phase compares well with the experimental data. Apparent enhancement of piezoelectric coefficient d33 is observed in an optimally oriented BaTiO3 single crystal. Based on the good agreement of results with the published data in single crystals, we proceed to apply the methodology in polycrystals. A configuration of crystallites, simultaneously constraining the orientation distribution of the c-axis (polar axis) while incorporating ab-plane randomness, which would multiply the overall piezoelectricity in ceramic BaTiO3 is also identified. The orientation distribution of the c-axes is found to be a narrow Gaussian distribution centered around 45°. The piezoelectric coefficient in such a ceramic is found to be nearly three times as that of the single crystal. Our optimization model provide designs for materials with enhanced piezoelectric performance, which would stimulate further studies involving materials possessing higher spontaneous polarization.

Deep Brain Stimulation for Essential Tremor: Aligning Thalamic and Posterior Subthalamic Targets in 1 Surgical Trajectory.

PubMed

Bot, Maarten; van Rootselaar, Fleur; Contarino, Maria Fiorella; Odekerken, Vincent; Dijk, Joke; de Bie, Rob; Schuurman, Richard; van den Munckhof, Pepijn

2017-12-21

Ventral intermediate nucleus (VIM) deep brain stimulation (DBS) and posterior subthalamic area (PSA) DBS suppress tremor in essential tremor (ET) patients, but it is not clear which target is optimal. Aligning both targets in 1 surgical trajectory would facilitate exploring stimulation of either target in a single patient. To evaluate aligning VIM and PSA in 1 surgical trajectory for DBS in ET. Technical aspects of trajectories, intraoperative stimulation findings, final electrode placement, target used for chronic stimulation, and adverse and beneficial effects were evaluated. In 17 patients representing 33 trajectories, we successfully aligned VIM and PSA targets in 26 trajectories. Trajectory distance between targets averaged 7.2 (range 6-10) mm. In all but 4 aligned trajectories, optimal intraoperative tremor suppression was obtained in the PSA. During follow-up, active electrode contacts were located in PSA in the majority of cases. Overall, successful tremor control was achieved in 69% of patients. Stimulation-induced dysarthria or gait ataxia occurred in, respectively, 56% and 44% of patients. Neither difference in tremor suppression or side effects was noted between aligned and nonaligned leads nor between the different locations of chronic stimulation. Alignment of VIM and PSA for DBS in ET is feasible and enables intraoperative exploration of both targets in 1 trajectory. This facilitates positioning of electrode contacts in both areas, where multiple effective points of stimulation can be found. In the majority of aligned leads, optimal intraoperative and chronic stimulation were located in the PSA. Copyright © 2017 by the Congress of Neurological Surgeons

Local alignment of two-base encoded DNA sequence

PubMed Central

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

2009-01-01

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

[Total and unicompartmental knee replacement. Patient-specific Instrumentation].

PubMed

Köster, G; Biró, C

2016-04-01

The objective of patient-specific instrumentation (PSI Zimmer®) technology is to optimize positioning and selection of components as well as surgical procedure in uni- and bicompartimental knee replacement. The article contains a description of the planning and surgical technique and evaluates the method based on own results and literature. Using MRI or CT scans a virtual 3D model of the joint is created in order to simulate and plan the implant positioning. According to these data, pin placement and/or cutting guides are produced, which enable the surgeon to transfer the planning to the surgical procedure. In a prospective comparative study 88 patients (44 per each of the two techniques) were operated by one surgeon receiving the same TKA using either MRI-based PSI or a conventional technique. The number of surgical trays, operating time, intraoperative changes and frontal alignment using a full leg x‑ray (70 cases) were compared. In 17 patients the method was applied with unicondylar knee replacement. Anatomical abnormalities could be detected preoperatively and considered during the operation. With PSI the number of trays could be reduced and predictability of the component size was more precise. Intraoperative changes became necessary only for distal femoral (25 %) and proximal tibial (36 %) resection and tibial rotation (40 %). Alignment was more precise in the PSI cases PSI using the applied technique proved to be practicable and reliable. The advantages of precise planning became obvious. Results concerning alignment are inconsistent in the literature. Soft tissue balancing has only been included in the technique to a limited degree so far. PSI is still in an early stage of development and further development opportunities should be exploited before final assessment.

The Dynamo package for tomography and subtomogram averaging: components for MATLAB, GPU computing and EC2 Amazon Web Services

PubMed Central

Castaño-Díez, Daniel

2017-01-01

Dynamo is a package for the processing of tomographic data. As a tool for subtomogram averaging, it includes different alignment and classification strategies. Furthermore, its data-management module allows experiments to be organized in groups of tomograms, while offering specialized three-dimensional tomographic browsers that facilitate visualization, location of regions of interest, modelling and particle extraction in complex geometries. Here, a technical description of the package is presented, focusing on its diverse strategies for optimizing computing performance. Dynamo is built upon mbtools (middle layer toolbox), a general-purpose MATLAB library for object-oriented scientific programming specifically developed to underpin Dynamo but usable as an independent tool. Its structure intertwines a flexible MATLAB codebase with precompiled C++ functions that carry the burden of numerically intensive operations. The package can be delivered as a precompiled standalone ready for execution without a MATLAB license. Multicore parallelization on a single node is directly inherited from the high-level parallelization engine provided for MATLAB, automatically imparting a balanced workload among the threads in computationally intense tasks such as alignment and classification, but also in logistic-oriented tasks such as tomogram binning and particle extraction. Dynamo supports the use of graphical processing units (GPUs), yielding considerable speedup factors both for native Dynamo procedures (such as the numerically intensive subtomogram alignment) and procedures defined by the user through its MATLAB-based GPU library for three-dimensional operations. Cloud-based virtual computing environments supplied with a pre-installed version of Dynamo can be publicly accessed through the Amazon Elastic Compute Cloud (EC2), enabling users to rent GPU computing time on a pay-as-you-go basis, thus avoiding upfront investments in hardware and longterm software maintenance. PMID:28580909

The Dynamo package for tomography and subtomogram averaging: components for MATLAB, GPU computing and EC2 Amazon Web Services.

PubMed

Castaño-Díez, Daniel

2017-06-01

Dynamo is a package for the processing of tomographic data. As a tool for subtomogram averaging, it includes different alignment and classification strategies. Furthermore, its data-management module allows experiments to be organized in groups of tomograms, while offering specialized three-dimensional tomographic browsers that facilitate visualization, location of regions of interest, modelling and particle extraction in complex geometries. Here, a technical description of the package is presented, focusing on its diverse strategies for optimizing computing performance. Dynamo is built upon mbtools (middle layer toolbox), a general-purpose MATLAB library for object-oriented scientific programming specifically developed to underpin Dynamo but usable as an independent tool. Its structure intertwines a flexible MATLAB codebase with precompiled C++ functions that carry the burden of numerically intensive operations. The package can be delivered as a precompiled standalone ready for execution without a MATLAB license. Multicore parallelization on a single node is directly inherited from the high-level parallelization engine provided for MATLAB, automatically imparting a balanced workload among the threads in computationally intense tasks such as alignment and classification, but also in logistic-oriented tasks such as tomogram binning and particle extraction. Dynamo supports the use of graphical processing units (GPUs), yielding considerable speedup factors both for native Dynamo procedures (such as the numerically intensive subtomogram alignment) and procedures defined by the user through its MATLAB-based GPU library for three-dimensional operations. Cloud-based virtual computing environments supplied with a pre-installed version of Dynamo can be publicly accessed through the Amazon Elastic Compute Cloud (EC2), enabling users to rent GPU computing time on a pay-as-you-go basis, thus avoiding upfront investments in hardware and longterm software maintenance.

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…

sc-PDB-Frag: a database of protein-ligand interaction patterns for Bioisosteric replacements.

PubMed

Desaphy, Jérémy; Rognan, Didier

2014-07-28

Bioisosteric replacement plays an important role in medicinal chemistry by keeping the biological activity of a molecule while changing either its core scaffold or substituents, thereby facilitating lead optimization and patenting. Bioisosteres are classically chosen in order to keep the main pharmacophoric moieties of the substructure to replace. However, notably when changing a scaffold, no attention is usually paid as whether all atoms of the reference scaffold are equally important for binding to the desired target. We herewith propose a novel database for bioisosteric replacement (scPDBFrag), capitalizing on our recently published structure-based approach to scaffold hopping, focusing on interaction pattern graphs. Protein-bound ligands are first fragmented and the interaction of the corresponding fragments with their protein environment computed-on-the-fly. Using an in-house developed graph alignment tool, interaction patterns graphs can be compared, aligned, and sorted by decreasing similarity to any reference. In the herein presented sc-PDB-Frag database ( http://bioinfo-pharma.u-strasbg.fr/scPDBFrag ), fragments, interaction patterns, alignments, and pairwise similarity scores have been extracted from the sc-PDB database of 8077 druggable protein-ligand complexes and further stored in a relational database. We herewith present the database, its Web implementation, and procedures for identifying true bioisosteric replacements based on conserved interaction patterns.

Optimal network alignment with graphlet degree vectors.

PubMed

Milenković, Tijana; Ng, Weng Leong; Hayes, Wayne; Przulj, Natasa

2010-06-30

Important biological information is encoded in the topology of biological networks. Comparative analyses of biological networks are proving to be valuable, as they can lead to transfer of knowledge between species and give deeper insights into biological function, disease, and evolution. We introduce a new method that uses the Hungarian algorithm to produce optimal global alignment between two networks using any cost function. We design a cost function based solely on network topology and use it in our network alignment. Our method can be applied to any two networks, not just biological ones, since it is based only on network topology. We use our new method to align protein-protein interaction networks of two eukaryotic species and demonstrate that our alignment exposes large and topologically complex regions of network similarity. At the same time, our alignment is biologically valid, since many of the aligned protein pairs perform the same biological function. From the alignment, we predict function of yet unannotated proteins, many of which we validate in the literature. Also, we apply our method to find topological similarities between metabolic networks of different species and build phylogenetic trees based on our network alignment score. The phylogenetic trees obtained in this way bear a striking resemblance to the ones obtained by sequence alignments. Our method detects topologically similar regions in large networks that are statistically significant. It does this independent of protein sequence or any other information external to network topology.

Sandia Corporation (Albuquerque, NM)

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.

Aligning Plasma-Arc Welding Oscillations

NASA Technical Reports Server (NTRS)

Norris, Jeff; Fairley, Mike

1989-01-01

Tool aids in alignment of oscillator probe on variable-polarity plasma-arc welding torch. Probe magnetically pulls arc from side to side as it moves along joint. Tensile strength of joint depends on alignment of weld bead and on alignment of probe. Operator installs new tool on front of torch body, levels it with built-in bubble glass, inserts probe in slot on tool, and locks probe in place. Procedure faster and easier and resulting alignment more accurate and repeatable.

The Influence of Component Alignment and Ligament Properties on Tibiofemoral Contact Forces in Total Knee Replacement.

PubMed

Smith, Colin R; Vignos, Michael F; Lenhart, Rachel L; Kaiser, Jarred; Thelen, Darryl G

2016-02-01

The study objective was to investigate the influence of coronal plane alignment and ligament properties on total knee replacement (TKR) contact loads during walking. We created a subject-specific knee model of an 83-year-old male who had an instrumented TKR. The knee model was incorporated into a lower extremity musculoskeletal model and included deformable contact, ligamentous structures, and six degrees-of-freedom (DOF) tibiofemoral and patellofemoral joints. A novel numerical optimization technique was used to simultaneously predict muscle forces, secondary knee kinematics, ligament forces, and joint contact pressures from standard gait analysis data collected on the subject. The nominal knee model predictions of medial, lateral, and total contact forces during gait agreed well with TKR measures, with root-mean-square (rms) errors of 0.23, 0.22, and 0.33 body weight (BW), respectively. Coronal plane component alignment did not affect total knee contact loads, but did alter the medial-lateral load distribution, with 4 deg varus and 4 deg valgus rotations in component alignment inducing +17% and -23% changes in the first peak medial tibiofemoral contact forces, respectively. A Monte Carlo analysis showed that uncertainties in ligament stiffness and reference strains induce ±0.2 BW uncertainty in tibiofemoral force estimates over the gait cycle. Ligament properties had substantial influence on the TKR load distributions, with the medial collateral ligament and iliotibial band (ITB) properties having the largest effects on medial and lateral compartment loading, respectively. The computational framework provides a viable approach for virtually designing TKR components, considering parametric uncertainty and predicting the effects of joint alignment and soft tissue balancing procedures on TKR function during movement.

The Influence of Component Alignment and Ligament Properties on Tibiofemoral Contact Forces in Total Knee Replacement

PubMed Central

Smith, Colin R.; Vignos, Michael F.; Lenhart, Rachel L.; Kaiser, Jarred; Thelen, Darryl G.

2016-01-01

The study objective was to investigate the influence of coronal plane alignment and ligament properties on total knee replacement (TKR) contact loads during walking. We created a subject-specific knee model of an 83-year-old male who had an instrumented TKR. The knee model was incorporated into a lower extremity musculoskeletal model and included deformable contact, ligamentous structures, and six degrees-of-freedom (DOF) tibiofemoral and patellofemoral joints. A novel numerical optimization technique was used to simultaneously predict muscle forces, secondary knee kinematics, ligament forces, and joint contact pressures from standard gait analysis data collected on the subject. The nominal knee model predictions of medial, lateral, and total contact forces during gait agreed well with TKR measures, with root-mean-square (rms) errors of 0.23, 0.22, and 0.33 body weight (BW), respectively. Coronal plane component alignment did not affect total knee contact loads, but did alter the medial–lateral load distribution, with 4 deg varus and 4 deg valgus rotations in component alignment inducing +17% and −23% changes in the first peak medial tibiofemoral contact forces, respectively. A Monte Carlo analysis showed that uncertainties in ligament stiffness and reference strains induce ±0.2 BW uncertainty in tibiofemoral force estimates over the gait cycle. Ligament properties had substantial influence on the TKR load distributions, with the medial collateral ligament and iliotibial band (ITB) properties having the largest effects on medial and lateral compartment loading, respectively. The computational framework provides a viable approach for virtually designing TKR components, considering parametric uncertainty and predicting the effects of joint alignment and soft tissue balancing procedures on TKR function during movement. PMID:26769446

An experimental apparatus for diffraction-limited soft x-ray nano-focusing

NASA Astrophysics Data System (ADS)

Merthe, Daniel J.; Goldberg, Kenneth A.; Yashchuk, Valeriy V.; Yuan, Sheng; McKinney, Wayne R.; Celestre, Richard; Mochi, Iacopo; Macdougall, James; Morrison, Gregory Y.; Rakawa, Senajith B.; Anderson, Erik; Smith, Brian V.; Domning, Edward E.; Warwick, Tony; Padmore, Howard

2011-09-01

Realizing the experimental potential of high-brightness, next generation synchrotron and free-electron laser light sources requires the development of reflecting x-ray optics capable of wavefront preservation and high-resolution nano-focusing. At the Advanced Light Source (ALS) beamline 5.3.1, we are developing broadly applicable, high-accuracy, in situ, at-wavelength wavefront measurement techniques to surpass 100-nrad slope measurement accuracy for diffraction-limited Kirkpatrick-Baez (KB) mirrors. The at-wavelength methodology we are developing relies on a series of wavefront-sensing tests with increasing accuracy and sensitivity, including scanning-slit Hartmann tests, grating-based lateral shearing interferometry, and quantitative knife-edge testing. We describe the original experimental techniques and alignment methodology that have enabled us to optimally set a bendable KB mirror to achieve a focused, FWHM spot size of 150 nm, with 1 nm (1.24 keV) photons at 3.7 mrad numerical aperture. The predictions of wavefront measurement are confirmed by the knife-edge testing. The side-profiled elliptically bent mirror used in these one-dimensional focusing experiments was originally designed for a much different glancing angle and conjugate distances. Visible-light long-trace profilometry was used to pre-align the mirror before installation at the beamline. This work demonstrates that high-accuracy, at-wavelength wavefront-slope feedback can be used to optimize the pitch, roll, and mirror-bending forces in situ, using procedures that are deterministic and repeatable.

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

MANGO: a new approach to multiple sequence alignment.

PubMed

Zhang, Zefeng; Lin, Hao; Li, Ming

2007-01-01

Multiple sequence alignment is a classical and challenging task for biological sequence analysis. The problem is NP-hard. The full dynamic programming takes too much time. The progressive alignment heuristics adopted by most state of the art multiple sequence alignment programs suffer from the 'once a gap, always a gap' phenomenon. Is there a radically new way to do multiple sequence alignment? This paper introduces a novel and orthogonal multiple sequence alignment method, using multiple optimized spaced seeds and new algorithms to handle these seeds efficiently. Our new algorithm processes information of all sequences as a whole, avoiding problems caused by the popular progressive approaches. Because the optimized spaced seeds are provably significantly more sensitive than the consecutive k-mers, the new approach promises to be more accurate and reliable. To validate our new approach, we have implemented MANGO: Multiple Alignment with N Gapped Oligos. Experiments were carried out on large 16S RNA benchmarks showing that MANGO compares favorably, in both accuracy and speed, against state-of-art multiple sequence alignment methods, including ClustalW 1.83, MUSCLE 3.6, MAFFT 5.861, Prob-ConsRNA 1.11, Dialign 2.2.1, DIALIGN-T 0.2.1, T-Coffee 4.85, POA 2.0 and Kalign 2.0.

Permanent bending and alignment of ZnO nanowires.

PubMed

Borschel, Christian; Spindler, Susann; Lerose, Damiana; Bochmann, Arne; Christiansen, Silke H; Nietzsche, Sandor; Oertel, Michael; Ronning, Carsten

2011-05-06

Ion beams can be used to permanently bend and re-align nanowires after growth. We have irradiated ZnO nanowires with energetic ions, achieving bending and alignment in different directions. Not only the bending of single nanowires is studied in detail, but also the simultaneous alignment of large ensembles of ZnO nanowires. Computer simulations reveal how the bending is initiated by ion beam induced damage. Detailed structural characterization identifies dislocations to relax stresses and make the bending and alignment permanent, even surviving annealing procedures.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oines, A; Oines, A; Kilian-Meneghin, J

2016-06-15

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

Photoluminescence and Band Alignment of Strained GaAsSb/GaAs QW Structures Grown by MBE on GaAs

PubMed Central

Sadofyev, Yuri G.; Samal, Nigamananda

2010-01-01

An in-depth optimization of growth conditions and investigation of optical properties including discussions on band alignment of GaAsSb/GaAs quantum well (QW) on GaAs by molecular beam epitaxy (MBE) are reported. Optimal MBE growth temperature of GaAsSb QW is found to be 470 ± 10 °C. GaAsSb/GaAs QW with Sb content ~0.36 has a weak type-II band alignment with valence band offset ratio QV ~1.06. A full width at half maximum (FWHM) of ~60 meV in room temperature (RT) photoluminescence (PL) indicates fluctuation in electrostatic potential to be less than 20 meV. Samples grown under optimal conditions do not exhibit any blue shift of peak in RT PL spectra under varying excitation.

Accuracy Estimation and Parameter Advising for Protein Multiple Sequence Alignment

PubMed Central

DeBlasio, Dan

2013-01-01

Abstract We develop a novel and general approach to estimating the accuracy of multiple sequence alignments without knowledge of a reference alignment, and use our approach to address a new task that we call parameter advising: the problem of choosing values for alignment scoring function parameters from a given set of choices to maximize the accuracy of a computed alignment. For protein alignments, we consider twelve independent features that contribute to a quality alignment. An accuracy estimator is learned that is a polynomial function of these features; its coefficients are determined by minimizing its error with respect to true accuracy using mathematical optimization. Compared to prior approaches for estimating accuracy, our new approach (a) introduces novel feature functions that measure nonlocal properties of an alignment yet are fast to evaluate, (b) considers more general classes of estimators beyond linear combinations of features, and (c) develops new regression formulations for learning an estimator from examples; in addition, for parameter advising, we (d) determine the optimal parameter set of a given cardinality, which specifies the best parameter values from which to choose. Our estimator, which we call Facet (for “feature-based accuracy estimator”), yields a parameter advisor that on the hardest benchmarks provides more than a 27% improvement in accuracy over the best default parameter choice, and for parameter advising significantly outperforms the best prior approaches to assessing alignment quality. PMID:23489379

A Low Power and High Throughput Self Synchronous FPGA Using 65nm CMOS with Throughput Optimization by Pipeline Alignment

NASA Astrophysics Data System (ADS)

Stefan Devlin, Benjamin; Nakura, Toru; Ikeda, Makoto; Asada, Kunihiro

We detail a self synchronous field programmable gate array (SSFPGA) with dual-pipeline (DP) architecture to conceal pre-charge time for dynamic logic, and its throughput optimization by using pipeline alignment implemented on benchmark circuits. A self synchronous LUT (SSLUT) consists of a three input tree-type structure with 8bits of SRAM for programming. A self synchronous switch box (SSSB) consists of both pass transistors and buffers to route signals, with 12bits of SRAM. One common block with one SSLUT and one SSSB occupies 2.2Mλ2 area with 35bits of SRAM, and the prototype SSFPGA with 34 × 30 (1020) blocks is designed and fabricated using 65nm CMOS. Measured results show at 1.2V 430MHz and 647MHz operation for a 3bit ripple carry adder, without and with throughput optimization, respectively. We find that using the proposed pipeline alignment techniques we can perform at maximum throughput of 647MHz in various benchmarks on the SSFPGA. We demonstrate up to 56.1 times throughput improvement with our pipeline alignment techniques. The pipeline alignment is carried out within the number of logic elements in the array and pipeline buffers in the switching matrix.

Mechanisms of Carrier Transport Induced by a Microswimmer Bath

DOE PAGES

Kaiser, Andreas; Sokolov, Andrey; Aranson, Igor S.; ...

2014-10-20

Recently, it was found that a wedgelike microparticle (referred to as ”carrier”) which is only allowed to translate but not to rotate exhibits a directed translational motion along the wedge cusp if it is exposed to a bath of microswimmers. Here we model this effect in detail by resolving the microswimmers explicitly using interaction models with different degrees of mutual alignment. Using computer simulations we study the impact of these interactions on the transport efficiency of V-shaped carrier. We show that the transport mechanisms itself strongly depends on the degree of alignment embodied in the modelling of the individual swimmermore » dynamics. For weak alignment, optimal carrier transport occurs in the turbulent microswimmer state and is induced by swirl depletion inside the carrier. For strong aligning interactions, optimal transport occurs already in the dilute regime and is mediated by a polar cloud of swimmers in the carrier wake pushing the wedge-particle forward. Finally, we also demonstrate that the optimal shape of the carrier leading to maximal transport speed depends on the kind of interaction model used.« less

Multiple DNA and protein sequence alignment on a workstation and a supercomputer.

PubMed

Tajima, K

1988-11-01

This paper describes a multiple alignment method using a workstation and supercomputer. The method is based on the alignment of a set of aligned sequences with the new sequence, and uses a recursive procedure of such alignment. The alignment is executed in a reasonable computation time on diverse levels from a workstation to a supercomputer, from the viewpoint of alignment results and computational speed by parallel processing. The application of the algorithm is illustrated by several examples of multiple alignment of 12 amino acid and DNA sequences of HIV (human immunodeficiency virus) env genes. Colour graphic programs on a workstation and parallel processing on a supercomputer are discussed.

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.

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

PubMed

Houben, L; Bar Sadan, M

2011-01-01

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

Optimization of an Offset Receiver Optics for Radio Telescopes

NASA Astrophysics Data System (ADS)

Yeap, Kim Ho; Tham, Choy Yoong

2018-01-01

The latest generation of Cassegrain radio astronomy antennas is designed for multiple frequency bands with receivers for individual bands offset from the antenna axis. The offset feed arrangement typically has two focusing elements in the form of ellipsoidal mirrors in the optical path between the feed horn and the antenna focus. This arrangement aligns the beam from the offset feed horn to illuminate the subreflector. The additional focusing elements increase the number of design variables, namely the distances between the horn aperture and the first mirror and that between the two mirrors, and their focal lengths. There are a huge number of possible combinations of these four variables in which the optics system can take on. The design aim is to seek the combination that will give the optimum antenna efficiency, not only at the centre frequency of the particular band but also across its bandwidth. To pick the optimum combination of the variables, it requires working through, by computational mean, a continuum range of variable values at different frequencies which will fit the optics system within the allocated physical space. Physical optics (PO) is a common technique used in optics design. However, due to the repeated iteration of the huge number of computation involved, the use of PO is not feasible. We present a procedure based on using multimode Gaussian optics to pick the optimum design and using PO for final verification of the system performance. The best antenna efficiency is achieved when the beam illuminating the subreflector is truncated with the optimum edge taper. The optimization procedure uses the beam's edge taper at the subreflector as the iteration target. The band 6 receiver optics design for the Atacama Large Millimetre Array (ALMA) antenna is used to illustrate the optimization procedure.

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

PubMed Central

2011-01-01

Background Comparing biological time series data across different conditions, or different specimens, is a common but still challenging task. Algorithms aligning two time series represent a valuable tool for such comparisons. While many powerful computation tools for time series alignment have been developed, they do not provide significance estimates for time shift measurements. Results Here, we present an extended version of the original DTW algorithm that allows us to determine the significance of time shift estimates in time series alignments, the DTW-Significance (DTW-S) algorithm. The DTW-S combines important properties of the original algorithm and other published time series alignment tools: DTW-S calculates the optimal alignment for each time point of each gene, it uses interpolated time points for time shift estimation, and it does not require alignment of the time-series end points. As a new feature, we implement a simulation procedure based on parameters estimated from real time series data, on a series-by-series basis, allowing us to determine the false positive rate (FPR) and the significance of the estimated time shift values. We assess the performance of our method using simulation data and real expression time series from two published primate brain expression datasets. Our results show that this method can provide accurate and robust time shift estimates for each time point on a gene-by-gene basis. Using these estimates, we are able to uncover novel features of the biological processes underlying human brain development and maturation. Conclusions The DTW-S provides a convenient tool for calculating accurate and robust time shift estimates at each time point for each gene, based on time series data. The estimates can be used to uncover novel biological features of the system being studied. The DTW-S is freely available as an R package TimeShift at http://www.picb.ac.cn/Comparative/data.html. PMID:21851598

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

PubMed

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

2011-08-18

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

The Meniscus-Deficient Knee

PubMed Central

Rao, Allison J.; Erickson, Brandon J.; Cvetanovich, Gregory L.; Yanke, Adam B.; Bach, Bernard R.; Cole, Brian J.

2015-01-01

Meniscal tears are the most common knee injury, and partial meniscectomies are the most common orthopaedic surgical procedure. The injured meniscus has an impaired ability to distribute load and resist tibial translation. Partial or complete loss of the meniscus promotes early development of chondromalacia and osteoarthritis. The primary goal of treatment for meniscus-deficient knees is to provide symptomatic relief, ideally to delay advanced joint space narrowing, and ultimately, joint replacement. Surgical treatments, including meniscal allograft transplantation (MAT), high tibial osteotomy (HTO), and distal femoral osteotomy (DFO), are options that attempt to decrease the loads on the articular cartilage of the meniscus-deficient compartment by replacing meniscal tissue or altering joint alignment. Clinical and biomechanical studies have reported promising outcomes for MAT, HTO, and DFO in the postmeniscectomized knee. These procedures can be performed alone or in conjunction with ligament reconstruction or chondral procedures (reparative, restorative, or reconstructive) to optimize stability and longevity of the knee. Complications can include fracture, nonunion, patella baja, compartment syndrome, infection, and deep venous thrombosis. MAT, HTO, and DFO are effective options for young patients suffering from pain and functional limitations secondary to meniscal deficiency. PMID:26779547

Differential evolution-simulated annealing for multiple sequence alignment

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

Novel Real-time Alignment and Calibration of the LHCb detector in Run2

NASA Astrophysics Data System (ADS)

Martinelli, Maurizio; LHCb Collaboration

2017-10-01

LHCb has introduced a novel real-time detector alignment and calibration strategy for LHC Run2. Data collected at the start of the fill are processed in a few minutes and used to update the alignment parameters, while the calibration constants are evaluated for each run. This procedure improves the quality of the online reconstruction. For example, the vertex locator is retracted and reinserted for stable beam conditions in each fill to be centred on the primary vertex position in the transverse plane. Consequently its position changes on a fill-by-fill basis. Critically, this new real-time alignment and calibration procedure allows identical constants to be used in the online and offline reconstruction, thus improving the correlation between triggered and offline-selected events. This offers the opportunity to optimise the event selection in the trigger by applying stronger constraints. The required computing time constraints are met thanks to a new dedicated framework using the multi-core farm infrastructure for the trigger. The motivation for a real-time alignment and calibration of the LHCb detector is discussed from both the operational and physics performance points of view. Specific challenges of this novel configuration are discussed, as well as the working procedures of the framework and its performance.

Lithographic process window optimization for mask aligner proximity lithography

NASA Astrophysics Data System (ADS)

Voelkel, Reinhard; Vogler, Uwe; Bramati, Arianna; Erdmann, Andreas; Ünal, Nezih; Hofmann, Ulrich; Hennemeyer, Marc; Zoberbier, Ralph; Nguyen, David; Brugger, Juergen

2014-03-01

We introduce a complete methodology for process window optimization in proximity mask aligner lithography. The commercially available lithography simulation software LAB from GenISys GmbH was used for simulation of light propagation and 3D resist development. The methodology was tested for the practical example of lines and spaces, 5 micron half-pitch, printed in a 1 micron thick layer of AZ® 1512HS1 positive photoresist on a silicon wafer. A SUSS MicroTec MA8 mask aligner, equipped with MO Exposure Optics® was used in simulation and experiment. MO Exposure Optics® is the latest generation of illumination systems for mask aligners. MO Exposure Optics® provides telecentric illumination and excellent light uniformity over the full mask field. MO Exposure Optics® allows the lithography engineer to freely shape the angular spectrum of the illumination light (customized illumination), which is a mandatory requirement for process window optimization. Three different illumination settings have been tested for 0 to 100 micron proximity gap. The results obtained prove, that the introduced process window methodology is a major step forward to obtain more robust processes in mask aligner lithography. The most remarkable outcome of the presented study is that a smaller exposure gap does not automatically lead to better print results in proximity lithography - what the "good instinct" of a lithographer would expect. With more than 5'000 mask aligners installed in research and industry worldwide, the proposed process window methodology might have significant impact on yield improvement and cost saving in industry.

Aligning Human Resource Development with the Strategic Priorities of Healthcare Organizations: The CFO Perspective

ERIC Educational Resources Information Center

Smith, Carla Breedlove

2013-01-01

The purpose of this qualitative study was to gain an understanding of how human resource development (HRD) can align more closely with the healthcare system's strategic priorities from the perspective of chief financial officers (CFOs). Five common themes emerged: (a) training is well aligned to the strategic priority to optimize clinical…

Asymmetric rotor-like probes to polarized fluorescence study of the macroscopically oriented uniaxial media: Model parameters recognition

NASA Astrophysics Data System (ADS)

Buczkowski, M.; Fisz, J. J.

2008-07-01

In this paper the possibility of the numerical data modelling in the case of angle- and time-resolved fluorescence spectroscopy is investigated. The asymmetric fluorescence probes are assumed to undergo the restricted rotational diffusion in a hosting medium. This process is described quantitatively by the diffusion tensor and the aligning potential. The evolution of the system is expressed in terms of the Smoluchowski equation with an appropriate time-developing operator. A matrix representation of this operator is calculated, then symmetrized and diagonalized. The resulting propagator is used to generate the synthetic noisy data set that imitates results of experimental measurements. The data set serves as a groundwork to the χ2 optimization, performed by the genetic algorithm followed by the gradient search, in order to recover model parameters, which are diagonal elements of the diffusion tensor, aligning potential expansion coefficients and directions of the electronic dipole moments. This whole procedure properly identifies model parameters, showing that the outlined formalism should be taken in the account in the case of analysing real experimental data.

Effect of band-aligned double absorber layers on photovoltaic characteristics of chemical bath deposited PbS/CdS thin film solar cells.

PubMed

Ho Yeon, Deuk; Chandra Mohanty, Bhaskar; Lee, Seung Min; Soo Cho, Yong

2015-09-23

Here we report the highest energy conversion efficiency and good stability of PbS thin film-based depleted heterojunction solar cells, not involving PbS quantum dots. The PbS thin films were grown by the low cost chemical bath deposition (CBD) process at relatively low temperatures. Compared to the quantum dot solar cells which require critical and multistep complex procedures for surface passivation, the present approach, leveraging the facile modulation of the optoelectronic properties of the PbS films by the CBD process, offers a simpler route for optimization of PbS-based solar cells. Through an architectural modification, wherein two band-aligned junctions are stacked without any intervening layers, an enhancement of conversion efficiency by as much as 30% from 3.10 to 4.03% facilitated by absorption of a wider range of solar spectrum has been obtained. As an added advantage of the low band gap PbS stacked over a wide gap PbS, the devices show stability over a period of 10 days.

RBT-GA: a novel metaheuristic for solving the Multiple Sequence Alignment problem.

PubMed

Taheri, Javid; Zomaya, Albert Y

2009-07-07

Multiple Sequence Alignment (MSA) has always been an active area of research in Bioinformatics. MSA is mainly focused on discovering biologically meaningful relationships among different sequences or proteins in order to investigate the underlying main characteristics/functions. This information is also used to generate phylogenetic trees. This paper presents a novel approach, namely RBT-GA, to solve the MSA problem using a hybrid solution methodology combining the Rubber Band Technique (RBT) and the Genetic Algorithm (GA) metaheuristic. RBT is inspired by the behavior of an elastic Rubber Band (RB) on a plate with several poles, which is analogues to locations in the input sequences that could potentially be biologically related. A GA attempts to mimic the evolutionary processes of life in order to locate optimal solutions in an often very complex landscape. RBT-GA is a population based optimization algorithm designed to find the optimal alignment for a set of input protein sequences. In this novel technique, each alignment answer is modeled as a chromosome consisting of several poles in the RBT framework. These poles resemble locations in the input sequences that are most likely to be correlated and/or biologically related. A GA-based optimization process improves these chromosomes gradually yielding a set of mostly optimal answers for the MSA problem. RBT-GA is tested with one of the well-known benchmarks suites (BALiBASE 2.0) in this area. The obtained results show that the superiority of the proposed technique even in the case of formidable sequences.

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.

Optimal design of an alignment-free two-DOF rehabilitation robot for the shoulder complex.

PubMed

Galinski, Daniel; Sapin, Julien; Dehez, Bruno

2013-06-01

This paper presents the optimal design of an alignment-free exoskeleton for the rehabilitation of the shoulder complex. This robot structure is constituted of two actuated joints and is linked to the arm through passive degrees of freedom (DOFs) to drive the flexion-extension and abduction-adduction movements of the upper arm. The optimal design of this structure is performed through two steps. The first step is a multi-objective optimization process aiming to find the best parameters characterizing the robot and its position relative to the patient. The second step is a comparison process aiming to select the best solution from the optimization results on the basis of several criteria related to practical considerations. The optimal design process leads to a solution outperforming an existing solution on aspects as kinematics or ergonomics while being more simple.

Genetic algorithms for protein threading.

PubMed

Yadgari, J; Amir, A; Unger, R

1998-01-01

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

Synthesis and orientation of barium hexaferrite ceramics by magnetic alignment

NASA Astrophysics Data System (ADS)

Autissier, Denis

1990-01-01

Particles of Ba 2Mn xZn 2- xFe 12O 22 with planar structure were prepared by chemical precipitation. They were processed by sleep casting in presence of a magnetic field. The degree of alignment was improved by a special sintering treatment. By this procedure an alignment as high as 99.9% is obtained.

Generating Models of Surgical Procedures using UMLS Concepts and Multiple Sequence Alignment

PubMed Central

Meng, Frank; D’Avolio, Leonard W.; Chen, Andrew A.; Taira, Ricky K.; Kangarloo, Hooshang

2005-01-01

Surgical procedures can be viewed as a process composed of a sequence of steps performed on, by, or with the patient’s anatomy. This sequence is typically the pattern followed by surgeons when generating surgical report narratives for documenting surgical procedures. This paper describes a methodology for semi-automatically deriving a model of conducted surgeries, utilizing a sequence of derived Unified Medical Language System (UMLS) concepts for representing surgical procedures. A multiple sequence alignment was computed from a collection of such sequences and was used for generating the model. These models have the potential of being useful in a variety of informatics applications such as information retrieval and automatic document generation. PMID:16779094

CORAL: aligning conserved core regions across domain families.

PubMed

Fong, Jessica H; Marchler-Bauer, Aron

2009-08-01

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

Piezoelectric Response of Aligned Electrospun Polyvinylidene Fluoride/Carbon Nanotube Nanofibrous Membranes.

PubMed

Wu, Chang-Mou; Chou, Min-Hui; Zeng, Wun-Yuan

2018-06-10

Polyvinylidene fluoride (PVDF) shows piezoelectricity related to its β-phase content and mechanical and electrical properties influenced by its morphology and crystallinity. Electrospinning (ES) can produce ultrafine and well-aligned PVDF nanofibers. In this study, the effects of the presence of carbon nanotubes (CNT) and optimized ES parameters on the crystal structures and piezoelectric properties of aligned PVDF/CNT nanofibrous membranes were examined. The optimal β content and piezoelectric coefficient (d 33 ) of the aligned electrospun PVDF reached 88% and 27.4 pC/N; CNT addition increased the β-phase content to 89% and d 33 to 31.3 pC/N. The output voltages of piezoelectric units with aligned electrospun PVDF/CNT membranes increased linearly with applied loading and showed good stability during cyclic dynamic compression and tension. The sensitivities of the piezoelectric units with the membranes under dynamic compression and tension were 2.26 mV/N and 4.29 mV/%, respectively. In bending tests, the output voltage increased nonlinearly with bending angle because complicated forces were involved. The output of the aligned membrane-based piezoelectric unit with CNT was 1.89 V at the bending angle of 100°. The high electric outputs indicate that the aligned electrospun PVDF/CNT membranes are potentially effective for flexible wearable sensor application with high sensitivity.

4D-CT motion estimation using deformable image registration and 5D respiratory motion modeling.

PubMed

Yang, Deshan; Lu, Wei; Low, Daniel A; Deasy, Joseph O; Hope, Andrew J; El Naqa, Issam

2008-10-01

Four-dimensional computed tomography (4D-CT) imaging technology has been developed for radiation therapy to provide tumor and organ images at the different breathing phases. In this work, a procedure is proposed for estimating and modeling the respiratory motion field from acquired 4D-CT imaging data and predicting tissue motion at the different breathing phases. The 4D-CT image data consist of series of multislice CT volume segments acquired in ciné mode. A modified optical flow deformable image registration algorithm is used to compute the image motion from the CT segments to a common full volume 3D-CT reference. This reference volume is reconstructed using the acquired 4D-CT data at the end-of-exhalation phase. The segments are optimally aligned to the reference volume according to a proposed a priori alignment procedure. The registration is applied using a multigrid approach and a feature-preserving image downsampling maxfilter to achieve better computational speed and higher registration accuracy. The registration accuracy is about 1.1 +/- 0.8 mm for the lung region according to our verification using manually selected landmarks and artificially deformed CT volumes. The estimated motion fields are fitted to two 5D (spatial 3D+tidal volume+airflow rate) motion models: forward model and inverse model. The forward model predicts tissue movements and the inverse model predicts CT density changes as a function of tidal volume and airflow rate. A leave-one-out procedure is used to validate these motion models. The estimated modeling prediction errors are about 0.3 mm for the forward model and 0.4 mm for the inverse model.

Handheld Navigation Device and Patient-Specific Cutting Guides Result in Similar Coronal Alignment for Primary Total Knee Arthroplasty: a Retrospective Matched Cohort Study.

PubMed

Steinhaus, Michael E; McLawhorn, Alexander S; Richardson, Shawn S; Maher, Patrick; Mayman, David J

2016-10-01

Proper alignment of total knee arthroplasty (TKA) is essential for TKA function and may reduce the risk of aseptic failure. Technologies that prevent malalignment may reduce the risk of revision surgery. The purpose of this study was to compare two competing TKA systems that purport improved alignment: patient-specific instrumentation (PSI), and a handheld portable navigation device (NAV). After IRB approval, 49 consecutive PSI TKAs (40 patients) were matched based on preoperative characteristics to 49 NAV TKAs (40 patients) performed by a single surgeon. A blinded observer measured alignment on digital radiographs. Operating room records were reviewed for procedure times. Two-tailed paired sample t tests and McNemar's test were used as appropriate. Alpha level was 0.05 for all tests. Preoperative cohort characteristics were not different. Mean postoperative long-leg mechanical alignment was within ±1° of neutral for both groups, although statistically different ( p  = 0.026). There were no other significant differences in coronal alignment. PSI exhibited significantly greater posterior tibial slope (4.4°) compared to NAV (2.7°) ( p  = 0.004); PSI resulted in significantly more outliers (>6°; p  = 0.004). Procedure time for unilateral TKAs was lower for PSI (74.4 min) compared to that for NAV (80.6 min; p  = 0.023). NAV and PSI technologies provided excellent coronal plane alignment. NAV was better for sagittal tibial slope, while PSI procedure times were shorter for unilateral TKA. The impact of these technologies on patient-reported outcomes and TKA survivorship is controversial and should be the focus of future research.

Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures

PubMed Central

2012-01-01

Background The NCBI Conserved Domain Database (CDD) consists of a collection of multiple sequence alignments of protein domains that are at various stages of being manually curated into evolutionary hierarchies based on conserved and divergent sequence and structural features. These domain models are annotated to provide insights into the relationships between sequence, structure and function via web-based BLAST searches. Results Here we automate the generation of conserved domain (CD) hierarchies using a combination of heuristic and Markov chain Monte Carlo (MCMC) sampling procedures and starting from a (typically very large) multiple sequence alignment. This procedure relies on statistical criteria to define each hierarchy based on the conserved and divergent sequence patterns associated with protein functional-specialization. At the same time this facilitates the sequence and structural annotation of residues that are functionally important. These statistical criteria also provide a means to objectively assess the quality of CD hierarchies, a non-trivial task considering that the protein subgroups are often very distantly related—a situation in which standard phylogenetic methods can be unreliable. Our aim here is to automatically generate (typically sub-optimal) hierarchies that, based on statistical criteria and visual comparisons, are comparable to manually curated hierarchies; this serves as the first step toward the ultimate goal of obtaining optimal hierarchical classifications. A plot of runtimes for the most time-intensive (non-parallelizable) part of the algorithm indicates a nearly linear time complexity so that, even for the extremely large Rossmann fold protein class, results were obtained in about a day. Conclusions This approach automates the rapid creation of protein domain hierarchies and thus will eliminate one of the most time consuming aspects of conserved domain database curation. At the same time, it also facilitates protein domain annotation by identifying those pattern residues that most distinguish each protein domain subgroup from other related subgroups. PMID:22726767

Alignment of sensor arrays in optical instruments using a geometric approach.

PubMed

Sawyer, Travis W

2018-02-01

Alignment of sensor arrays in optical instruments is critical to maximize the instrument's performance. While many commercial systems use standardized mounting threads for alignment, custom systems require specialized equipment and alignment procedures. These alignment procedures can be time-consuming, dependent on operator experience, and have low repeatability. Furthermore, each alignment solution must be considered on a case-by-case basis, leading to additional time and resource cost. Here I present a method to align a sensor array using geometric analysis. By imaging a grid pattern of dots, I show that it is possible to calculate the misalignment for a sensor in five degrees of freedom simultaneously. I first test the approach by simulating different cases of misalignment using Zemax before applying the method to experimentally acquired data of sensor misalignment for an echelle spectrograph. The results show that the algorithm effectively quantifies misalignment in five degrees of freedom for an F/5 imaging system, accurate to within ±0.87  deg in rotation and ±0.86  μm in translation. Furthermore, the results suggest that the method can also be applied to non-imaging systems with a small penalty to precision. This general approach can potentially improve the alignment of sensor arrays in custom instruments by offering an accurate, quantitative approach to calculating misalignment in five degrees of freedom simultaneously.

Management of idiopathic and nonidiopathic flatfoot.

PubMed

Frances, Jenny M; Feldman, David S

2015-01-01

Flatfoot in a child may be normal before development of the arch, but the prevalence decreases with age. Treatment is indicated only in the presence of pain and should begin with nonsurgical management options such as stretching of the Achilles tendon and the use of soft shoe orthotics. If pain persists, a modified Evans procedure, together with additional procedures to address forefoot supination, can be successful in correcting deformity and addressing pain. A thorough understanding of the pathology and correction desired will help minimize complications and recurrence. If neuromuscular pathology is present, treatment principles are altered and greatly depend on the severity of the deformity, the association of tibialis posterior spasticity, and ambulatory status. In mild to moderate pathology in walking patients with cerebral palsy, osteotomies can be successful. Various forms of arthrodesis can decrease recurrence when the deformity is severe in a nonambulatory patient with cerebral palsy and a symptomatic valgus foot deformity. In cases of collagen disorders, where soft-tissue laxity complicates management, deformity correction may be of higher importance. Overall alignment always should be evaluated and corrected when necessary to optimize the outcome in patients with valgus foot deformities. The successful treatment of flexible or rigid flatfoot deformity must take into account underlying pathology to optimize outcomes.

Concentration solar power optimization system and method of using the same

DOEpatents

Andraka, Charles E

2014-03-18

A system and method for optimizing at least one mirror of at least one CSP system is provided. The system has a screen for displaying light patterns for reflection by the mirror, a camera for receiving a reflection of the light patterns from the mirror, and a solar characterization tool. The solar characterization tool has a characterizing unit for determining at least one mirror parameter of the mirror based on an initial position of the camera and the screen, and a refinement unit for refining the determined parameter(s) based on an adjusted position of the camera and screen whereby the mirror is characterized. The system may also be provided with a solar alignment tool for comparing at least one mirror parameter of the mirror to a design geometry whereby an alignment error is defined, and at least one alignment unit for adjusting the mirror to reduce the alignment error.

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

PubMed

Kokiopoulou, Effrosyni; Kressner, Daniel; Frossard, Pascal

2011-06-01

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

A Coarse-Alignment Method Based on the Optimal-REQUEST Algorithm

PubMed Central

Zhu, Yongyun

2018-01-01

In this paper, we proposed a coarse-alignment method for strapdown inertial navigation systems based on attitude determination. The observation vectors, which can be obtained by inertial sensors, usually contain various types of noise, which affects the convergence rate and the accuracy of the coarse alignment. Given this drawback, we studied an attitude-determination method named optimal-REQUEST, which is an optimal method for attitude determination that is based on observation vectors. Compared to the traditional attitude-determination method, the filtering gain of the proposed method is tuned autonomously; thus, the convergence rate of the attitude determination is faster than in the traditional method. Within the proposed method, we developed an iterative method for determining the attitude quaternion. We carried out simulation and turntable tests, which we used to validate the proposed method’s performance. The experiment’s results showed that the convergence rate of the proposed optimal-REQUEST algorithm is faster and that the coarse alignment’s stability is higher. In summary, the proposed method has a high applicability to practical systems. PMID:29337895

Highly aligned arrays of high aspect ratio barium titanate nanowires via hydrothermal synthesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bowland, Christopher C.; Zhou, Zhi; Malakooti, Mohammad H.

2015-06-01

We report on the development of a hydrothermal synthesis procedure that results in the growth of highly aligned arrays of high aspect ratio barium titanate nanowires. Using a multiple step, scalable hydrothermal reaction, a textured titanium dioxide film is deposited on titanium foil upon which highly aligned nanowires are grown via homoepitaxy and converted to barium titanate. Scanning electron microscope images clearly illustrate the effect the textured film has on the degree of orientation of the nanowires. The alignment of nanowires is quantified by calculating the Herman's Orientation Factor, which reveals a 58% improvement in orientation as compared to growthmore » in the absence of the textured film. The ferroelectric properties of barium titanate combined with the development of this scalable growth procedure provide a powerful route towards increasing the efficiency and performance of nanowire-based devices in future real-world applications such as sensing and power harvesting.« less

Photocathode Optimization for a Dynamic Transmission Electron Microscope: Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ellis, P; Flom, Z; Heinselman, K

2011-08-04

The Dynamic Transmission Electron Microscope (DTEM) team at Harvey Mudd College has been sponsored by LLNL to design and build a test setup for optimizing the performance of the DTEM's electron source. Unlike a traditional TEM, the DTEM achieves much faster exposure times by using photoemission from a photocathode to produce electrons for imaging. The DTEM team's work is motivated by the need to improve the coherence and current density of the electron cloud produced by the electron gun in order to increase the image resolution and contrast achievable by DTEM. The photoemission test setup is nearly complete and themore » team will soon complete baseline tests of electron gun performance. The photoemission laser and high voltage power supply have been repaired; the optics path for relaying the laser to the photocathode has been finalized, assembled, and aligned; the internal setup of the vacuum chamber has been finalized and mostly implemented; and system control, synchronization, and data acquisition has been implemented in LabVIEW. Immediate future work includes determining a consistent alignment procedure to place the laser waist on the photocathode, and taking baseline performance measurements of the tantalum photocathode. Future research will examine the performance of the electron gun as a function of the photoemission laser profile, the photocathode material, and the geometry and voltages of the accelerating and focusing components in the electron gun. This report presents the team's progress and outlines the work that remains.« less

Reappraisal of the 2010 Maule, 2014 Iquique, 2015 Illapel through Inversion of Geodetic Data and Tsunami Waveforms Using the Optimal Time Alignment (OTA) Method

NASA Astrophysics Data System (ADS)

Romano, F.; Lorito, S.; Piatanesi, A.; Volpe, M.; Lay, T.; Tolomei, C.; Murphy, S.; Tonini, R.; Escalante, C.; Castro, M. J.; Gonzalez-Vida, J. M.; Macias, J.

2017-12-01

The Chile subduction zone is one of the most seismically active regions in the world and it hosted a number of great tsunamigenic earthquakes in the past. In particular, during the last 7 years three M8+ earthquakes occurred nearby the Chilean coasts, that is the 2010 M8.8 Maule, the 2014 M8.1 Iquique, and the M8.3 2015 Illapel earthquakes. The rupture process of these earthquakes has been studied by using different kind of geophysical observations such as seismic, geodetic, and tsunami data; in particular, tsunami waveforms are important for constraining the slip on the offshore portion of the fault. However, it has been shown that forward modelling of tsunami data can be affected by unavailability of accurate bathymetric models, especially in the vicinity of the tide-gauges; and in the far field by water density gradients, ocean floor elasticity, or geopotential gravity changes, generally neglected. This could result in a mismatch between observed and predicted tsunami signals thus affecting the retrieved tsunami source image. Recently, a method has been proposed for automatic correction during the nonlinear inversion of the mismatch (optimal time alignment, OTA; Romano et al., GRL, 2016). Here, we present a reappraisal of the joint inversion of tsunami data with OTA procedure and geodetic data, for the Maule, Iquique, and Illapel earthquakes. We compare the results with those obtained by tsunami inversion without using OTA and with other published inversion results.

Half a billion surgical cases: Aligning surgical delivery with best-performing health systems.

PubMed

Shrime, Mark G; Daniels, Kimberly M; Meara, John G

2015-07-01

Surgical delivery varies 200-fold across countries. No direct correlation exists, however, between surgical delivery and health outcomes, making it difficult to pinpoint a goal for surgical scale-up. This report determines the amount of surgery that would be delivered worldwide if the world aligned itself with countries providing the best health outcomes. Annual rates of surgical delivery have been published previously for 129 countries. Five health outcomes were plotted against reported surgical delivery. Univariate and multivariate polynomial regression curves were fit, and the optimal point on each regression curve was determined by solving for first-order conditions. The country closest to the optimum for each health outcome was taken as representative of the best-performing health system. Monetary inputs to and surgical procedures provided by these systems were scaled to the global population. For 3 of the 5 health outcomes, optima could be found. Globally, 315 million procedures currently are provided annually. If global delivery mirrored the 3 best-performing countries, between 360 million and 460 million cases would be provided annually. With population growth, this will increase to approximately half a billion cases by 2030. Health systems delivering these outcomes spend approximately 10% of their GDP on health. This is the first study to provide empirical evidence for the surgical output that an ideal health system would provide. Our results project ideal delivery worldwide of approximately 550 million annual surgical cases by 2030. Copyright © 2015 Elsevier Inc. All rights reserved.

Half a billion surgical cases: Aligning surgical delivery with best-performing health systems

PubMed Central

Shrime, Mark G.; Daniels, Kimberly M.; Meara, John G.

2015-01-01

Background Surgical delivery varies 200-fold across countries. No direct correlation exists, however, between surgical delivery and health outcomes, making it difficult to pinpoint a goal for surgical scale-up. This report determines the amount of surgery that would be delivered worldwide if the world aligned itself with countries providing the best health outcomes. Methods Annual rates of surgical delivery have been published previously for 129 countries. Five health outcomes were plotted against reported surgical delivery. Univariate and multivariate polynomial regression curves were fit, and the optimal point on each regression curve was determined by solving for first-order conditions. The country closest to the optimum for each health outcome was taken as representative of the best-performing health system. Monetary inputs to and surgical procedures provided by these systems were scaled to the global population. Results For 3 of the 5 health outcomes, optima could be found. Globally, 315 million procedures currently are provided annually. If global delivery mirrored the 3 best-performing countries, between 360 million and 460 million cases would be provided annually. With population growth, this will increase to approximately half a billion cases by 2030. Health systems delivering these outcomes spend approximately 10% of their GDP on health. Conclusion This is the first study to provide empirical evidence for the surgical output that an ideal health system would provide. Our results project ideal delivery worldwide of approximately 550 million annual surgical cases by 2030. PMID:25934078

RBT-GA: a novel metaheuristic for solving the multiple sequence alignment problem

PubMed Central

Taheri, Javid; Zomaya, Albert Y

2009-01-01

Background Multiple Sequence Alignment (MSA) has always been an active area of research in Bioinformatics. MSA is mainly focused on discovering biologically meaningful relationships among different sequences or proteins in order to investigate the underlying main characteristics/functions. This information is also used to generate phylogenetic trees. Results This paper presents a novel approach, namely RBT-GA, to solve the MSA problem using a hybrid solution methodology combining the Rubber Band Technique (RBT) and the Genetic Algorithm (GA) metaheuristic. RBT is inspired by the behavior of an elastic Rubber Band (RB) on a plate with several poles, which is analogues to locations in the input sequences that could potentially be biologically related. A GA attempts to mimic the evolutionary processes of life in order to locate optimal solutions in an often very complex landscape. RBT-GA is a population based optimization algorithm designed to find the optimal alignment for a set of input protein sequences. In this novel technique, each alignment answer is modeled as a chromosome consisting of several poles in the RBT framework. These poles resemble locations in the input sequences that are most likely to be correlated and/or biologically related. A GA-based optimization process improves these chromosomes gradually yielding a set of mostly optimal answers for the MSA problem. Conclusion RBT-GA is tested with one of the well-known benchmarks suites (BALiBASE 2.0) in this area. The obtained results show that the superiority of the proposed technique even in the case of formidable sequences. PMID:19594869

Bokeh mirror alignment for Cherenkov telescopes

NASA Astrophysics Data System (ADS)

Ahnen, M. L.; Baack, D.; Balbo, M.; Bergmann, M.; Biland, A.; Blank, M.; Bretz, T.; Bruegge, K. A.; Buss, J.; Domke, M.; Dorner, D.; Einecke, S.; Hempfling, C.; Hildebrand, D.; Hughes, G.; Lustermann, W.; Mannheim, K.; Mueller, S. A.; Neise, D.; Neronov, A.; Noethe, M.; Overkemping, A.-K.; Paravac, A.; Pauss, F.; Rhode, W.; Shukla, A.; Temme, F.; Thaele, J.; Toscano, S.; Vogler, P.; Walter, R.; Wilbert, A.

2016-09-01

Imaging Atmospheric Cherenkov Telescopes (IACTs) need imaging optics with large apertures and high image intensities to map the faint Cherenkov light emitted from cosmic ray air showers onto their image sensors. Segmented reflectors fulfill these needs, and composed from mass production mirror facets they are inexpensive and lightweight. However, as the overall image is a superposition of the individual facet images, alignment remains a challenge. Here we present a simple, yet extendable method, to align a segmented reflector using its Bokeh. Bokeh alig nment does not need a star or good weather nights but can be done even during daytime. Bokeh alignment optimizes the facet orientations by comparing the segmented reflectors Bokeh to a predefined template. The optimal Bokeh template is highly constricted by the reflector's aperture and is easy accessible. The Bokeh is observed using the out of focus image of a near by point like light source in a distance of about 10 focal lengths. We introduce Bokeh alignment on segmented reflectors and demonstrate it on the First Geiger-mode Avalanche Cherenkov Telescope (FACT) on La Palma, Spain.

Global Positioning System data collection, processing, and analysis conducted by the U.S. Geological Survey Earthquake Hazards Program

USGS Publications Warehouse

Murray, Jessica R.; Svarc, Jerry L.

2017-01-01

The U.S. Geological Survey Earthquake Science Center collects and processes Global Positioning System (GPS) data throughout the western United States to measure crustal deformation related to earthquakes and tectonic processes as part of a long‐term program of research and monitoring. Here, we outline data collection procedures and present the GPS dataset built through repeated temporary deployments since 1992. This dataset consists of observations at ∼1950 locations. In addition, this article details our data processing and analysis procedures, which consist of the following. We process the raw data collected through temporary deployments, in addition to data from continuously operating western U.S. GPS stations operated by multiple agencies, using the GIPSY software package to obtain position time series. Subsequently, we align the positions to a common reference frame, determine the optimal parameters for a temporally correlated noise model, and apply this noise model when carrying out time‐series analysis to derive deformation measures, including constant interseismic velocities, coseismic offsets, and transient postseismic motion.

Prototype of the novel CAMEA concept—A backend for neutron spectrometers

NASA Astrophysics Data System (ADS)

Markó, Márton; Groitl, Felix; Birk, Jonas Okkels; Freeman, Paul Gregory; Lefmann, Kim; Christensen, Niels Bech; Niedermayer, Christof; Jurányi, Fanni; Lass, Jakob; Hansen, Allan; Rønnow, Henrik M.

2018-01-01

The continuous angle multiple energy analysis concept is a backend for both time-of-flight and analyzer-based neutron spectrometers optimized for neutron spectroscopy with highly efficient mapping in the horizontal scattering plane. The design employs a series of several upward scattering analyzer arcs placed behind each other, which are set to different final energies allowing a wide angular coverage with multiple energies recorded simultaneously. For validation of the concept and the model calculations, a prototype was installed at the Swiss neutron source SINQ, Paul Scherrer Institut. The design of the prototype, alignment and calibration procedures, experimental results of background measurements, and proof-of-concept inelastic measurements on LiHoF4 and h-YMnO3 are presented here.

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

PubMed

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

2015-08-01

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

Mango: multiple alignment with N gapped oligos.

PubMed

Zhang, Zefeng; Lin, Hao; Li, Ming

2008-06-01

Multiple sequence alignment is a classical and challenging task. The problem is NP-hard. The full dynamic programming takes too much time. The progressive alignment heuristics adopted by most state-of-the-art works suffer from the "once a gap, always a gap" phenomenon. Is there a radically new way to do multiple sequence alignment? In this paper, we introduce a novel and orthogonal multiple sequence alignment method, using both multiple optimized spaced seeds and new algorithms to handle these seeds efficiently. Our new algorithm processes information of all sequences as a whole and tries to build the alignment vertically, avoiding problems caused by the popular progressive approaches. Because the optimized spaced seeds have proved significantly more sensitive than the consecutive k-mers, the new approach promises to be more accurate and reliable. To validate our new approach, we have implemented MANGO: Multiple Alignment with N Gapped Oligos. Experiments were carried out on large 16S RNA benchmarks, showing that MANGO compares favorably, in both accuracy and speed, against state-of-the-art multiple sequence alignment methods, including ClustalW 1.83, MUSCLE 3.6, MAFFT 5.861, ProbConsRNA 1.11, Dialign 2.2.1, DIALIGN-T 0.2.1, T-Coffee 4.85, POA 2.0, and Kalign 2.0. We have further demonstrated the scalability of MANGO on very large datasets of repeat elements. MANGO can be downloaded at http://www.bioinfo.org.cn/mango/ and is free for academic usage.

A comparison of radiographic anatomic axis knee alignment measurements and cross-sectional associations with knee osteoarthritis.

PubMed

Goulston, L M; Sanchez-Santos, M T; D'Angelo, S; Leyland, K M; Hart, D J; Spector, T D; Cooper, C; Dennison, E M; Hunter, D; Arden, N K

2016-04-01

Malalignment is associated with knee osteoarthritis (KOA), however, the optimal anatomic axis (AA) knee alignment measurement on a standard limb radiograph (SLR) is unknown. This study compares one-point (1P) and two-point (2P) AA methods using three knee joint centre locations and examines cross-sectional associations with symptomatic radiographic knee osteoarthritis (SRKOA), radiographic knee osteoarthritis (RKOA) and knee pain. AA alignment was measured six different ways using the KneeMorf software on 1058 SLRs from 584 women in the Chingford Study. Cross-sectional associations with principal outcome SRKOA combined with greatest reproducibility determined the optimal 1P and 2P AA method. Appropriate varus/neutral/valgus alignment categories were established using logistic regression with generalised estimating equation models fitted with restricted cubic spline function. The tibial plateau centre displayed greatest reproducibility and associations with SRKOA. As mean 1P and 2P values differed by >2°, new alignment categories were generated for 1P: varus <178°, neutral 178-182°, valgus >182° and for 2P methods: varus <180°, neutral 180-185°, valgus >185°. Varus vs neutral alignment was associated with a near 2-fold increase in SRKOA and RKOA, and valgus vs neutral for RKOA using 2P method. Nonsignificant associations were seen for 1P method for SRKOA, RKOA and knee pain. AA alignment was associated with SRKOA and the tibial plateau centre had the strongest association. Differences in AA alignment when 1P vs 2P methods were compared indicated bespoke alignment categories were necessary. Further replication and validation with mechanical axis alignment comparison is required. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

A comparison of radiographic anatomic axis knee alignment measurements and cross-sectional associations with knee osteoarthritis

PubMed Central

Goulston, L.M.; Sanchez-Santos, M.T.; D'Angelo, S.; Leyland, K.M.; Hart, D.J.; Spector, T.D.; Cooper, C.; Dennison, E.M.; Hunter, D.; Arden, N.K.

2016-01-01

Summary Objective Malalignment is associated with knee osteoarthritis (KOA), however, the optimal anatomic axis (AA) knee alignment measurement on a standard limb radiograph (SLR) is unknown. This study compares one-point (1P) and two-point (2P) AA methods using three knee joint centre locations and examines cross-sectional associations with symptomatic radiographic knee osteoarthritis (SRKOA), radiographic knee osteoarthritis (RKOA) and knee pain. Methods AA alignment was measured six different ways using the KneeMorf software on 1058 SLRs from 584 women in the Chingford Study. Cross-sectional associations with principal outcome SRKOA combined with greatest reproducibility determined the optimal 1P and 2P AA method. Appropriate varus/neutral/valgus alignment categories were established using logistic regression with generalised estimating equation models fitted with restricted cubic spline function. Results The tibial plateau centre displayed greatest reproducibility and associations with SRKOA. As mean 1P and 2P values differed by >2°, new alignment categories were generated for 1P: varus <178°, neutral 178–182°, valgus >182° and for 2P methods: varus <180°, neutral 180–185°, valgus >185°. Varus vs neutral alignment was associated with a near 2-fold increase in SRKOA and RKOA, and valgus vs neutral for RKOA using 2P method. Nonsignificant associations were seen for 1P method for SRKOA, RKOA and knee pain. Conclusions AA alignment was associated with SRKOA and the tibial plateau centre had the strongest association. Differences in AA alignment when 1P vs 2P methods were compared indicated bespoke alignment categories were necessary. Further replication and validation with mechanical axis alignment comparison is required. PMID:26700504

VANLO - Interactive visual exploration of aligned biological networks

PubMed Central

Brasch, Steffen; Linsen, Lars; Fuellen, Georg

2009-01-01

Background Protein-protein interaction (PPI) is fundamental to many biological processes. In the course of evolution, biological networks such as protein-protein interaction networks have developed. Biological networks of different species can be aligned by finding instances (e.g. proteins) with the same common ancestor in the evolutionary process, so-called orthologs. For a better understanding of the evolution of biological networks, such aligned networks have to be explored. Visualization can play a key role in making the various relationships transparent. Results We present a novel visualization system for aligned biological networks in 3D space that naturally embeds existing 2D layouts. In addition to displaying the intra-network connectivities, we also provide insight into how the individual networks relate to each other by placing aligned entities on top of each other in separate layers. We optimize the layout of the entire alignment graph in a global fashion that takes into account inter- as well as intra-network relationships. The layout algorithm includes a step of merging aligned networks into one graph, laying out the graph with respect to application-specific requirements, splitting the merged graph again into individual networks, and displaying the network alignment in layers. In addition to representing the data in a static way, we also provide different interaction techniques to explore the data with respect to application-specific tasks. Conclusion Our system provides an intuitive global understanding of aligned PPI networks and it allows the investigation of key biological questions. We evaluate our system by applying it to real-world examples documenting how our system can be used to investigate the data with respect to these key questions. Our tool VANLO (Visualization of Aligned Networks with Layout Optimization) can be accessed at . PMID:19821976

Long Read Alignment with Parallel MapReduce Cloud Platform

PubMed Central

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

2015-01-01

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

Long Read Alignment with Parallel MapReduce Cloud Platform.

PubMed

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

2015-01-01

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

Protein alignment algorithms with an efficient backtracking routine on multiple GPUs.

PubMed

Blazewicz, Jacek; Frohmberg, Wojciech; Kierzynka, Michal; Pesch, Erwin; Wojciechowski, Pawel

2011-05-20

Pairwise sequence alignment methods are widely used in biological research. The increasing number of sequences is perceived as one of the upcoming challenges for sequence alignment methods in the nearest future. To overcome this challenge several GPU (Graphics Processing Unit) computing approaches have been proposed lately. These solutions show a great potential of a GPU platform but in most cases address the problem of sequence database scanning and computing only the alignment score whereas the alignment itself is omitted. Thus, the need arose to implement the global and semiglobal Needleman-Wunsch, and Smith-Waterman algorithms with a backtracking procedure which is needed to construct the alignment. In this paper we present the solution that performs the alignment of every given sequence pair, which is a required step for progressive multiple sequence alignment methods, as well as for DNA recognition at the DNA assembly stage. Performed tests show that the implementation, with performance up to 6.3 GCUPS on a single GPU for affine gap penalties, is very efficient in comparison to other CPU and GPU-based solutions. Moreover, multiple GPUs support with load balancing makes the application very scalable. The article shows that the backtracking procedure of the sequence alignment algorithms may be designed to fit in with the GPU architecture. Therefore, our algorithm, apart from scores, is able to compute pairwise alignments. This opens a wide range of new possibilities, allowing other methods from the area of molecular biology to take advantage of the new computational architecture. Performed tests show that the efficiency of the implementation is excellent. Moreover, the speed of our GPU-based algorithms can be almost linearly increased when using more than one graphics card.

Optimal geometrical design of inertial vibration DC piezoelectric nanogenerators based on obliquely aligned InN nanowire arrays.

PubMed

Ku, Nai-Jen; Liu, Guocheng; Wang, Chao-Hung; Gupta, Kapil; Liao, Wei-Shun; Ban, Dayan; Liu, Chuan-Pu

2017-09-28

Piezoelectric nanogenerators have been investigated to generate electricity from environmental vibrations due to their energy conversion capabilities. In this study, we demonstrate an optimal geometrical design of inertial vibration direct-current piezoelectric nanogenerators based on obliquely aligned InN nanowire (NW) arrays with an optimized oblique angle of ∼58°, and driven by the inertial force of their own weight, using a mechanical shaker without any AC/DC converters. The nanogenerator device manifests potential applications not only as a unique energy harvesting device capable of scavenging energy from weak mechanical vibrations, but also as a sensitive strain sensor. The maximum output power density of the nanogenerator is estimated to be 2.9 nW cm -2 , leading to an improvement of about 3-12 times that of vertically aligned ZnO NW DC nanogenerators. Integration of two nanogenerators also exhibits a linear increase in the output power, offering an enormous potential for the creation of self-powered sustainable nanosystems utilizing incessantly natural ambient energy sources.

Improved, ACMG-Compliant, in silico prediction of pathogenicity for missense substitutions encoded by TP53 variants.

PubMed

Fortuno, Cristina; James, Paul A; Young, Erin L; Feng, Bing; Olivier, Magali; Pesaran, Tina; Tavtigian, Sean V; Spurdle, Amanda B

2018-05-18

Clinical interpretation of germline missense variants represents a major challenge, including those in the TP53 Li-Fraumeni syndrome gene. Bioinformatic prediction is a key part of variant classification strategies. We aimed to optimize the performance of the Align-GVGD tool used for p53 missense variant prediction, and compare its performance to other bioinformatic tools (SIFT, PolyPhen-2) and ensemble methods (REVEL, BayesDel). Reference sets of assumed pathogenic and assumed benign variants were defined using functional and/or clinical data. Area under the curve and Matthews correlation coefficient (MCC) values were used as objective functions to select an optimized protein multi-sequence alignment with best performance for Align-GVGD. MCC comparison of tools using binary categories showed optimized Align-GVGD (C15 cut-off) combined with BayesDel (0.16 cut-off), or with REVEL (0.5 cut-off), to have the best overall performance. Further, a semi-quantitative approach using multiple tiers of bioinformatic prediction, validated using an independent set of non-functional and functional variants, supported use of Align-GVGD and BayesDel prediction for different strength of evidence levels in ACMG/AMP rules. We provide rationale for bioinformatic tool selection for TP53 variant classification, and have also computed relevant bioinformatic predictions for every possible p53 missense variant to facilitate their use by the scientific and medical community. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Simulation-based comprehensive benchmarking of RNA-seq aligners

PubMed Central

Baruzzo, Giacomo; Hayer, Katharina E; Kim, Eun Ji; Di Camillo, Barbara; FitzGerald, Garret A; Grant, Gregory R

2018-01-01

Alignment is the first step in most RNA-seq analysis pipelines, and the accuracy of downstream analyses depends heavily on it. Unlike most steps in the pipeline, alignment is particularly amenable to benchmarking with simulated data. We performed a comprehensive benchmarking of 14 common splice-aware aligners for base, read, and exon junction-level accuracy and compared default with optimized parameters. We found that performance varied by genome complexity, and accuracy and popularity were poorly correlated. The most widely cited tool underperforms for most metrics, particularly when using default settings. PMID:27941783

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.

Integration of Microdialysis Sampling and Microchip Electrophoresis with Electrochemical Detection

PubMed Central

Mecker, Laura C.; Martin, R. Scott

2009-01-01

Here we describe the fabrication, optimization, and application of a microfluidic device that integrates microdialysis (MD) sampling, microchip electrophoresis (ME), and electrochemical detection (EC). The manner in which the chip is produced is reproducible and enables the fixed alignment of the MD/ME and ME/EC interfaces. Poly(dimethylsiloxane) (PDMS) -based valves were used for the discrete injection of sample from the hydrodynamic MD dialysate stream into a separation channel for analysis with ME. To enable the integration of ME with EC detection, a palladium decoupler was used to isolate the high voltages associated with electrophoresis from micron-sized carbon ink detection electrodes. Optimization of the ME/EC interface was needed to allow the use of biologically appropriate perfusate buffers containing high salt content. This optimization included changes in the fabrication procedure, increases in the decoupler surface area, and a programmed voltage shutoff. The ability of the MD/ME/EC system to sample a biological system was demonstrated by using a linear probe to monitor the stimulated release of dopamine from a confluent layer of PC 12 cells. To our knowledge, this is the first report of a microchip-based system that couples microdialysis sampling with microchip electrophoresis and electrochemical detection. PMID:19551945

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.

Study of optical techniques for the Ames unitary wind tunnels. Part 1: Schlieren

NASA Technical Reports Server (NTRS)

Lee, George

1992-01-01

Alignment procedures and conceptual designs for the rapid alignment of the Ames Unitary Wind Tunnel schlieren systems were devised. The schlieren systems can be aligned by translating the light source, the mirrors, and the knife edge equal distances. One design for rapid alignment consists of a manual pin locking scheme. The other is a motorized electronic position scheme. A study of two optical concepts which can be used with the schlieren system was made. These are the 'point diffraction interferometers' and the 'focus schlieren'. Effects of vibrations were studied.

An optimization-based approach for high-order accurate discretization of conservation laws with discontinuous solutions

NASA Astrophysics Data System (ADS)

Zahr, M. J.; Persson, P.-O.

2018-07-01

This work introduces a novel discontinuity-tracking framework for resolving discontinuous solutions of conservation laws with high-order numerical discretizations that support inter-element solution discontinuities, such as discontinuous Galerkin or finite volume methods. The proposed method aims to align inter-element boundaries with discontinuities in the solution by deforming the computational mesh. A discontinuity-aligned mesh ensures the discontinuity is represented through inter-element jumps while smooth basis functions interior to elements are only used to approximate smooth regions of the solution, thereby avoiding Gibbs' phenomena that create well-known stability issues. Therefore, very coarse high-order discretizations accurately resolve the piecewise smooth solution throughout the domain, provided the discontinuity is tracked. Central to the proposed discontinuity-tracking framework is a discrete PDE-constrained optimization formulation that simultaneously aligns the computational mesh with discontinuities in the solution and solves the discretized conservation law on this mesh. The optimization objective is taken as a combination of the deviation of the finite-dimensional solution from its element-wise average and a mesh distortion metric to simultaneously penalize Gibbs' phenomena and distorted meshes. It will be shown that our objective function satisfies two critical properties that are required for this discontinuity-tracking framework to be practical: (1) possesses a local minima at a discontinuity-aligned mesh and (2) decreases monotonically to this minimum in a neighborhood of radius approximately h / 2, whereas other popular discontinuity indicators fail to satisfy the latter. Another important contribution of this work is the observation that traditional reduced space PDE-constrained optimization solvers that repeatedly solve the conservation law at various mesh configurations are not viable in this context since severe overshoot and undershoot in the solution, i.e., Gibbs' phenomena, may make it impossible to solve the discrete conservation law on non-aligned meshes. Therefore, we advocate a gradient-based, full space solver where the mesh and conservation law solution converge to their optimal values simultaneously and therefore never require the solution of the discrete conservation law on a non-aligned mesh. The merit of the proposed method is demonstrated on a number of one- and two-dimensional model problems including the L2 projection of discontinuous functions, Burgers' equation with a discontinuous source term, transonic flow through a nozzle, and supersonic flow around a bluff body. We demonstrate optimal O (h p + 1) convergence rates in the L1 norm for up to polynomial order p = 6 and show that accurate solutions can be obtained on extremely coarse meshes.

Mechanical alignment of particles for use in fabricating superconducting and permanent magnetic materials

DOEpatents

Nellis, William J.; Maple, M. Brian

1992-01-01

A method for mechanically aligning oriented superconducting or permanently magnetic materials for further processing into constructs. This pretreatment optimizes the final crystallographic orientation and, thus, properties in these constructs. Such materials as superconducting fibers, needles and platelets are utilized.

Studies on in situ magnetic alignment of bonded anisotropic Nd-Fe-B alloy powders

DOE PAGES

Nlebedim, I. C.; Ucar, Huseyin; Hatter, Christine B.; ...

2016-08-30

We presented some considerations for achieving high degree of alignment in polymer bonded permanent magnets via the results of a study on in situ magnetic alignment of anisotropic Nd-Fe-B magnet powders. Contributions from effect of the alignment temperature, alignment magnetic field and the properties of the polymer on the hard magnetic properties of the bonded magnet were considered. Moreover, the thermo-rheological properties of the polymer and the response of the magnet powders to the applied magnetic field indicate that hard magnetic properties were optimized at an alignment temperature just above the melting temperature of the EVA co-polymer. This agrees withmore » an observed correlation between the change in magnetization due to improved magnetic alignment of the anisotropic powders and the change in viscosity of the binder. Finally, manufacturing cost can be minimized by identifying optimum alignment temperatures and magnetic field strengths.« less

Studies on in situ magnetic alignment of bonded anisotropic Nd-Fe-B alloy powders

NASA Astrophysics Data System (ADS)

Nlebedim, I. C.; Ucar, Huseyin; Hatter, Christine B.; McCallum, R. W.; McCall, Scott K.; Kramer, M. J.; Paranthaman, M. Parans

2017-01-01

Considerations for achieving high degree of alignment in polymer bonded permanent magnets are presented via the results of a study on in situ magnetic alignment of anisotropic Nd-Fe-B magnet powders. Contributions from effect of the alignment temperature, alignment magnetic field and the properties of the polymer on the hard magnetic properties of the bonded magnet were considered. The thermo-rheological properties of the polymer and the response of the magnet powders to the applied magnetic field indicate that hard magnetic properties were optimized at an alignment temperature just above the melting temperature of the EVA co-polymer. This agrees with an observed correlation between the change in magnetization due to improved magnetic alignment of the anisotropic powders and the change in viscosity of the binder. Manufacturing cost can be minimized by identifying optimum alignment temperatures and magnetic field strengths.

Feature Based Retention Time Alignment for Improved HDX MS Analysis

NASA Astrophysics Data System (ADS)

Venable, John D.; Scuba, William; Brock, Ansgar

2013-04-01

An algorithm for retention time alignment of mass shifted hydrogen-deuterium exchange (HDX) data based on an iterative distance minimization procedure is described. The algorithm performs pairwise comparisons in an iterative fashion between a list of features from a reference file and a file to be time aligned to calculate a retention time mapping function. Features are characterized by their charge, retention time and mass of the monoisotopic peak. The algorithm is able to align datasets with mass shifted features, which is a prerequisite for aligning hydrogen-deuterium exchange mass spectrometry datasets. Confidence assignments from the fully automated processing of a commercial HDX software package are shown to benefit significantly from retention time alignment prior to extraction of deuterium incorporation values.

Aligning Greek-English parallel texts

NASA Astrophysics Data System (ADS)

Galiotou, Eleni; Koronakis, George; Lazari, Vassiliki

2015-02-01

In this paper, we discuss issues concerning the alignment of parallel texts written in languages with different alphabets based on an experiment of aligning texts from the proceedings of the European Parliament in Greek and English. First, we describe our implementation of the k-vec algorithm and its application to the bilingual corpus. Then the output of the algorithm is used as a starting point for an alignment procedure at a sentence level which also takes into account mark-ups of meta-information. The results of the implementation are compared to those of the application of the Church and Gale alignment algorithm on the Europarl corpus. The conclusions of this comparison can give useful insights as for the efficiency of alignment algorithms when applied to the particular bilingual corpus.

Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments.

PubMed

Daily, Jeff

2016-02-10

Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. A faster intra-sequence local pairwise alignment implementation is described and benchmarked, including new global and semi-global variants. Using a 375 residue query sequence a speed of 136 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon E5-2670 24-core processor system, the highest reported for an implementation based on Farrar's 'striped' approach. Rognes's SWIPE optimal database search application is still generally the fastest available at 1.2 to at best 2.4 times faster than Parasail for sequences shorter than 500 amino acids. However, Parasail was faster for longer sequences. For global alignments, Parasail's prefix scan implementation is generally the fastest, faster even than Farrar's 'striped' approach, however the opal library is faster for single-threaded applications. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. Applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.

Magnetic field design for selecting and aligning immunomagnetic labeled cells.

PubMed

Tibbe, Arjan G J; de Grooth, Bart G; Greve, Jan; Dolan, Gerald J; Rao, Chandra; Terstappen, Leon W M M

2002-03-01

Recently we introduced the CellTracks cell analysis system, in which samples are prepared based on a combination of immunomagnetic selection, separation, and alignment of cells along ferromagnetic lines. Here we describe the underlying magnetic principles and considerations made in the magnetic field design to achieve the best possible cell selection and alignment of magnetically labeled cells. Materials and Methods Computer simulations, in combination with experimental data, were used to optimize the design of the magnets and Ni lines to obtain the optimal magnetic configuration. A homogeneous cell distribution on the upper surface of the sample chamber was obtained with a magnet where the pole faces were tilted towards each other. The spatial distribution of magnetically aligned objects in between the Ni lines was dependent on the ratio of the diameter of the aligned object and the line spacing, which was tested with magnetically and fluorescently labeled 6 microm polystyrene beads. The best result was obtained when the line spacing was equal to or smaller than the diameter of the aligned object. The magnetic gradient of the designed permanent magnet extracts magnetically labeled cells from any cell suspension to a desired plane, providing a homogeneous cell distribution. In addition, it magnetizes ferro-magnetic Ni lines in this plane whose additional local gradient adds to the gradient of the permanent magnet. The resultant gradient aligns the magnetically labeled cells first brought to this plane. This combination makes it possible, in a single step, to extract and align cells on a surface from any cell suspension. Copyright 2002 Wiley-Liss, Inc.

CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment

PubMed Central

Manavski, Svetlin A; Valle, Giorgio

2008-01-01

Background Searching for similarities in protein and DNA databases has become a routine procedure in Molecular Biology. The Smith-Waterman algorithm has been available for more than 25 years. It is based on a dynamic programming approach that explores all the possible alignments between two sequences; as a result it returns the optimal local alignment. Unfortunately, the computational cost is very high, requiring a number of operations proportional to the product of the length of two sequences. Furthermore, the exponential growth of protein and DNA databases makes the Smith-Waterman algorithm unrealistic for searching similarities in large sets of sequences. For these reasons heuristic approaches such as those implemented in FASTA and BLAST tend to be preferred, allowing faster execution times at the cost of reduced sensitivity. The main motivation of our work is to exploit the huge computational power of commonly available graphic cards, to develop high performance solutions for sequence alignment. Results In this paper we present what we believe is the fastest solution of the exact Smith-Waterman algorithm running on commodity hardware. It is implemented in the recently released CUDA programming environment by NVidia. CUDA allows direct access to the hardware primitives of the last-generation Graphics Processing Units (GPU) G80. Speeds of more than 3.5 GCUPS (Giga Cell Updates Per Second) are achieved on a workstation running two GeForce 8800 GTX. Exhaustive tests have been done to compare our implementation to SSEARCH and BLAST, running on a 3 GHz Intel Pentium IV processor. Our solution was also compared to a recently published GPU implementation and to a Single Instruction Multiple Data (SIMD) solution. These tests show that our implementation performs from 2 to 30 times faster than any other previous attempt available on commodity hardware. Conclusions The results show that graphic cards are now sufficiently advanced to be used as efficient hardware accelerators for sequence alignment. Their performance is better than any alternative available on commodity hardware platforms. The solution presented in this paper allows large scale alignments to be performed at low cost, using the exact Smith-Waterman algorithm instead of the largely adopted heuristic approaches. PMID:18387198

Overcoming low-alignment signal contrast induced alignment failure by alignment signal enhancement

NASA Astrophysics Data System (ADS)

Lee, Byeong Soo; Kim, Young Ha; Hwang, Hyunwoo; Lee, Jeongjin; Kong, Jeong Heung; Kang, Young Seog; Paarhuis, Bart; Kok, Haico; de Graaf, Roelof; Weichselbaum, Stefan; Droste, Richard; Mason, Christopher; Aarts, Igor; de Boeij, Wim P.

2016-03-01

Overlay is one of the key factors which enables optical lithography extension to 1X node DRAM manufacturing. It is natural that accurate wafer alignment is a prerequisite for good device overlay. However, alignment failures or misalignments are commonly observed in a fab. There are many factors which could induce alignment problems. Low alignment signal contrast is one of the main issues. Alignment signal contrast can be degraded by opaque stack materials or by alignment mark degradation due to processes like CMP. This issue can be compounded by mark sub-segmentation from design rules in combination with double or quadruple spacer process. Alignment signal contrast can be improved by applying new material or process optimization, which sometimes lead to the addition of another process-step with higher costs. If we can amplify the signal components containing the position information and reduce other unwanted signal and background contributions then we can improve alignment performance without process change. In this paper we use ASML's new alignment sensor (as was introduced and released on the NXT:1980Di) and sample wafers with special stacks which can induce poor alignment signal to demonstrate alignment and overlay improvement.

Determination of aberration center of Ronchigram for automated aberration correctors in scanning transmission electron microscopy.

PubMed

Sannomiya, Takumi; Sawada, Hidetaka; Nakamichi, Tomohiro; Hosokawa, Fumio; Nakamura, Yoshio; Tanishiro, Yasumasa; Takayanagi, Kunio

2013-12-01

A generic method to determine the aberration center is established, which can be utilized for aberration calculation and axis alignment for aberration corrected electron microscopes. In this method, decentering induced secondary aberrations from inherent primary aberrations are minimized to find the appropriate axis center. The fitness function to find the optimal decentering vector for the axis was defined as a sum of decentering induced secondary aberrations with properly distributed weight values according to the aberration order. Since the appropriate decentering vector is determined from the aberration values calculated at an arbitrary center axis, only one aberration measurement is in principle required to find the center, resulting in /very fast center search. This approach was tested for the Ronchigram based aberration calculation method for aberration corrected scanning transmission electron microscopy. Both in simulation and in experiments, the center search was confirmed to work well although the convergence to find the best axis becomes slower with larger primary aberrations. Such aberration center determination is expected to fully automatize the aberration correction procedures, which used to require pre-alignment of experienced users. This approach is also applicable to automated aperture positioning. Copyright © 2013 Elsevier B.V. All rights reserved.

Evaluation of peak picking quality in LC-MS metabolomics data.

PubMed

Brodsky, Leonid; Moussaieff, Arieh; Shahaf, Nir; Aharoni, Asaph; Rogachev, Ilana

2010-11-15

The output of LC-MS metabolomics experiments consists of mass-peak intensities identified through a peak-picking/alignment procedure. Besides imperfections in biological samples and instrumentation, data accuracy is highly dependent on the applied algorithms and their parameters. Consequently, quality control (QC) is essential for further data analysis. Here, we present a QC approach that is based on discrepancies between replicate samples. First, the quantile normalization of per-sample log-signal distributions is applied to each group of biologically homogeneous samples. Next, the overall quality of each replicate group is characterized by the Z-transformed correlation coefficients between samples. This general QC allows a tuning of the procedure's parameters which minimizes the inter-replicate discrepancies in the generated output. Subsequently, an in-depth QC measure detects local neighborhoods on a template of aligned chromatograms that are enriched by divergences between intensity profiles of replicate samples. These neighborhoods are determined through a segmentation algorithm. The retention time (RT)-m/z positions of the neighborhoods with local divergences are indicative of either: incorrect alignment of chromatographic features, technical problems in the chromatograms, or to a true biological discrepancy between replicates for particular metabolites. We expect this method to aid in the accurate analysis of metabolomics data and in the development of new peak-picking/alignment procedures.

Energy level alignment at molecule-metal interfaces from an optimally tuned range-separated hybrid functional

DOE PAGES

Liu, Zhen-Fei; Egger, David A.; Refaely-Abramson, Sivan; ...

2017-02-21

The alignment of the frontier orbital energies of an adsorbed molecule with the substrate Fermi level at metal-organic interfaces is a fundamental observable of significant practical importance in nanoscience and beyond. Typical density functional theory calculations, especially those using local and semi-local functionals, often underestimate level alignment leading to inaccurate electronic structure and charge transport properties. Here, we develop a new fully self-consistent predictive scheme to accurately compute level alignment at certain classes of complex heterogeneous molecule-metal interfaces based on optimally tuned range-separated hybrid functionals. Starting from a highly accurate description of the gas-phase electronic structure, our method by constructionmore » captures important nonlocal surface polarization effects via tuning of the long-range screened exchange in a range-separated hybrid in a non-empirical and system-specific manner. We implement this functional in a plane-wave code and apply it to several physisorbed and chemisorbed molecule-metal interface systems. Our results are in quantitative agreement with experiments, the both the level alignment and work function changes. This approach constitutes a new practical scheme for accurate and efficient calculations of the electronic structure of molecule-metal interfaces.« less

Energy level alignment at molecule-metal interfaces from an optimally tuned range-separated hybrid functional

NASA Astrophysics Data System (ADS)

Liu, Zhen-Fei; Egger, David A.; Refaely-Abramson, Sivan; Kronik, Leeor; Neaton, Jeffrey B.

2017-03-01

The alignment of the frontier orbital energies of an adsorbed molecule with the substrate Fermi level at metal-organic interfaces is a fundamental observable of significant practical importance in nanoscience and beyond. Typical density functional theory calculations, especially those using local and semi-local functionals, often underestimate level alignment leading to inaccurate electronic structure and charge transport properties. In this work, we develop a new fully self-consistent predictive scheme to accurately compute level alignment at certain classes of complex heterogeneous molecule-metal interfaces based on optimally tuned range-separated hybrid functionals. Starting from a highly accurate description of the gas-phase electronic structure, our method by construction captures important nonlocal surface polarization effects via tuning of the long-range screened exchange in a range-separated hybrid in a non-empirical and system-specific manner. We implement this functional in a plane-wave code and apply it to several physisorbed and chemisorbed molecule-metal interface systems. Our results are in quantitative agreement with experiments, the both the level alignment and work function changes. Our approach constitutes a new practical scheme for accurate and efficient calculations of the electronic structure of molecule-metal interfaces.

Downsizing in the public sector: Metro-Toronto's hospitals.

PubMed

Flint, Douglas H

2003-01-01

This study has two objectives. First, to predict the outcomes of a public sector downsizing; second to measure effects of downsizing at organizational and inter-organizational levels. Primary data to assess the organizational level effects was collected through interviews with senior executives at two of Metro-Toronto's hospitals. Secondary data, to assess the inter-organizational effects, was collected from government documents and media reports. Due to the exploratory nature of the study's objectives a case study method was employed. Most institutional downsizing practices aligned with successful outcomes. Procedures involved at the inter-organizational level aligned with unsuccessful outcomes and negated organizational initiatives. This resulted in an overall alignment with unsuccessful procedures. The implication, based on private sector downsizings, is that the post-downsized hospital system was more costly and less effective.

23 CFR 620.203 - Procedures.

Code of Federal Regulations, 2012 CFR

2012-04-01

... grade and/or alignment, including new right-of-way required for adjustments. Eligibility for Federal-aid... eliminating the necessity of a formal transfer later. Such procedure would be subject to prior FHWA approval...

23 CFR 620.203 - Procedures.

Code of Federal Regulations, 2014 CFR

2014-04-01

... grade and/or alignment, including new right-of-way required for adjustments. Eligibility for Federal-aid... eliminating the necessity of a formal transfer later. Such procedure would be subject to prior FHWA approval...

23 CFR 620.203 - Procedures.

Code of Federal Regulations, 2013 CFR

2013-04-01

... grade and/or alignment, including new right-of-way required for adjustments. Eligibility for Federal-aid... eliminating the necessity of a formal transfer later. Such procedure would be subject to prior FHWA approval...

Relation between film character and wafer alignment: critical alignment issues on HV device for VLSI manufacturing

NASA Astrophysics Data System (ADS)

Lo, Yi-Chuan; Lee, Chih-Hsiung; Lin, Hsun-Peng; Peng, Chiou-Shian

1998-06-01

Several continuous splits for wafer alignment target topography conditions to improve epitaxy film alignment were applied. The alignment evaluation among former layer pad oxide thickness (250 angstrom - 500 angstrom), drive oxide thickness (6000 angstrom - 10000 angstrom), nitride film thickness (600 angstrom - 1500 angstrom), initial oxide etch (fully wet etch, fully dry etch and dry plus wet etch) will be split to this experiment. Also various epitaxy deposition recipe such as: epitaxy source (SiHCl2 or SiCHCl3) and growth rate (1.3 micrometer/min approximately 2.0 micrometer/min) will be used to optimize the process window for alignment issue. All the reflectance signal and cross section photography of alignment target during NIKON stepper alignment process will be examined. Experimental results show epitaxy recipe plays an important role to wafer alignment. Low growth rate with good performance conformity epitaxy lead to alignment target avoid washout, pattern shift and distortion. All the results (signal monitor and film character) combined with NIKON's stepper standard laser scanning alignment system will be discussed in this paper.

A Figure-of-Merit for Designing High-Performance Inductive Power Transmission Links

PubMed Central

Kiani, Mehdi; Ghovanloo, Maysam

2014-01-01

Power transfer efficiency (PTE) and power delivered to the load (PDL) are two key inductive link design parameters that relate to the power source and driver specs, power loss, transmission range, robustness against misalignment, variations in loading, and interference with other devices. Designers need to strike a delicate balance between these two because designing the link to achieve high PTE will degrade the PDL and vice versa. We are proposing a new figure-of-merit (FoM), which can help designers to find out whether a two-, three-, or four-coil link is appropriate for their particular application and guide them through an iterative design procedure to reach optimal coil geometries based on how they weigh the PTE versus PDL for that application. Three design examples at three different power levels have been presented based on the proposed FoM for implantable microelectronic devices, handheld mobile devices, and electric vehicles. The new FoM suggests that the two-coil links are suitable when the coils are strongly coupled, and a large PDL is needed. Three-coil links are the best when the coils are loosely coupled, the coupling distance varies considerably, and large PDL is necessary. Finally, four-coil links are optimal when the PTE is paramount, the coils are loosely coupled, and their relative distance and alignment are stable. Measurement results support the accuracy of the theoretical design procedure and conclusions. PMID:25382898

A Figure-of-Merit for Designing High-Performance Inductive Power Transmission Links.

PubMed

Kiani, Mehdi; Ghovanloo, Maysam

2012-11-16

Power transfer efficiency (PTE) and power delivered to the load (PDL) are two key inductive link design parameters that relate to the power source and driver specs, power loss, transmission range, robustness against misalignment, variations in loading, and interference with other devices. Designers need to strike a delicate balance between these two because designing the link to achieve high PTE will degrade the PDL and vice versa. We are proposing a new figure-of-merit (FoM), which can help designers to find out whether a two-, three-, or four-coil link is appropriate for their particular application and guide them through an iterative design procedure to reach optimal coil geometries based on how they weigh the PTE versus PDL for that application. Three design examples at three different power levels have been presented based on the proposed FoM for implantable microelectronic devices, handheld mobile devices, and electric vehicles. The new FoM suggests that the two-coil links are suitable when the coils are strongly coupled, and a large PDL is needed. Three-coil links are the best when the coils are loosely coupled, the coupling distance varies considerably, and large PDL is necessary. Finally, four-coil links are optimal when the PTE is paramount, the coils are loosely coupled, and their relative distance and alignment are stable. Measurement results support the accuracy of the theoretical design procedure and conclusions.

A generalized global alignment algorithm.

PubMed

Huang, Xiaoqiu; Chao, Kun-Mao

2003-01-22

Homologous sequences are sometimes similar over some regions but different over other regions. Homologous sequences have a much lower global similarity if the different regions are much longer than the similar regions. We present a generalized global alignment algorithm for comparing sequences with intermittent similarities, an ordered list of similar regions separated by different regions. A generalized global alignment model is defined to handle sequences with intermittent similarities. A dynamic programming algorithm is designed to compute an optimal general alignment in time proportional to the product of sequence lengths and in space proportional to the sum of sequence lengths. The algorithm is implemented as a computer program named GAP3 (Global Alignment Program Version 3). The generalized global alignment model is validated by experimental results produced with GAP3 on both DNA and protein sequences. The GAP3 program extends the ability of standard global alignment programs to recognize homologous sequences of lower similarity. The GAP3 program is freely available for academic use at http://bioinformatics.iastate.edu/aat/align/align.html.

Constructing Aligned Assessments Using Automated Test Construction

ERIC Educational Resources Information Center

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

2013-01-01

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

Precise Alignment and Permanent Mounting of Thin and Lightweight X-ray Segments

NASA Technical Reports Server (NTRS)

Biskach, Michael P.; Chan, Kai-Wing; Hong, Melinda N.; Mazzarella, James R.; McClelland, Ryan S.; Norman, Michael J.; Saha, Timo T.; Zhang, William W.

2012-01-01

To provide observations to support current research efforts in high energy astrophysics. future X-ray telescope designs must provide matching or better angular resolution while significantly increasing the total collecting area. In such a design the permanent mounting of thin and lightweight segments is critical to the overall performance of the complete X-ray optic assembly. The thin and lightweight segments used in the assemhly of the modules are desigued to maintain and/or exceed the resolution of existing X-ray telescopes while providing a substantial increase in collecting area. Such thin and delicate X-ray segments are easily distorted and yet must be aligned to the arcsecond level and retain accurate alignment for many years. The Next Generation X-ray Optic (NGXO) group at NASA Goddard Space Flight Center has designed, assembled. and implemented new hardware and procedures mth the short term goal of aligning three pairs of X-ray segments in a technology demonstration module while maintaining 10 arcsec alignment through environmental testing as part of the eventual design and construction of a full sized module capable of housing hundreds of X-ray segments. The recent attempts at multiple segment pair alignment and permanent mounting is described along with an overview of the procedure used. A look into what the next year mll bring for the alignment and permanent segment mounting effort illustrates some of the challenges left to overcome before an attempt to populate a full sized module can begin.

Measurement of the translation and rotation of a sphere in fluid flow

NASA Astrophysics Data System (ADS)

Barros, Diogo; Hiltbrand, Ben; Longmire, Ellen K.

2018-06-01

The problem of determining the translation and rotation of a spherical particle moving in fluid flow is considered. Lagrangian tracking of markers printed over the surface of a sphere is employed to compute the center motion and the angular velocity of the solid body. The method initially calculates the sphere center from the 3D coordinates of the reconstructed markers, then finds the optimal rotation matrix that aligns a set of markers tracked at sequential time steps. The parameters involved in the experimental implementation of this procedure are discussed, and the associated uncertainty is estimated from numerical analysis. Finally, the proposed methodology is applied to characterize the motion of a large spherical particle released in a turbulent boundary layer developing in a water channel.

Functional annotation by sequence-weighted structure alignments: statistical analysis and case studies from the Protein 3000 structural genomics project in Japan.

PubMed

Standley, Daron M; Toh, Hiroyuki; Nakamura, Haruki

2008-09-01

A method to functionally annotate structural genomics targets, based on a novel structural alignment scoring function, is proposed. In the proposed score, position-specific scoring matrices are used to weight structurally aligned residue pairs to highlight evolutionarily conserved motifs. The functional form of the score is first optimized for discriminating domains belonging to the same Pfam family from domains belonging to different families but the same CATH or SCOP superfamily. In the optimization stage, we consider four standard weighting functions as well as our own, the "maximum substitution probability," and combinations of these functions. The optimized score achieves an area of 0.87 under the receiver-operating characteristic curve with respect to identifying Pfam families within a sequence-unique benchmark set of domain pairs. Confidence measures are then derived from the benchmark distribution of true-positive scores. The alignment method is next applied to the task of functionally annotating 230 query proteins released to the public as part of the Protein 3000 structural genomics project in Japan. Of these queries, 78 were found to align to templates with the same Pfam family as the query or had sequence identities > or = 30%. Another 49 queries were found to match more distantly related templates. Within this group, the template predicted by our method to be the closest functional relative was often not the most structurally similar. Several nontrivial cases are discussed in detail. Finally, 103 queries matched templates at the fold level, but not the family or superfamily level, and remain functionally uncharacterized. 2008 Wiley-Liss, Inc.

An Approach to Quad Meshing Based On Cross Valued Maps and the Ginzburg-Landau Theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Viertel, Ryan; Osting, Braxton

2017-08-01

A generalization of vector fields, referred to as N-direction fields or cross fields when N=4, has been recently introduced and studied for geometry processing, with applications in quadrilateral (quad) meshing, texture mapping, and parameterization. We make the observation that cross field design for two-dimensional quad meshing is related to the well-known Ginzburg-Landau problem from mathematical physics. This identification yields a variety of theoretical tools for efficiently computing boundary-aligned quad meshes, with provable guarantees on the resulting mesh, for example, the number of mesh defects and bounds on the defect locations. The procedure for generating the quad mesh is to (i)more » find a complex-valued "representation" field that minimizes the Dirichlet energy subject to a boundary constraint, (ii) convert the representation field into a boundary-aligned, smooth cross field, (iii) use separatrices of the cross field to partition the domain into four sided regions, and (iv) mesh each of these four-sided regions using standard techniques. Under certain assumptions on the geometry of the domain, we prove that this procedure can be used to produce a cross field whose separatrices partition the domain into four sided regions. To solve the energy minimization problem for the representation field, we use an extension of the Merriman-Bence-Osher (MBO) threshold dynamics method, originally conceived as an algorithm to simulate motion by mean curvature, to minimize the Ginzburg-Landau energy for the optimal representation field. Lastly, we demonstrate the method on a variety of test domains.« less

Accelerating large-scale protein structure alignments with graphics processing units

PubMed Central

2012-01-01

Background Large-scale protein structure alignment, an indispensable tool to structural bioinformatics, poses a tremendous challenge on computational resources. To ensure structure alignment accuracy and efficiency, efforts have been made to parallelize traditional alignment algorithms in grid environments. However, these solutions are costly and of limited accessibility. Others trade alignment quality for speedup by using high-level characteristics of structure fragments for structure comparisons. Findings We present ppsAlign, a parallel protein structure Alignment framework designed and optimized to exploit the parallelism of Graphics Processing Units (GPUs). As a general-purpose GPU platform, ppsAlign could take many concurrent methods, such as TM-align and Fr-TM-align, into the parallelized algorithm design. We evaluated ppsAlign on an NVIDIA Tesla C2050 GPU card, and compared it with existing software solutions running on an AMD dual-core CPU. We observed a 36-fold speedup over TM-align, a 65-fold speedup over Fr-TM-align, and a 40-fold speedup over MAMMOTH. Conclusions ppsAlign is a high-performance protein structure alignment tool designed to tackle the computational complexity issues from protein structural data. The solution presented in this paper allows large-scale structure comparisons to be performed using massive parallel computing power of GPU. PMID:22357132

AlignMe—a membrane protein sequence alignment web server

PubMed Central

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

2014-01-01

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

Optimal Alignment of Structures for Finite and Periodic Systems.

PubMed

Griffiths, Matthew; Niblett, Samuel P; Wales, David J

2017-10-10

Finding the optimal alignment between two structures is important for identifying the minimum root-mean-square distance (RMSD) between them and as a starting point for calculating pathways. Most current algorithms for aligning structures are stochastic, scale exponentially with the size of structure, and the performance can be unreliable. We present two complementary methods for aligning structures corresponding to isolated clusters of atoms and to condensed matter described by a periodic cubic supercell. The first method (Go-PERMDIST), a branch and bound algorithm, locates the global minimum RMSD deterministically in polynomial time. The run time increases for larger RMSDs. The second method (FASTOVERLAP) is a heuristic algorithm that aligns structures by finding the global maximum kernel correlation between them using fast Fourier transforms (FFTs) and fast SO(3) transforms (SOFTs). For periodic systems, FASTOVERLAP scales with the square of the number of identical atoms in the system, reliably finds the best alignment between structures that are not too distant, and shows significantly better performance than existing algorithms. The expected run time for Go-PERMDIST is longer than FASTOVERLAP for periodic systems. For finite clusters, the FASTOVERLAP algorithm is competitive with existing algorithms. The expected run time for Go-PERMDIST to find the global RMSD between two structures deterministically is generally longer than for existing stochastic algorithms. However, with an earlier exit condition, Go-PERMDIST exhibits similar or better performance.

Approximate matching of regular expressions.

PubMed

Myers, E W; Miller, W

1989-01-01

Given a sequence A and regular expression R, the approximate regular expression matching problem is to find a sequence matching R whose optimal alignment with A is the highest scoring of all such sequences. This paper develops an algorithm to solve the problem in time O(MN), where M and N are the lengths of A and R. Thus, the time requirement is asymptotically no worse than for the simpler problem of aligning two fixed sequences. Our method is superior to an earlier algorithm by Wagner and Seiferas in several ways. First, it treats real-valued costs, in addition to integer costs, with no loss of asymptotic efficiency. Second, it requires only O(N) space to deliver just the score of the best alignment. Finally, its structure permits implementation techniques that make it extremely fast in practice. We extend the method to accommodate gap penalties, as required for typical applications in molecular biology, and further refine it to search for sub-strings of A that strongly align with a sequence in R, as required for typical data base searches. We also show how to deliver an optimal alignment between A and R in only O(N + log M) space using O(MN log M) time. Finally, an O(MN(M + N) + N2log N) time algorithm is presented for alignment scoring schemes where the cost of a gap is an arbitrary increasing function of its length.

Rapid alignment of nanotomography data using joint iterative reconstruction and reprojection.

PubMed

Gürsoy, Doğa; Hong, Young P; He, Kuan; Hujsak, Karl; Yoo, Seunghwan; Chen, Si; Li, Yue; Ge, Mingyuan; Miller, Lisa M; Chu, Yong S; De Andrade, Vincent; He, Kai; Cossairt, Oliver; Katsaggelos, Aggelos K; Jacobsen, Chris

2017-09-18

As x-ray and electron tomography is pushed further into the nanoscale, the limitations of rotation stages become more apparent, leading to challenges in the alignment of the acquired projection images. Here we present an approach for rapid post-acquisition alignment of these projections to obtain high quality three-dimensional images. Our approach is based on a joint estimation of alignment errors, and the object, using an iterative refinement procedure. With simulated data where we know the alignment error of each projection image, our approach shows a residual alignment error that is a factor of a thousand smaller, and it reaches the same error level in the reconstructed image in less than half the number of iterations. We then show its application to experimental data in x-ray and electron nanotomography.

Memory-efficient dynamic programming backtrace and pairwise local sequence alignment.

PubMed

Newberg, Lee A

2008-08-15

A backtrace through a dynamic programming algorithm's intermediate results in search of an optimal path, or to sample paths according to an implied probability distribution, or as the second stage of a forward-backward algorithm, is a task of fundamental importance in computational biology. When there is insufficient space to store all intermediate results in high-speed memory (e.g. cache) existing approaches store selected stages of the computation, and recompute missing values from these checkpoints on an as-needed basis. Here we present an optimal checkpointing strategy, and demonstrate its utility with pairwise local sequence alignment of sequences of length 10,000. Sample C++-code for optimal backtrace is available in the Supplementary Materials. Supplementary data is available at Bioinformatics online.

Optical alignment of electrodes on electrical discharge machines

NASA Technical Reports Server (NTRS)

Boissevain, A. G.; Nelson, B. W.

1972-01-01

Shadowgraph system projects magnified image on screen so that alignment of small electrodes mounted on electrical discharge machines can be corrected and verified. Technique may be adapted to other machine tool equipment where physical contact cannot be made during inspection and access to tool limits conventional runout checking procedures.

In-flight alignment using H ∞ filter for strapdown INS on aircraft.

PubMed

Pei, Fu-Jun; Liu, Xuan; Zhu, Li

2014-01-01

In-flight alignment is an effective way to improve the accuracy and speed of initial alignment for strapdown inertial navigation system (INS). During the aircraft flight, strapdown INS alignment was disturbed by lineal and angular movements of the aircraft. To deal with the disturbances in dynamic initial alignment, a novel alignment method for SINS is investigated in this paper. In this method, an initial alignment error model of SINS in the inertial frame is established. The observability of the system is discussed by piece-wise constant system (PWCS) theory and observable degree is computed by the singular value decomposition (SVD) theory. It is demonstrated that the system is completely observable, and all the system state parameters can be estimated by optimal filter. Then a H ∞ filter was designed to resolve the uncertainty of measurement noise. The simulation results demonstrate that the proposed algorithm can reach a better accuracy under the dynamic disturbance condition.

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

Optical Modeling of the Alignment and Test of the NASA James Webb Space Telescope

NASA Technical Reports Server (NTRS)

Howard, Joseph M.; Hayden, Bill; Keski-Kuha, Ritva; Feinberg, Lee

2007-01-01

Optical modeling challenges of the ground alignment plan and optical test and verification of the NASA James Webb Space Telescope are discussed. Issues such as back-out of the gravity sag of light-weighted mirrors, as well as the use of a sparse-aperture auto-collimating flat system are discussed. A walk-through of the interferometer based alignment procedure is summarized, and sensitivities from the sparse aperture wavefront test are included as examples.'

Aligning HST Images to Gaia: A Faster Mosaicking Workflow

NASA Astrophysics Data System (ADS)

Bajaj, V.

2017-11-01

We present a fully programmatic workflow for aligning HST images using the high-quality astrometry provided by Gaia Data Release 1. Code provided in a Jupyter Notebook works through this procedure, including parsing the data to determine the query area parameters, querying Gaia for the coordinate catalog, and using the catalog with TweakReg as reference catalog. This workflow greatly simplifies the normally time-consuming process of aligning HST images, especially those taken as part of mosaics.

Effect of Alignment on Transport Properties of Carbon Nanotube/Metallic Junctions

NASA Technical Reports Server (NTRS)

Wincheski, Buzz; Namkung, Min; Smits, Jan; Williams, Phillip; Harvey, Robert

2003-01-01

Ballistic and spin coherent transport in single walled carbon nanotubes (SWCNT) are predicted to enable high sensitivity single-nanotube devices for strain and magnetic field sensing. Based upon these phenomena, electron beam lithography procedures have been developed to study the transport properties of purified HiPCO single walled carbon nanotubes for development into sensory materials for nondestructive evaluation. Purified nanotubes are dispersed in solvent suspension and then deposited on the device substrate before metallic contacts are defined and deposited through electron beam lithography. This procedure produces randomly dispersed ropes, typically 2 - 20 nm in diameter, of single walled carbon nanotubes. Transport and scanning probe microscopy studies have shown a good correlation between the junction resistance and tube density, alignment, and contact quality. In order to improve transport properties of the junctions a technique has been developed to align and concentrate nanotubes at specific locations on the substrate surface. Lithographic techniques are used to define local areas where high frequency electric fields are to be concentrated. Application of the fields while the substrate is exposed to nanotube-containing solution results in nanotube arrays aligned with the electric field lines. A second electron beam lithography layer is then used to deposit metallic contacts across the aligned tubes. Experimental measurements are presented showing the increased tube alignment and improvement in the transport properties of the junctions.

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

PubMed Central

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

2015-01-01

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

Alignment of dynamic networks.

PubMed

Vijayan, V; Critchlow, D; Milenkovic, T

2017-07-15

Network alignment (NA) aims to find a node mapping that conserves similar regions between compared networks. NA is applicable to many fields, including computational biology, where NA can guide the transfer of biological knowledge from well- to poorly-studied species across aligned network regions. Existing NA methods can only align static networks. However, most complex real-world systems evolve over time and should thus be modeled as dynamic networks. We hypothesize that aligning dynamic network representations of evolving systems will produce superior alignments compared to aligning the systems' static network representations, as is currently done. For this purpose, we introduce the first ever dynamic NA method, DynaMAGNA ++. This proof-of-concept dynamic NA method is an extension of a state-of-the-art static NA method, MAGNA++. Even though both MAGNA++ and DynaMAGNA++ optimize edge as well as node conservation across the aligned networks, MAGNA++ conserves static edges and similarity between static node neighborhoods, while DynaMAGNA++ conserves dynamic edges (events) and similarity between evolving node neighborhoods. For this purpose, we introduce the first ever measure of dynamic edge conservation and rely on our recent measure of dynamic node conservation. Importantly, the two dynamic conservation measures can be optimized with any state-of-the-art NA method and not just MAGNA++. We confirm our hypothesis that dynamic NA is superior to static NA, on synthetic and real-world networks, in computational biology and social domains. DynaMAGNA++ is parallelized and has a user-friendly graphical interface. http://nd.edu/∼cone/DynaMAGNA++/ . tmilenko@nd.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Alignment of dynamic networks

PubMed Central

Vijayan, V.; Critchlow, D.; Milenković, T.

2017-01-01

Abstract Motivation: Network alignment (NA) aims to find a node mapping that conserves similar regions between compared networks. NA is applicable to many fields, including computational biology, where NA can guide the transfer of biological knowledge from well- to poorly-studied species across aligned network regions. Existing NA methods can only align static networks. However, most complex real-world systems evolve over time and should thus be modeled as dynamic networks. We hypothesize that aligning dynamic network representations of evolving systems will produce superior alignments compared to aligning the systems’ static network representations, as is currently done. Results: For this purpose, we introduce the first ever dynamic NA method, DynaMAGNA ++. This proof-of-concept dynamic NA method is an extension of a state-of-the-art static NA method, MAGNA++. Even though both MAGNA++ and DynaMAGNA++ optimize edge as well as node conservation across the aligned networks, MAGNA++ conserves static edges and similarity between static node neighborhoods, while DynaMAGNA++ conserves dynamic edges (events) and similarity between evolving node neighborhoods. For this purpose, we introduce the first ever measure of dynamic edge conservation and rely on our recent measure of dynamic node conservation. Importantly, the two dynamic conservation measures can be optimized with any state-of-the-art NA method and not just MAGNA++. We confirm our hypothesis that dynamic NA is superior to static NA, on synthetic and real-world networks, in computational biology and social domains. DynaMAGNA++ is parallelized and has a user-friendly graphical interface. Availability and implementation: http://nd.edu/∼cone/DynaMAGNA++/. Contact: tmilenko@nd.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28881980

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

Smart grid initialization reduces the computational complexity of multi-objective image registration based on a dual-dynamic transformation model to account for large anatomical differences

NASA Astrophysics Data System (ADS)

Bosman, Peter A. N.; Alderliesten, Tanja

2016-03-01

We recently demonstrated the strong potential of using dual-dynamic transformation models when tackling deformable image registration problems involving large anatomical differences. Dual-dynamic transformation models employ two moving grids instead of the common single moving grid for the target image (and single fixed grid for the source image). We previously employed powerful optimization algorithms to make use of the additional flexibility offered by a dual-dynamic transformation model with good results, directly obtaining insight into the trade-off between important registration objectives as a result of taking a multi-objective approach to optimization. However, optimization has so far been initialized using two regular grids, which still leaves a great potential of dual-dynamic transformation models untapped: a-priori grid alignment with image structures/areas that are expected to deform more. This allows (far) less grid points to be used, compared to using a sufficiently refined regular grid, leading to (far) more efficient optimization, or, equivalently, more accurate results using the same number of grid points. We study the implications of exploiting this potential by experimenting with two new smart grid initialization procedures: one manual expert-based and one automated image-feature-based. We consider a CT test case with large differences in bladder volume with and without a multi-resolution scheme and find a substantial benefit of using smart grid initialization.

Evaluation of mathematical algorithms for automatic patient alignment in radiosurgery.

PubMed

Williams, Kenneth M; Schulte, Reinhard W; Schubert, Keith E; Wroe, Andrew J

2015-06-01

Image registration techniques based on anatomical features can serve to automate patient alignment for intracranial radiosurgery procedures in an effort to improve the accuracy and efficiency of the alignment process as well as potentially eliminate the need for implanted fiducial markers. To explore this option, four two-dimensional (2D) image registration algorithms were analyzed: the phase correlation technique, mutual information (MI) maximization, enhanced correlation coefficient (ECC) maximization, and the iterative closest point (ICP) algorithm. Digitally reconstructed radiographs from the treatment planning computed tomography scan of a human skull were used as the reference images, while orthogonal digital x-ray images taken in the treatment room were used as the captured images to be aligned. The accuracy of aligning the skull with each algorithm was compared to the alignment of the currently practiced procedure, which is based on a manual process of selecting common landmarks, including implanted fiducials and anatomical skull features. Of the four algorithms, three (phase correlation, MI maximization, and ECC maximization) demonstrated clinically adequate (ie, comparable to the standard alignment technique) translational accuracy and improvements in speed compared to the interactive, user-guided technique; however, the ICP algorithm failed to give clinically acceptable results. The results of this work suggest that a combination of different algorithms may provide the best registration results. This research serves as the initial groundwork for the translation of automated, anatomy-based 2D algorithms into a real-world system for 2D-to-2D image registration and alignment for intracranial radiosurgery. This may obviate the need for invasive implantation of fiducial markers into the skull and may improve treatment room efficiency and accuracy. © The Author(s) 2014.

Focus determination for the James Webb Space Telescope Science Instruments: A Survey of Methods

NASA Technical Reports Server (NTRS)

Davila, Pamela S.; Bolcar, Matthew R.; Boss, B.; Dean, B.; Hapogian, J.; Howard, J.; Unger, B.; Wilson, M.

2006-01-01

The James Webb Space Telescope (JWST) is a segmented deployable telescope that will require on-orbit alignment using the Near Infrared Camera as a wavefront sensor. The telescope will be aligned by adjusting seven degrees of freedom on each of 18 primary mirror segments and five degrees of freedom on the secondary mirror to optimize the performance of the telescope and camera at a wavelength of 2 microns. With the completion of these adjustments, the telescope focus is set and the optical performance of each of the other science instruments should then be optimal without making further telescope focus adjustments for each individual instrument. This alignment approach requires confocality of the instruments after integration and alignment to the composite metering structure, which will be verified during instrument level testing at Goddard Space Flight Center with a telescope optical simulator. In this paper, we present the results from a study of several analytical approaches to determine the focus for each instrument. The goal of the study is to compare the accuracies obtained for each method, and to select the most feasible for use during optical testing.

Protein docking by the interface structure similarity: how much structure is needed?

PubMed

Sinha, Rohita; Kundrotas, Petras J; Vakser, Ilya A

2012-01-01

The increasing availability of co-crystallized protein-protein complexes provides an opportunity to use template-based modeling for protein-protein docking. Structure alignment techniques are useful in detection of remote target-template similarities. The size of the structure involved in the alignment is important for the success in modeling. This paper describes a systematic large-scale study to find the optimal definition/size of the interfaces for the structure alignment-based docking applications. The results showed that structural areas corresponding to the cutoff values <12 Å across the interface inadequately represent structural details of the interfaces. With the increase of the cutoff beyond 12 Å, the success rate for the benchmark set of 99 protein complexes, did not increase significantly for higher accuracy models, and decreased for lower-accuracy models. The 12 Å cutoff was optimal in our interface alignment-based docking, and a likely best choice for the large-scale (e.g., on the scale of the entire genome) applications to protein interaction networks. The results provide guidelines for the docking approaches, including high-throughput applications to modeled structures.

Optimization of Buckypaper-enhanced Multifunctional Thermoplastic Composites

PubMed Central

Li, Zhongrui; Liang, Zhiyong

2017-01-01

A series of flattened-nanotube reinforced thermoplastic composites are sizably fabricated as a function of buckypaper loading. The effects of the volume fraction, nanotube alignment and length on the tensile performance of the composites are factored into a general expression. The incorporation of self-reinforcing polyphenylene resin (Parmax) into a highly aligned buckypaper frame at an optimal weight ratio boosts the tensile strength and Young’s modulus of the buckypaper/Parmax composite to 1145 MPa and 150 GPa, respectively, far exceeding those of Parmax and aligned buckypaper individually. The composite also exhibits improved thermal (>65 W/m-K) and electrical (~700 S/cm) conductivities, as well as high thermoelectric power (22 μV/K) at room temperature. Meanwhile, the composite displays a heterogeneously complex structure. The hexyl groups of Parmax noncovalently interact with the honeycomb structure of the flattened nanotube through π-stacking and CH-π interaction, correspondingly improving the dispersity of polymer on the nanotube surface and the interfacial stress transferring while the high alignment degrees of nanotube facilitate phonon and charge transport in the composites. PMID:28205637

Development of a reinforced electrochemically aligned collagen bioscaffold for tendon tissue engineering applications

NASA Astrophysics Data System (ADS)

Uquillas Paredes, Jorge Alfredo

Type-I collagen is a promising biomaterial that can be used to synthesize bioscaffolds as a strategy to regenerate and repair damaged tendons. The existing in vitro prepared collagen bioscaffolds are in the form of gels, foams, or extruded fibers. These bioscaffolds readily present sites for attachment of biological factors and cells; however, they have extremely poor biomechanical properties in comparison to the properties of native tendons. The biomechanical function of type-I collagen bioscaffolds needs to be elevated to the level of natural tissues for this biomaterial to replace mechanically challenged tendons in a functionally meaningful way. The overall goal of this dissertation is to develop a reinforced electrochemically aligned collagenous bioscaffold for applications in tendon tissue engineering. The bioscaffold is synthesized by a unique electrochemical process via isoelectric focusing (IEF) to attain a very high degree of molecular alignment and packing density. This dissertation presents progress made on four aims: A) development of simple and descriptive electrochemical theory via the mathematical model of IEF and the forces acting on collagen alignment under an electric field; B) optimization of the post-alignment PBS treatment step to achieve d- banding pattern in uncrosslinked electrochemically aligned collagen (ELAC) bioscaffolds; C) optimization of the best crosslinking protocol to produce the strongest possible ELAC biomaterial with excellent cellular compatibility; and D) in vivo evaluation of the biocompatibility and biodegradability properties of electronically aligned collagen bioscaffolds. The results of this dissertation provide strong evidence showing that reinforced ELAC bioscaffolds could be used clinically in the future to repair damaged tendons.

A multiple-alignment based primer design algorithm for genetically highly variable DNA targets

PubMed Central

2013-01-01

Background Primer design for highly variable DNA sequences is difficult, and experimental success requires attention to many interacting constraints. The advent of next-generation sequencing methods allows the investigation of rare variants otherwise hidden deep in large populations, but requires attention to population diversity and primer localization in relatively conserved regions, in addition to recognized constraints typically considered in primer design. Results Design constraints include degenerate sites to maximize population coverage, matching of melting temperatures, optimizing de novo sequence length, finding optimal bio-barcodes to allow efficient downstream analyses, and minimizing risk of dimerization. To facilitate primer design addressing these and other constraints, we created a novel computer program (PrimerDesign) that automates this complex procedure. We show its powers and limitations and give examples of successful designs for the analysis of HIV-1 populations. Conclusions PrimerDesign is useful for researchers who want to design DNA primers and probes for analyzing highly variable DNA populations. It can be used to design primers for PCR, RT-PCR, Sanger sequencing, next-generation sequencing, and other experimental protocols targeting highly variable DNA samples. PMID:23965160

Alignment verification procedures

NASA Technical Reports Server (NTRS)

Edwards, P. R.; Phillips, E. P.; Newman, J. C., Jr.

1988-01-01

In alignment verification procedures each laboratory is required to align its test machines and gripping fixtures to produce a nearly uniform tensile stress field on an un-notched sheet specimen. The blank specimens (50 mm w X 305 mm l X 2.3 mm th) supplied by the coordinators were strain gauged. Strain gauge readings were taken at all gauges (n = 1 through 10). The alignment verification procedures are as follows: (1) zero all strain gauges while specimen is in a free-supported condition; (2) put strain-gauged specimen in the test machine so that specimen front face (face 1) is in contact with reference jaw (standard position of specimen), tighten grips, and at zero load measure strains on all gauges. (epsilon sub nS0 is strain at gauge n, standard position, zero load); (3) with specimen in machine and at a tensile load of 10 kN measure strains (specimen in standard position). (Strain = epsilon sub nS10); (4) remove specimen from machine. Put specimen in machine so that specimen back face (face 2) is in contact with reference jaw (reverse position of specimen), tighten grips, and at zero load measure strains on all gauges. (Strain - epsilon sub nR0); and (5) with specimen in machine and at tensile load of 10 kN measure strains (specimen in reverse position). (epsilon sub nR10 is strain at gauge n, reverse position, 10 kN load).

Alignment of gold nanorods by angular photothermal depletion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taylor, Adam B.; Chow, Timothy T. Y.; Chon, James W. M., E-mail: jchon@swin.edu.au

2014-02-24

In this paper, we demonstrate that a high degree of alignment can be imposed upon randomly oriented gold nanorod films by angular photothermal depletion with linearly polarized laser irradiation. The photothermal reshaping of gold nanorods is observed to follow quadratic melting model rather than the threshold melting model, which distorts the angular and spectral hole created on 2D distribution map of nanorods to be an open crater shape. We have accounted these observations to the alignment procedures and demonstrated good agreement between experiment and simulations. The use of multiple laser depletion wavelengths allowed alignment criteria over a large range ofmore » aspect ratios, achieving 80% of the rods in the target angular range. We extend the technique to demonstrate post-alignment in a multilayer of randomly oriented gold nanorod films, with arbitrary control of alignment shown across the layers. Photothermal angular depletion alignment of gold nanorods is a simple, promising post-alignment method for creating future 3D or multilayer plasmonic nanorod based devices and structures.« less

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

PubMed Central

2013-01-01

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

Implant alignment in total elbow arthroplasty: conventional vs. navigated techniques

NASA Astrophysics Data System (ADS)

McDonald, Colin P.; Johnson, James A.; King, Graham J. W.; Peters, Terry M.

2009-02-01

Incorrect selection of the native flexion-extension axis during implant alignment in elbow replacement surgery is likely a significant contributor to failure of the prosthesis. Computer and image-assisted surgery is emerging as a useful surgical tool in terms of improving the accuracy of orthopaedic procedures. This study evaluated the accuracy of implant alignment using an image-based navigation technique compared against a conventional non-navigated approach. Implant alignment error was 0.8 +/- 0.3 mm in translation and 1.1 +/- 0.4° in rotation for the navigated alignment, compared with 3.1 +/- 1.3 mm and 5.0 +/- 3.8° for the non-navigated alignment. Five (5) of the 11 non-navigated alignments were malaligned greater than 5° while none of the navigated alignments were placed with an error of greater than 2.0°. It is likely that improved implant positioning will lead to reduced implant loading and wear, resulting in fewer implantrelated complications and revision surgeries.

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

PubMed

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

2014-01-01

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

Laparoscopic Suturing as a Barrier to Broader Adoption of Laparoscopic Surgery.

PubMed

Lim, Sangtaeck; Ghosh, Sudip; Niklewski, Paul; Roy, Sanjoy

2017-01-01

Laparoscopic surgery is increasingly replacing the open procedure because of its many patient-related benefits that are well aligned with policies and programs that seek to optimize health system performance. However, widespread adoption of laparoscopic surgery has been slow, in part, because of the complexity of laparoscopic suturing. The objective of this study was to review the clinical and economic impacts of laparoscopic suturing in key procedures and to assess its role as a barrier to the broader adoption of laparoscopic surgery. A medical literature search of MEDLINE, EMBASE, and BIOSIS from January 2010 through June 2016 identified 47 relevant articles. Laparoscopic suturing and intracorporeal knot tying may result in extended surgical time, complications, and surgeon errors, while improving patient quality of life through improved cosmesis, diet toleration, and better bowel movements. Despite advancement in surgical techniques and the availability of newer surgical tools, the complexity of laparoscopic suturing continues to be a barrier to greater adoption of MIS. The results of the study underscore the need for development of proficiency in laparoscopic suturing, which may help improve patient outcomes and reduce healthcare costs.

[The "Würzburg T". A concept for optimization of early multiple trauma care in the emergency department].

PubMed

Kuhnigk, H; Steinhübel, B; Keil, T; Roewer, N

2004-07-01

Anaesthesia management, radiological diagnostic and the concept of damage control surgery should be combined in the resuscitation room. Defined clinical targets and their realisation are a CT-scan and complete damage control surgery in the shock room. Furthermore minimised patient transfer and positioning with continuous access to the head, upper parts of the body and anaesthesia machine should be realised during diagnostic procedures. Based on a carbon-slide fixed on a turntable and innovative alignment of diagnostic devices, a three phase treatment algorithm has been established. Phase A includes primary survey, anaesthetic management and ultrasound examination. Following a turn of the table conventional x-ray diagnostic is assessed in phase B. Tracks for the slide enable immediate transfer to a spiral CT-scan without additional patient positioning (phase C). Following complete CT-scan rearrangement of the table to phase A facilitates immediate damage control surgery. To accelerate device operation and treatment the integrated anaesthesia workstation is ceiling-mounted and manoeuvres close to the patient. This concept realizes complete diagnostic procedures and damage control surgery without time consuming patient transfer or rearrangement.

Multiple network alignment via multiMAGNA+.

PubMed

Vijayan, Vipin; Milenkovic, Tijana

2017-08-21

Network alignment (NA) aims to find a node mapping that identifies topologically or functionally similar network regions between molecular networks of different species. Analogous to genomic sequence alignment, NA can be used to transfer biological knowledge from well- to poorly-studied species between aligned network regions. Pairwise NA (PNA) finds similar regions between two networks while multiple NA (MNA) can align more than two networks. We focus on MNA. Existing MNA methods aim to maximize total similarity over all aligned nodes (node conservation). Then, they evaluate alignment quality by measuring the amount of conserved edges, but only after the alignment is constructed. Directly optimizing edge conservation during alignment construction in addition to node conservation may result in superior alignments. Thus, we present a novel MNA method called multiMAGNA++ that can achieve this. Indeed, multiMAGNA++ outperforms or is on par with existing MNA methods, while often completing faster than existing methods. That is, multiMAGNA++ scales well to larger network data and can be parallelized effectively. During method evaluation, we also introduce new MNA quality measures to allow for more fair MNA method comparison compared to the existing alignment quality measures. MultiMAGNA++ code is available on the method's web page at http://nd.edu/~cone/multiMAGNA++/.

The preliminary checkout, evaluation and calibration of a 3-component force measurement system for calibrating propulsion simulators for wind tunnel models

NASA Technical Reports Server (NTRS)

Scott, W. A.

1984-01-01

The propulsion simulator calibration laboratory (PSCL) in which calibrations can be performed to determine the gross thrust and airflow of propulsion simulators installed in wind tunnel models is described. The preliminary checkout, evaluation and calibration of the PSCL's 3 component force measurement system is reported. Methods and equipment were developed for the alignment and calibration of the force measurement system. The initial alignment of the system demonstrated the need for more efficient means of aligning system's components. The use of precision alignment jigs increases both the speed and accuracy with which the system is aligned. The calibration of the force measurement system shows that the methods and equipment for this procedure can be successful.

Rapid alignment of nanotomography data using joint iterative reconstruction and reprojection

DOE PAGES

Gürsoy, Doğa; Hong, Young P.; He, Kuan; ...

2017-09-18

As x-ray and electron tomography is pushed further into the nanoscale, the limitations of rotation stages become more apparent, leading to challenges in the alignment of the acquired projection images. Here we present an approach for rapid post-acquisition alignment of these projections to obtain high quality three-dimensional images. Our approach is based on a joint estimation of alignment errors, and the object, using an iterative refinement procedure. With simulated data where we know the alignment error of each projection image, our approach shows a residual alignment error that is a factor of a thousand smaller, and it reaches the samemore » error level in the reconstructed image in less than half the number of iterations. We then show its application to experimental data in x-ray and electron nanotomography.« less

Therapeutic Exercise for Body Alignment and Function.

ERIC Educational Resources Information Center

Daniels, Lucille; Worthingham, Catherine

This textbook is designed for the use of persons dealing with the problems of body alignment and function, primarily the physical therapist, the physical educator, and the physician. Those procedures are included that appear to be best suited for prevention of disability, improvement of impaired function, and maintenance of the optimum level of…

Classroom EFL Writing: The Alignment-Oriented Approach

ERIC Educational Resources Information Center

Haiyan, Miao; Rilong, Liu

2016-01-01

This paper outlines the alignment-oriented approach in classroom EFL writing. Based on a review of the characteristics of the written language and comparison between the product-focused approach and the process-focused approach, the paper proposes a practical classroom procedure as to how to teach EFL writing. A follow-up empirical study is…

LAMBADA and InflateGRO2: efficient membrane alignment and insertion of membrane proteins for molecular dynamics simulations.

PubMed

Schmidt, Thomas H; Kandt, Christian

2012-10-22

At the beginning of each molecular dynamics membrane simulation stands the generation of a suitable starting structure which includes the working steps of aligning membrane and protein and seamlessly accommodating the protein in the membrane. Here we introduce two efficient and complementary methods based on pre-equilibrated membrane patches, automating these steps. Using a voxel-based cast of the coarse-grained protein, LAMBADA computes a hydrophilicity profile-derived scoring function based on which the optimal rotation and translation operations are determined to align protein and membrane. Employing an entirely geometrical approach, LAMBADA is independent from any precalculated data and aligns even large membrane proteins within minutes on a regular workstation. LAMBADA is the first tool performing the entire alignment process automatically while providing the user with the explicit 3D coordinates of the aligned protein and membrane. The second tool is an extension of the InflateGRO method addressing the shortcomings of its predecessor in a fully automated workflow. Determining the exact number of overlapping lipids based on the area occupied by the protein and restricting expansion, compression and energy minimization steps to a subset of relevant lipids through automatically calculated and system-optimized operation parameters, InflateGRO2 yields optimal lipid packing and reduces lipid vacuum exposure to a minimum preserving as much of the equilibrated membrane structure as possible. Applicable to atomistic and coarse grain structures in MARTINI format, InflateGRO2 offers high accuracy, fast performance, and increased application flexibility permitting the easy preparation of systems exhibiting heterogeneous lipid composition as well as embedding proteins into multiple membranes. Both tools can be used separately, in combination with other methods, or in tandem permitting a fully automated workflow while retaining a maximum level of usage control and flexibility. To assess the performance of both methods, we carried out test runs using 22 membrane proteins of different size and transmembrane structure.

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.

Design and realization of the optical and electron beam alignment system for the HUST-FEL oscillator

NASA Astrophysics Data System (ADS)

Fu, Q.; Tan, P.; Liu, K. F.; Qin, B.; Liu, X.

2018-06-01

A Free Electron Laser(FEL) oscillator with radiation wavelength at 30-100 μ m is under commissioning at Huazhong University of Science and Technology (HUST). This work presents the schematic design and realization procedures for the optical and beam alignment system in the HUST FEL facility. The optical cavity misalignment effects are analyzed with the code OPC + Genesis 1.3, and the tolerance of misalignment is proposed with the simulation result. Depending on undulator mechanical benchmarks, a laser indicating system has been built up as reference datum. The alignment of both optical axis and beam trajectory were achieved by this alignment system.

Multianode Photomultiplier Tube Alignment for the MINERvA Experiment at Fermilab

NASA Astrophysics Data System (ADS)

Bruno, Jorge

2006-10-01

The MINERvA experiment (Main INjector ExpeRiment vA) at FNAL will study the neutrino-nucleon and neutrino-nucleus interaction. The light collection from the detector will be done via optic fibers using Hamamatsu H8804 64-channel photomultiplier tubes (PMT). Each PMT channel needs to be precisely aligned with the corresponding optic fiber. The MINERvA PMT optical boxes contain precision machined optic ``cookies'' which capture the 8x8 array of optic fibers. Each PMT-cookie pair needs to be aligned as precisely as possible. This contribution will describe the alignment setup and procedure implemented at James Madison University.

Computerized planning of prostate cryosurgery using variable cryoprobe insertion depth.

PubMed

Rossi, Michael R; Tanaka, Daigo; Shimada, Kenji; Rabin, Yoed

2010-02-01

The current study presents a computerized planning scheme for prostate cryosurgery using a variable insertion depth strategy. This study is a part of an ongoing effort to develop computerized tools for cryosurgery. Based on typical clinical practices, previous automated planning schemes have required that all cryoprobes be aligned at a single insertion depth. The current study investigates the benefit of removing this constraint, in comparison with results based on uniform insertion depth planning as well as the so-called "pullback procedure". Planning is based on the so-called "bubble-packing method", and its quality is evaluated with bioheat transfer simulations. This study is based on five 3D prostate models, reconstructed from ultrasound imaging, and cryoprobe active length in the range of 15-35 mm. The variable insertion depth technique is found to consistently provide superior results when compared to the other placement methods. Furthermore, it is shown that both the optimal active length and the optimal number of cryoprobes vary among prostate models, based on the size and shape of the target region. Due to its low computational cost, the new scheme can be used to determine the optimal cryoprobe layout for a given prostate model in real time. Copyright 2008 Elsevier Inc. All rights reserved.

Fine-tuning structural RNA alignments in the twilight zone.

PubMed

Bremges, Andreas; Schirmer, Stefanie; Giegerich, Robert

2010-04-30

A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance. This method works best around 75% sequence similarity. However, in a "twilight zone" below 55% similarity, the sequence alignment tends to obscure the covariance signal used in the second phase. Therefore, while the overall shape of the consensus structure may still be found, the degree of conservation cannot be estimated reliably. Based on a combination of available methods, we present a method named planACstar for improving structure conservation in structural alignments in the twilight zone. After constructing a consensus structure by alignment folding, planACstar abandons the original sequence alignment, refolds the sequences individually, but consistent with the consensus, aligns the structures, irrespective of sequence, by a pure structure alignment method, and derives an improved sequence alignment from the alignment of structures, to be re-submitted to alignment folding, etc.. This circle may be iterated as long as structural conservation improves, but normally, one step suffices. Employing the tools ClustalW, RNAalifold, and RNAforester, we find that for sequences with 30-55% sequence identity, structural conservation can be improved by 10% on average, with a large variation, measured in terms of RNAalifold's own criterion, the structure conservation index.

Validating Coherence Measurements Using Aligned and Unaligned Coherence Functions

NASA Technical Reports Server (NTRS)

Miles, Jeffrey Hilton

2006-01-01

This paper describes a novel approach based on the use of coherence functions and statistical theory for sensor validation in a harsh environment. By the use of aligned and unaligned coherence functions and statistical theory one can test for sensor degradation, total sensor failure or changes in the signal. This advanced diagnostic approach and the novel data processing methodology discussed provides a single number that conveys this information. This number as calculated with standard statistical procedures for comparing the means of two distributions is compared with results obtained using Yuen's robust statistical method to create confidence intervals. Examination of experimental data from Kulite pressure transducers mounted in a Pratt & Whitney PW4098 combustor using spectrum analysis methods on aligned and unaligned time histories has verified the effectiveness of the proposed method. All the procedures produce good results which demonstrates how robust the technique is.

Nurses' Satisfaction With Using Nursing Information Systems From Technology Acceptance Model and Information Systems Success Model Perspectives: A Reductionist Approach.

PubMed

Lin, Hsien-Cheng

2017-02-01

Nursing information systems can enhance nursing practice and the efficiency and quality of administrative affairs within the nursing department and thus have been widely considered for implementation. Close alignment of human-computer interaction can advance optimal clinical performance with the use of information systems. However, a lack of introduction of the concept of alignment between users' perceptions and technological functionality has caused dissatisfaction, as shown in the existing literature. This study provides insight into the alignment between nurses' perceptions and how technological functionality affects their satisfaction with Nursing Information System use through a reductionist perspective of alignment. This cross-sectional study collected data from 531 registered nurses in Taiwan. The results indicated that "perceived usefulness in system quality alignment," "perceived usefulness in information quality alignment," "perceived ease of use in system quality alignment," "perceived ease of use in information quality alignment," and "perceived ease of use in service quality alignment" have significantly affected nurses' satisfaction with Nursing Information System use. However, "perceived usefulness in service quality alignment" had no significant effect on nurses' satisfaction. This study also provides some meaningful implications for theoretical and practical aspects of design.

In-Flight Alignment Using H ∞ Filter for Strapdown INS on Aircraft

PubMed Central

Pei, Fu-Jun; Liu, Xuan; Zhu, Li

2014-01-01

In-flight alignment is an effective way to improve the accuracy and speed of initial alignment for strapdown inertial navigation system (INS). During the aircraft flight, strapdown INS alignment was disturbed by lineal and angular movements of the aircraft. To deal with the disturbances in dynamic initial alignment, a novel alignment method for SINS is investigated in this paper. In this method, an initial alignment error model of SINS in the inertial frame is established. The observability of the system is discussed by piece-wise constant system (PWCS) theory and observable degree is computed by the singular value decomposition (SVD) theory. It is demonstrated that the system is completely observable, and all the system state parameters can be estimated by optimal filter. Then a H ∞ filter was designed to resolve the uncertainty of measurement noise. The simulation results demonstrate that the proposed algorithm can reach a better accuracy under the dynamic disturbance condition. PMID:24511300

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilbur, Jeffrey D.; Gomez, Enrique D.; Ellsworth, Mark W.

A procedure for creating samples that can be repeatedly cycled between weakly aligned and strongly aligned states is described. Poly(styrene-b-isoprene) block copolymer samples were first shear-aligned and then cross-linked using a high energy electron beam. Samples with more than 1.0 cross-links per chain on average showed almost complete recovery of their initial alignment state even after 20 cycles of heating above the order–disorder transition temperature of the un-cross-linked block copolymer. Samples with 1.1 cross-links per chain, which showed over 90% loss of alignment on heating and almost 100% recovery of alignment on cooling, provided the best example of a reversiblemore » aligned-to-unaligned transition. Samples with lower cross-linking densities exhibited irreversible loss of alignment upon heating, while those with higher cross-linking densities exhibited less than 90% loss of alignment upon heating. Alignment was quantified by a technique that we call two color depolarized light scattering (TCDLS), an extension of the traditional depolarized light scattering experiment used to determine the state of order in block copolymers. Qualitative confirmation of our interpretation of TCDLS data was obtained by small-angle X-ray scattering and transmission electron microscopy.« less

Multistage Complexity in Language Proficiency Assessment: A Framework for Aligning Theoretical Perspectives, Test Development, and Psychometrics

ERIC Educational Resources Information Center

Luecht, Richard M.

2003-01-01

This article contends that the necessary links between constructs and test scores/decisions in language assessment must be established through principled design procedures that align three models: (1) a theoretical construct model; (2) a test development model; and (3) a psychometric scoring model. The theoretical construct model articulates the…

Methodological Choices in the Content Analysis of Textbooks for Measuring Alignment with Standards

ERIC Educational Resources Information Center

Polikoff, Morgan S.; Zhou, Nan; Campbell, Shauna E.

2015-01-01

With the recent adoption of the Common Core standards in many states, there is a need for quality information about textbook alignment to standards. While there are many existing content analysis procedures, these generally have little, if any, validity or reliability evidence. One exception is the Surveys of Enacted Curriculum (SEC), which has…

Alignment and calibration of the MgF2 biplate compensator for applications in rotating-compensator multichannel ellipsometry.

PubMed

Lee, J; Rovira, P I; An, I; Collins, R W

2001-08-01

Biplate compensators made from MgF2 are being used increasingly in rotating-element single-channel and multichannel ellipsometers. For the measurement of accurate ellipsometric spectra, the compensator must be carefully (i) aligned internally to ensure that the fast axes of the two plates are perpendicular and (ii) calibrated to determine the phase retardance delta versus photon energy E. We present alignment and calibration procedures for multichannel ellipsometer configurations with special attention directed to the precision, accuracy, and reproducibility in the determination of delta (E). Run-to-run variations in external compensator alignment, i.e., alignment with respect to the incident beam, can lead to irreproducibilities in delta of approximately 0.2 degrees . Errors in the ellipsometric measurement of a sample can be minimized by calibrating with an external compensator alignment that matches as closely as possible that used in the measurement.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gürsoy, Doğa; Hong, Young P.; He, Kuan

As x-ray and electron tomography is pushed further into the nanoscale, the limitations of rotation stages become more apparent, leading to challenges in the alignment of the acquired projection images. Here we present an approach for rapid post-acquisition alignment of these projections to obtain high quality three-dimensional images. Our approach is based on a joint estimation of alignment errors, and the object, using an iterative refinement procedure. With simulated data where we know the alignment error of each projection image, our approach shows a residual alignment error that is a factor of a thousand smaller, and it reaches the samemore » error level in the reconstructed image in less than half the number of iterations. We then show its application to experimental data in x-ray and electron nanotomography.« less

Freeze Tape Casting of Functionally Graded Porous Ceramics

NASA Technical Reports Server (NTRS)

Sofie, Stephen W.

2007-01-01

Freeze tape casting is a means of making preforms of ceramic sheets that, upon subsequent completion of fabrication processing, can have anisotropic and/or functionally graded properties that notably include aligned and graded porosity. Freeze tape casting was developed to enable optimization of the microstructures of porous ceramic components for use as solid oxide electrodes in fuel cells: Through alignment and grading of pores, one can tailor surface areas and diffusion channels for flows of gas and liquid species involved in fuel-cell reactions. Freeze tape casting offers similar benefits for fabrication of optimally porous ceramics for use as catalysts, gas sensors, and filters.

Resolving the multiple sequence alignment problem using biogeography-based optimization with multiple populations.

PubMed

Zemali, El-Amine; Boukra, Abdelmadjid

2015-08-01

The multiple sequence alignment (MSA) is one of the most challenging problems in bioinformatics, it involves discovering similarity between a set of protein or DNA sequences. This paper introduces a new method for the MSA problem called biogeography-based optimization with multiple populations (BBOMP). It is based on a recent metaheuristic inspired from the mathematics of biogeography named biogeography-based optimization (BBO). To improve the exploration ability of BBO, we have introduced a new concept allowing better exploration of the search space. It consists of manipulating multiple populations having each one its own parameters. These parameters are used to build up progressive alignments allowing more diversity. At each iteration, the best found solution is injected in each population. Moreover, to improve solution quality, six operators are defined. These operators are selected with a dynamic probability which changes according to the operators efficiency. In order to test proposed approach performance, we have considered a set of datasets from Balibase 2.0 and compared it with many recent algorithms such as GAPAM, MSA-GA, QEAMSA and RBT-GA. The results show that the proposed approach achieves better average score than the previously cited methods.

Self-optimizing approach for automated laser resonator alignment

NASA Astrophysics Data System (ADS)

Brecher, C.; Schmitt, R.; Loosen, P.; Guerrero, V.; Pyschny, N.; Pavim, A.; Gatej, A.

2012-02-01

Nowadays, the assembly of laser systems is dominated by manual operations, involving elaborate alignment by means of adjustable mountings. From a competition perspective, the most challenging problem in laser source manufacturing is price pressure, a result of cost competition exerted mainly from Asia. From an economical point of view, an automated assembly of laser systems defines a better approach to produce more reliable units at lower cost. However, the step from today's manual solutions towards an automated assembly requires parallel developments regarding product design, automation equipment and assembly processes. This paper introduces briefly the idea of self-optimizing technical systems as a new approach towards highly flexible automation. Technically, the work focuses on the precision assembly of laser resonators, which is one of the final and most crucial assembly steps in terms of beam quality and laser power. The paper presents a new design approach for miniaturized laser systems and new automation concepts for a robot-based precision assembly, as well as passive and active alignment methods, which are based on a self-optimizing approach. Very promising results have already been achieved, considerably reducing the duration and complexity of the laser resonator assembly. These results as well as future development perspectives are discussed.

Electrospun Collagen/Silk Tissue Engineering Scaffolds: Fiber Fabrication, Post-Treatment Optimization, and Application in Neural Differentiation of Stem Cells

NASA Astrophysics Data System (ADS)

Zhu, Bofan

Biocompatible scaffolds mimicking the locally aligned fibrous structure of native extracellular matrix (ECM) are in high demand in tissue engineering. In this thesis research, unidirectionally aligned fibers were generated via a home-built electrospinning system. Collagen type I, as a major ECM component, was chosen in this study due to its support of cell proliferation and promotion of neuroectodermal commitment in stem cell differentiation. Synthetic dragline silk proteins, as biopolymers with remarkable tensile strength and superior elasticity, were also used as a model material. Good alignment, controllable fiber size and morphology, as well as a desirable deposition density of fibers were achieved via the optimization of solution and electrospinning parameters. The incorporation of silk proteins into collagen was found to significantly enhance mechanical properties and stability of electrospun fibers. Glutaraldehyde (GA) vapor post-treatment was demonstrated as a simple and effective way to tune the properties of collagen/silk fibers without changing their chemical composition. With 6-12 hours GA treatment, electrospun collagen/silk fibers were not only biocompatible, but could also effectively induce the polarization and neural commitment of stem cells, which were optimized on collagen rich fibers due to the unique combination of biochemical and biophysical cues imposed to cells. Taken together, electrospun collagen rich composite fibers are mechanically strong, stable and provide excellent cell adhesion. The unidirectionally aligned fibers can accelerate neural differentiation of stem cells, representing a promising therapy for neural tissue degenerative diseases and nerve injuries.

The relative phases of basal ganglia activities dynamically shape effective connectivity in Parkinson's disease.

PubMed

Cagnan, Hayriye; Duff, Eugene Paul; Brown, Peter

2015-06-01

Optimal phase alignment between oscillatory neural circuits is hypothesized to optimize information flow and enhance system performance. This theory is known as communication-through-coherence. The basal ganglia motor circuit exhibits exaggerated oscillatory and coherent activity patterns in Parkinson's disease. Such activity patterns are linked to compromised motor system performance as evinced by bradykinesia, rigidity and tremor, suggesting that network function might actually deteriorate once a certain level of net synchrony is exceeded in the motor circuit. Here, we characterize the processes underscoring excessive synchronization and its termination. To this end, we analysed local field potential recordings from the subthalamic nucleus and globus pallidus of five patients with Parkinson's disease (four male and one female, aged 37-64 years). We observed that certain phase alignments between subthalamic nucleus and globus pallidus amplified local neural synchrony in the beta frequency band while others either suppressed it or did not induce any significant change with respect to surrogates. The increase in local beta synchrony directly correlated with how long the two nuclei locked to beta-amplifying phase alignments. Crucially, administration of the dopamine prodrug, levodopa, reduced the frequency and duration of periods during which subthalamic and pallidal populations were phase-locked to beta-amplifying alignments. Conversely ON dopamine, the total duration over which subthalamic and pallidal populations were aligned to phases that left beta-amplitude unchanged with respect to surrogates increased. Thus dopaminergic input shifted circuit dynamics from persistent periods of locking to amplifying phase alignments, associated with compromised motoric function, to more dynamic phase alignment and improved motoric function. This effect of dopamine on local circuit resonance suggests means by which novel electrical interventions might prevent resonance-related pathological circuit interactions. © The Author (2015). Published by Oxford University Press on behalf of the Guarantors of Brain.

Beam shaping for laser-based adaptive optics in astronomy.

PubMed

Béchet, Clémentine; Guesalaga, Andrés; Neichel, Benoit; Fesquet, Vincent; González-Núñez, Héctor; Zúñiga, Sebastián; Escarate, Pedro; Guzman, Dani

2014-06-02

The availability and performance of laser-based adaptive optics (AO) systems are strongly dependent on the power and quality of the laser beam before being projected to the sky. Frequent and time-consuming alignment procedures are usually required in the laser systems with free-space optics to optimize the beam. Despite these procedures, significant distortions of the laser beam have been observed during the first two years of operation of the Gemini South multi-conjugate adaptive optics system (GeMS). A beam shaping concept with two deformable mirrors is investigated in order to provide automated optimization of the laser quality for astronomical AO. This study aims at demonstrating the correction of quasi-static aberrations of the laser, in both amplitude and phase, testing a prototype of this two-deformable mirror concept on GeMS. The paper presents the results of the preparatory study before the experimental phase. An algorithm to control amplitude and phase correction, based on phase retrieval techniques, is presented with a novel unwrapping method. Its performance is assessed via numerical simulations, using aberrations measured at GeMS as reference. The results predict effective amplitude and phase correction of the laser distortions with about 120 actuators per mirror and a separation of 1.4 m between the mirrors. The spot size is estimated to be reduced by up to 15% thanks to the correction. In terms of AO noise level, this has the same benefit as increasing the photon flux by 40%.

Statistical Significance of Optical Map Alignments

PubMed Central

Sarkar, Deepayan; Goldstein, Steve; Schwartz, David C.

2012-01-01

Abstract The Optical Mapping System constructs ordered restriction maps spanning entire genomes through the assembly and analysis of large datasets comprising individually analyzed genomic DNA molecules. Such restriction maps uniquely reveal mammalian genome structure and variation, but also raise computational and statistical questions beyond those that have been solved in the analysis of smaller, microbial genomes. We address the problem of how to filter maps that align poorly to a reference genome. We obtain map-specific thresholds that control errors and improve iterative assembly. We also show how an optimal self-alignment score provides an accurate approximation to the probability of alignment, which is useful in applications seeking to identify structural genomic abnormalities. PMID:22506568

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

PubMed

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

2017-12-15

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

3D patterned substrates for bioartificial blood vessels - The effect of hydrogels on aligned cells on a biomaterial surface.

PubMed

Zhao, Xinxin; Irvine, Scott Alexander; Agrawal, Animesh; Cao, Ye; Lim, Pei Qi; Tan, Si Ying; Venkatraman, Subbu S

2015-10-01

The optimal bio-artificial blood vessel construct is one that has a compliant tubular core with circumferentially aligned smooth muscle cells (SMCs). Obtaining this well-aligned pattern of SMCs on a scaffold is highly beneficial as this cellular orientation preserves the SMC contractile phenotype. We used 3D patterning to create channels on a polycaprolactone (PCL) scaffold; SMCs were then found to be aligned within the microchannels. To preserve this alignment, and to provide a protective coating that could further incorporate cells, we evaluated the use of two hydrogels, one based on poly(ethylene glycol) diacrylate (PEGDA) and the other based on gelatin. Hydrogels were either physically coated on the PCL surfaces or covalently linked via suitable surface modification of PCL. For covalent immobilization of PEGDA hydrogel, alkene groups were introduced on PCL, while for gelatin covalent linkage, serum proteins were introduced. It is, however, crucial that the hydrogel coating does not disrupt the cellular patterning and distribution. We show in this work that both the process of coating as well as the nature of the coating are critical to preservation of the aligned SMCs. The covalent coating methods involving the crosslinking of hydrogels with the surface of PCL films promoted hydrogel retention time on the film as compared with physical deposition. Furthermore, subsequent hydrogel degradation is affected by the components of the cell culture medium, hinting at a possible route to in vivo biodegradation. Surface features control cellular orientation and subsequently influence their functionality, a useful effect for cellularized biomedical devices. Such devices also can benefit from protective and cell friendly hydrogel coatings. However, literature is lacking on the fate of cells that have endured hydrogel coating whilst orientated on a biomaterial surface. In particular, elucidation of the cells ability to remain adherent and orientated post hydrogel addition. Coating requires two procedures that may be deleterious to the orientated cells: the surface pretreatment for gel binding and the hydrogel crosslinking reaction. We compare transglutaminase gelatin crosslinking and UV initiated PEGDA crosslinking, coated onto smooth muscle cells orientated on patterned PCL surfaces. This original study will be of considerable use to the wider biomaterials community. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Can three-dimensional patient-specific cutting guides be used to achieve optimal correction for high tibial osteotomy? Pilot study.

PubMed

Munier, M; Donnez, M; Ollivier, M; Flecher, X; Chabrand, P; Argenson, J-N; Parratte, S

2017-04-01

Treatment of medial tibiofemoral osteoarthritis with a high-tibial osteotomy (HTO) is most effective when the optimal angular correction is achieved. However, conventional instrumentation is limited when multiplanar correction is needed. Use of patient-specific cutting guides (PSCGs) for HTO provides an accurate correction (difference<2°) relative to the preoperative planning. Between February 2014 and February 2015, 10 patients (mean age: 46 years [range: 31-59]; grade 1 or 2 osteoarthritis in Ahlbäck's classification) were included prospectively in this reliability and safety study. All patients were operated using the same medial opening-wedge osteotomy technique. Preoperative planning was based on long-leg radiographs and CT scans with 3D reconstruction. The PSGCs were used to align the osteotomy cut and position the screw holes for the plate. The desired correction was achieved in the three planes when the holes on the plate were aligned with the holes drilled based on the PSCG. Preoperatively, the mean HKA angle was 171.9° (range: 166-179°), the mean proximal tibial angle was 87° (86-88°) and the mean tibial slope was 7.8° (1-22°). The postoperative correction was compared to the planned correction using 3D CT scan transformations. Intraoperative and postoperative complications were assessed at a minimum follow-up of 1 year. The procedure was successfully carried out in all patients with the PSCGs. On postoperative long-leg radiographs, the mean HKA was 182.3° (180-185°); on the CT scan, the mean tibial mechanical angle was 94° (90-98°) and the mean tibial slope was 7.1° (4-11°). In 19 out of 20 postoperative HKA and slope measurements, the difference between the planned and achieved correction was <2° based on the 3D analysis of the three planes in space; in the other case, the slope was 13° instead of the planned 10°. The intra-class correlation coefficients between the postoperative and planned parameters were 0.98 [0.92-0.99] for the HKA and 0.96 [0.79-0.99] for the tibial slope. There were no surgical site infections; one patient had a postoperative hematoma that resolved spontaneously. The results of this study showed that use of PSCGs in HTO procedures helps to achieve optimal correction in a safe and reliable manner. IV - Prospective cohort study. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

PrimerDesign-M: A multiple-alignment based multiple-primer design tool for walking across variable genomes

DOE PAGES

Yoon, Hyejin; Leitner, Thomas

2014-12-17

Analyses of entire viral genomes or mtDNA requires comprehensive design of many primers across their genomes. In addition, simultaneous optimization of several DNA primer design criteria may improve overall experimental efficiency and downstream bioinformatic processing. To achieve these goals, we developed PrimerDesign-M. It includes several options for multiple-primer design, allowing researchers to efficiently design walking primers that cover long DNA targets, such as entire HIV-1 genomes, and that optimizes primers simultaneously informed by genetic diversity in multiple alignments and experimental design constraints given by the user. PrimerDesign-M can also design primers that include DNA barcodes and minimize primer dimerization. PrimerDesign-Mmore » finds optimal primers for highly variable DNA targets and facilitates design flexibility by suggesting alternative designs to adapt to experimental conditions.« less

Pinning down high-performance Cu-chalcogenides as thin-film solar cell absorbers: A successive screening approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yubo; Zhang, Wenqing, E-mail: wqzhang@mail.sic.ac.cn, E-mail: pzhang3@buffalo.edu; State Key Laboratory of High Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050

2016-05-21

Photovoltaic performances of Cu-chalcogenides solar cells are strongly correlated with the absorber fundamental properties such as optimal bandgap, desired band alignment with window material, and high photon absorption ability. According to these criteria, we carry out a successive screening for 90 Cu-chalcogenides using efficient theoretical approaches. Besides the well-recognized CuInSe{sub 2} and Cu{sub 2}ZnSnSe{sub 4} materials, several novel candidates are identified to have optimal bandgaps of around 1.0–1.5 eV, spike-like band alignments with CdS window layer, sharp photon absorption edges, and high absorption coefficients. These new systems have great potential to be superior absorbers for photovolatic applications if their carrriermore » transport and defect properties are properly optimized.« less

Spreadsheet macros for coloring sequence alignments.

PubMed

Haygood, M G

1993-12-01

This article describes a set of Microsoft Excel macros designed to color amino acid and nucleotide sequence alignments for review and preparation of visual aids. The colored alignments can then be modified to emphasize features of interest. Procedures for importing and coloring sequences are described. The macro file adds a new menu to the menu bar containing sequence-related commands to enable users unfamiliar with Excel to use the macros more readily. The macros were designed for use with Macintosh computers but will also run with the DOS version of Excel.

DIALIGN P: fast pair-wise and multiple sequence alignment using parallel processors.

PubMed

Schmollinger, Martin; Nieselt, Kay; Kaufmann, Michael; Morgenstern, Burkhard

2004-09-09

Parallel computing is frequently used to speed up computationally expensive tasks in Bioinformatics. Herein, a parallel version of the multi-alignment program DIALIGN is introduced. We propose two ways of dividing the program into independent sub-routines that can be run on different processors: (a) pair-wise sequence alignments that are used as a first step to multiple alignment account for most of the CPU time in DIALIGN. Since alignments of different sequence pairs are completely independent of each other, they can be distributed to multiple processors without any effect on the resulting output alignments. (b) For alignments of large genomic sequences, we use a heuristics by splitting up sequences into sub-sequences based on a previously introduced anchored alignment procedure. For our test sequences, this combined approach reduces the program running time of DIALIGN by up to 97%. By distributing sub-routines to multiple processors, the running time of DIALIGN can be crucially improved. With these improvements, it is possible to apply the program in large-scale genomics and proteomics projects that were previously beyond its scope.

A comparison of registration errors with imageless computer navigation during MIS total knee arthroplasty versus standard incision total knee arthroplasty: a cadaveric study.

PubMed

Davis, Edward T; Pagkalos, Joseph; Gallie, Price A M; Macgroarty, Kelly; Waddell, James P; Schemitsch, Emil H

2015-01-01

Optimal component alignment in total knee arthroplasty has been associated with better functional outcome as well as improved implant longevity. The ability to align components optimally during minimally invasive (MIS) total knee replacement (TKR) has been a cause of concern. Computer navigation is a useful aid in achieving the desired alignment although it is limited by the error during the manual registration of landmarks. Our study aims to compare the registration process error between a standard and a MIS surgical approach. We hypothesized that performing the registration error via an MIS approach would increase the registration process error. Five fresh frozen lower limbs were routinely prepared and draped. The registration process was performed through an MIS approach. This was then extended to the standard approach and the registration was performed again. Two surgeons performed the registration process five times with each approach. Performing the registration process through the MIS approach was not associated with higher error compared to the standard approach in the alignment parameters of interest. This rejects our hypothesis. Image-free navigated MIS TKR does not appear to carry higher risk of component malalignment due to the registration process error. Navigation can be used during MIS TKR to improve alignment without reduced accuracy due to the approach.

Feasibility and optical performance of one axis three positions sun-tracking polar-axis aligned CPCs for photovoltaic applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang, Runsheng; Yu, Yamei

2010-09-15

A new design concept, called one axis three positions sun-tracking polar-axis aligned CPCs (3P-CPCs, in short), was proposed and theoretically studied in this work for photovoltaic applications. The proposed trough-like CPC is oriented in the polar-axis direction, and the aperture is daily adjusted eastward, southward, and westward in the morning, noon and afternoon, respectively, by rotating the CPC trough, to ensure efficient collection of beam radiation nearly all day. To investigate the optical performance of such CPCs, an analytical mathematical procedure is developed to estimate daily and annual solar gain captured by such CPCs based on extraterrestrial radiation and monthlymore » horizontal radiation. Results show that the acceptance half-angle of 3P-CPCs is a unique parameter to determine their optical performance according to extraterrestrial radiation, and the annual solar gain stays constant if the acceptance half-angle, {theta}{sub a}, is less than one third of {omega}{sub 0,min}, the sunset hour angle in the winter solstice, otherwise decreases with the increase of {theta}{sub a}. For 3P-CPCs used in China, the annual solar gain, depending on the climatic conditions in site, decreased with the acceptance half-angle, but such decrease was slow for the case of {theta}{sub a}{<=}{omega}{sub 0,min}/3, indicating that the acceptance half-angle should be less than one third of {omega}{sub 0,min} for maximizing annual energy collection. Compared to fixed east-west aligned CPCs (EW-CPCs) with a yearly optimal acceptance half-angle, the fixed south-facing polar-axis aligned CPCs (1P-CPCs) with the same acceptance half-angle as the EW-CPCs annually collected about 65-74% of that EW-CPCs did, whereas 3P-CPCs annually collected 1.26-1.45 times of that EW-CPCs collected, indicating that 3P-CPCs were more efficient for concentrating solar radiation onto their coupling solar cells. (author)« less

Software for Alignment of Segments of a Telescope Mirror

NASA Technical Reports Server (NTRS)

Hall, Drew P.; Howard, Richard T.; Ly, William C.; Rakoczy, John M.; Weir, John M.

2006-01-01

The Segment Alignment Maintenance System (SAMS) software is designed to maintain the overall focus and figure of the large segmented primary mirror of the Hobby-Eberly Telescope. This software reads measurements made by sensors attached to the segments of the primary mirror and from these measurements computes optimal control values to send to actuators that move the mirror segments.

Optimizing wind farm layout via LES-calibrated geometric models inclusive of wind direction and atmospheric stability effects

NASA Astrophysics Data System (ADS)

Archer, Cristina; Ghaisas, Niranjan

2015-04-01

The energy generation at a wind farm is controlled primarily by the average wind speed at hub height. However, two other factors impact wind farm performance: 1) the layout of the wind turbines, in terms of spacing between turbines along and across the prevailing wind direction; staggering or aligning consecutive rows; angles between rows, columns, and prevailing wind direction); and 2) atmospheric stability, which is a measure of whether vertical motion is enhanced (unstable), suppressed (stable), or neither (neutral). Studying both factors and their complex interplay with Large-Eddy Simulation (LES) is a valid approach because it produces high-resolution, 3D, turbulent fields, such as wind velocity, temperature, and momentum and heat fluxes, and it properly accounts for the interactions between wind turbine blades and the surrounding atmospheric and near-surface properties. However, LES are computationally expensive and simulating all the possible combinations of wind directions, atmospheric stabilities, and turbine layouts to identify the optimal wind farm configuration is practically unfeasible today. A new, geometry-based method is proposed that is computationally inexpensive and that combines simple geometric quantities with a minimal number of LES simulations to identify the optimal wind turbine layout, taking into account not only the actual frequency distribution of wind directions (i.e., wind rose) at the site of interest, but also atmospheric stability. The geometry-based method is calibrated with LES of the Lillgrund wind farm conducted with the Software for Offshore/onshore Wind Farm Applications (SOWFA), based on the open-access OpenFOAM libraries. The geometric quantities that offer the best correlations (>0.93) with the LES results are the blockage ratio, defined as the fraction of the swept area of a wind turbine that is blocked by an upstream turbine, and the blockage distance, the weighted distance from a given turbine to all upstream turbines that can potentially block it. Based on blockage ratio and distance, an optimization procedure is proposed that explores many different layout variables and identifies, given actual wind direction and stability distributions, the optimal wind farm layout, i.e., the one with the highest wind energy production. The optimization procedure is applied to both the calibration wind farm (Lillgrund) and a test wind farm (Horns Rev) and a number of layouts more efficient than the existing ones are identified. The optimization procedure based on geometric models proposed here can be applied very quickly (within a few hours) to any proposed wind farm, once enough information on wind direction frequency and, if available, atmospheric stability frequency has been gathered and once the number of turbines and/or the areal extent of the wind farm have been identified.

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

PubMed

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

2010-06-01

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

Fine-tuning structural RNA alignments in the twilight zone

PubMed Central

2010-01-01

Background A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance. This method works best around 75% sequence similarity. However, in a "twilight zone" below 55% similarity, the sequence alignment tends to obscure the covariance signal used in the second phase. Therefore, while the overall shape of the consensus structure may still be found, the degree of conservation cannot be estimated reliably. Results Based on a combination of available methods, we present a method named planACstar for improving structure conservation in structural alignments in the twilight zone. After constructing a consensus structure by alignment folding, planACstar abandons the original sequence alignment, refolds the sequences individually, but consistent with the consensus, aligns the structures, irrespective of sequence, by a pure structure alignment method, and derives an improved sequence alignment from the alignment of structures, to be re-submitted to alignment folding, etc.. This circle may be iterated as long as structural conservation improves, but normally, one step suffices. Conclusions Employing the tools ClustalW, RNAalifold, and RNAforester, we find that for sequences with 30-55% sequence identity, structural conservation can be improved by 10% on average, with a large variation, measured in terms of RNAalifold's own criterion, the structure conservation index. PMID:20433706

Score distributions of gapped multiple sequence alignments down to the low-probability tail

NASA Astrophysics Data System (ADS)

Fieth, Pascal; Hartmann, Alexander K.

2016-08-01

Assessing the significance of alignment scores of optimally aligned DNA or amino acid sequences can be achieved via the knowledge of the score distribution of random sequences. But this requires obtaining the distribution in the biologically relevant high-scoring region, where the probabilities are exponentially small. For gapless local alignments of infinitely long sequences this distribution is known analytically to follow a Gumbel distribution. Distributions for gapped local alignments and global alignments of finite lengths can only be obtained numerically. To obtain result for the small-probability region, specific statistical mechanics-based rare-event algorithms can be applied. In previous studies, this was achieved for pairwise alignments. They showed that, contrary to results from previous simple sampling studies, strong deviations from the Gumbel distribution occur in case of finite sequence lengths. Here we extend the studies to multiple sequence alignments with gaps, which are much more relevant for practical applications in molecular biology. We study the distributions of scores over a large range of the support, reaching probabilities as small as 10-160, for global and local (sum-of-pair scores) multiple alignments. We find that even after suitable rescaling, eliminating the sequence-length dependence, the distributions for multiple alignment differ from the pairwise alignment case. Furthermore, we also show that the previously discussed Gaussian correction to the Gumbel distribution needs to be refined, also for the case of pairwise alignments.

Paraplegic patients: how to measure balance and what is normal or functional?

PubMed

Barkoh, Kaku; Lucas, Joshua W; Lee, Larry; Hsieh, Patrick C; Wang, Jeffrey C; Rolfe, Kevin

2018-02-01

To review the current understanding and data of sagittal balance and alignment considerations in paraplegic patients. A PubMed literature search was conducted to identify all relevant articles relating to sagittal alignment and sagittal balance considerations in paraplegic and spinal cord injury patients. While there are numerous studies and publications on sagittal balance in the ambulatory patient with spinal deformity or complex spine disorders, there is paucity of the literature on "normal" sagittal balance in the paraplegic patients. Studies have reported significantly alterations of the sagittal alignment parameters in the non-ambulatory paraplegic patients compared to ambulatory patients. The variability of the alignment changes is related to the differences in the level of the spinal cord injury and their differences in the activations of truncal muscles to allow functional movements in those patients, particularly in optimizing sitting and transferring. Surgical goal in treating paraplegic patients with complex pathologies should not be solely directed to achieve the "normal" radiographic parameters of sagittal alignment in the ambulatory patients. The goal should be to maintain good coronal balance to allow ideal sitting position and to preserve motion segment to optimize functions of paraplegia patients. Current available literature data have not defined normal sagittal parameters for paraplegic patients. There are significant differences in postural sagittal parameters and muscle activations in paraplegic and non-spinal cord injury patients that can lead to differences in sagittal alignment and balance. Treatment goal in spine surgery for paraplegic patients should address their global function, sitting balance, and ability to perform self-care rather than the accepted radiographic parameters for adult spinal deformity in ambulatory patients.

Lamellar boundary alignment of DS-processed TiAl-W alloys by a solidification procedure

NASA Astrophysics Data System (ADS)

Jung, In-Soo; Oh, Myung-Hoon; Park, No-Jin; Kumar, K. Sharvan; Wee, Dang-Moon

2007-12-01

In this study, a β solidification procedure was used to align the lamellae in a Ti-47Al-2W (at.%) alloy parallel to the growth direction. The Bridgman technique and the floating zone process were used for directional solidification. The mechanical properties of the directionally solidified alloy were evaluated in tension at room temperature and at 800°C. At a growth rate of 30 mm/h (with the floating zone approach), the lamellae were well aligned parallel to the growth direction. The aligned lamellae yielded excellent room temperature tensile ductility. The tensile yield strength at 800°C was similar to that at room temperature. The orientation of the γ lamellar laths in the directionally solidified ingots, which were manufactured by means of a floating zone process, was identified with the aid of electron backscattered diffraction analysis. On the basis of this analysis, the preferred growth direction of the bcc-β dendrites that formed at high temperatures close to the melting point was inferred to be [001]β at a growth rate of 30 mm/h and [111]β at a growth rate of 90 mm/h.

Fast Gaussian kernel learning for classification tasks based on specially structured global optimization.

PubMed

Zhong, Shangping; Chen, Tianshun; He, Fengying; Niu, Yuzhen

2014-09-01

For a practical pattern classification task solved by kernel methods, the computing time is mainly spent on kernel learning (or training). However, the current kernel learning approaches are based on local optimization techniques, and hard to have good time performances, especially for large datasets. Thus the existing algorithms cannot be easily extended to large-scale tasks. In this paper, we present a fast Gaussian kernel learning method by solving a specially structured global optimization (SSGO) problem. We optimize the Gaussian kernel function by using the formulated kernel target alignment criterion, which is a difference of increasing (d.i.) functions. Through using a power-transformation based convexification method, the objective criterion can be represented as a difference of convex (d.c.) functions with a fixed power-transformation parameter. And the objective programming problem can then be converted to a SSGO problem: globally minimizing a concave function over a convex set. The SSGO problem is classical and has good solvability. Thus, to find the global optimal solution efficiently, we can adopt the improved Hoffman's outer approximation method, which need not repeat the searching procedure with different starting points to locate the best local minimum. Also, the proposed method can be proven to converge to the global solution for any classification task. We evaluate the proposed method on twenty benchmark datasets, and compare it with four other Gaussian kernel learning methods. Experimental results show that the proposed method stably achieves both good time-efficiency performance and good classification performance. Copyright © 2014 Elsevier Ltd. All rights reserved.

Preservation or Restoration of Segmental and Regional Spinal Lordosis Using Minimally Invasive Interbody Fusion Techniques in Degenerative Lumbar Conditions: A Literature Review.

PubMed

Uribe, Juan S; Myhre, Sue Lynn; Youssef, Jim A

2016-04-01

A literature review. The purpose of this study was to review lumbar segmental and regional alignment changes following treatment with a variety of minimally invasive surgery (MIS) interbody fusion procedures for short-segment, degenerative conditions. An increasing number of lumbar fusions are being performed with minimally invasive exposures, despite a perception that minimally invasive lumbar interbody fusion procedures are unable to affect segmental and regional lordosis. Through a MEDLINE and Google Scholar search, a total of 23 articles were identified that reported alignment following minimally invasive lumbar fusion for degenerative (nondeformity) lumbar spinal conditions to examine aggregate changes in postoperative alignment. Of the 23 studies identified, 28 study cohorts were included in the analysis. Procedural cohorts included MIS ALIF (two), extreme lateral interbody fusion (XLIF) (16), and MIS posterior/transforaminal lumbar interbody fusion (P/TLIF) (11). Across 19 study cohorts and 720 patients, weighted average of lumbar lordosis preoperatively for all procedures was 43.5° (range 28.4°-52.5°) and increased 3.4° (9%) (range -2° to 7.4°) postoperatively (P < 0.001). Segmental lordosis increased, on average, by 4° from a weighted average of 8.3° preoperatively (range -0.8° to 15.8°) to 11.2° at postoperative time points (range -0.2° to 22.8°) (P < 0.001) in 1182 patient from 24 study cohorts. Simple linear regression revealed a significant relationship between preoperative lumbar lordosis and change in lumbar lordosis (r = 0.413; P = 0.003), wherein lower preoperative lumbar lordosis predicted a greater increase in postoperative lumbar lordosis. Significant gains in both weighted average lumbar lordosis and segmental lordosis were seen following MIS interbody fusion. None of the segmental lordosis cohorts and only two of the 19 lumbar lordosis cohorts showed decreases in lordosis postoperatively. These results suggest that MIS approaches are able to impact regional and local segmental alignment and that preoperative patient factors can impact the extent of correction gained (preserving vs. restoring alignment). 4.

Construction and assembly of the wire planes for the MicroBooNE Time Projection Chamber

DOE PAGES

Acciarri, R.; Adams, C.; Asaadi, J.; ...

2017-03-09

As x-ray and electron tomography is pushed further into the nanoscale, the limitations of rotation stages become more apparent, leading to challenges in the alignment of the acquired projection images. Here we present an approach for rapid post-acquisition alignment of these projections to obtain high quality three-dimensional images. Our approach is based on a joint estimation of alignment errors, and the object, using an iterative refinement procedure. With simulated data where we know the alignment error of each projection image, our approach shows a residual alignment error that is a factor of a thousand smaller, and it reaches the samemore » error level in the reconstructed image in less than half the number of iterations. We then show its application to experimental data in x-ray and electron nanotomography.« less

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

PubMed

Paleo, Pierre; Pouyet, Emeline; Kieffer, Jérôme

2014-03-01

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

Construction and assembly of the wire planes for the MicroBooNE Time Projection Chamber

DOE Office of Scientific and Technical Information (OSTI.GOV)

Acciarri, R.; Adams, C.; Asaadi, J.

As x-ray and electron tomography is pushed further into the nanoscale, the limitations of rotation stages become more apparent, leading to challenges in the alignment of the acquired projection images. Here we present an approach for rapid post-acquisition alignment of these projections to obtain high quality three-dimensional images. Our approach is based on a joint estimation of alignment errors, and the object, using an iterative refinement procedure. With simulated data where we know the alignment error of each projection image, our approach shows a residual alignment error that is a factor of a thousand smaller, and it reaches the samemore » error level in the reconstructed image in less than half the number of iterations. We then show its application to experimental data in x-ray and electron nanotomography.« less

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

PubMed

Löytynoja, Ari

2012-01-01

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

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

PubMed

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

2014-07-01

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

Vertically aligned N-doped CNTs growth using Taguchi experimental design

NASA Astrophysics Data System (ADS)

Silva, Ricardo M.; Fernandes, António J. S.; Ferro, Marta C.; Pinna, Nicola; Silva, Rui F.

2015-07-01

The Taguchi method with a parameter design L9 orthogonal array was implemented for optimizing the nitrogen incorporation in the structure of vertically aligned N-doped CNTs grown by thermal chemical deposition (TCVD). The maximization of the ID/IG ratio of the Raman spectra was selected as the target value. As a result, the optimal deposition configuration was NH3 = 90 sccm, growth temperature = 825 °C and catalyst pretreatment time of 2 min, the first parameter having the main effect on nitrogen incorporation. A confirmation experiment with these values was performed, ratifying the predicted ID/IG ratio of 1.42. Scanning electron microscopy (SEM) characterization revealed a uniform completely vertically aligned array of multiwalled CNTs which individually exhibit a bamboo-like structure, consisting of periodically curved graphitic layers, as depicted by high resolution transmission electron microscopy (HRTEM). The X-ray photoelectron spectroscopy (XPS) results indicated a 2.00 at.% of N incorporation in the CNTs in pyridine-like and graphite-like, as the predominant species.

Optimization methods of pulse-to-pulse alignment using femtosecond pulse laser based on temporal coherence function for practical distance measurement

NASA Astrophysics Data System (ADS)

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

2018-02-01

An interferometer technique based on temporal coherence function of femtosecond pulses is demonstrated for practical distance measurement. Here, the pulse-to-pulse alignment is analyzed for large delay distance measurement. Firstly, a temporal coherence function model between two femtosecond pulses is developed in the time domain for the dispersive unbalanced Michelson interferometer. Then, according to this model, the fringes analysis and the envelope extraction process are discussed. Meanwhile, optimization methods of pulse-to-pulse alignment for practical long distance measurement are presented. The order of the curve fitting and the selection of points for envelope extraction are analyzed. Furthermore, an averaging method based on the symmetry of the coherence function is demonstrated. Finally, the performance of the proposed methods is evaluated in the absolute distance measurement of 20 μ m with path length difference of 9 m. The improvement of standard deviation in experimental results shows that these approaches have the potential for practical distance measurement.

A greedy, graph-based algorithm for the alignment of multiple homologous gene lists.

PubMed

Fostier, Jan; Proost, Sebastian; Dhoedt, Bart; Saeys, Yvan; Demeester, Piet; Van de Peer, Yves; Vandepoele, Klaas

2011-03-15

Many comparative genomics studies rely on the correct identification of homologous genomic regions using accurate alignment tools. In such case, the alphabet of the input sequences consists of complete genes, rather than nucleotides or amino acids. As optimal multiple sequence alignment is computationally impractical, a progressive alignment strategy is often employed. However, such an approach is susceptible to the propagation of alignment errors in early pairwise alignment steps, especially when dealing with strongly diverged genomic regions. In this article, we present a novel accurate and efficient greedy, graph-based algorithm for the alignment of multiple homologous genomic segments, represented as ordered gene lists. Based on provable properties of the graph structure, several heuristics are developed to resolve local alignment conflicts that occur due to gene duplication and/or rearrangement events on the different genomic segments. The performance of the algorithm is assessed by comparing the alignment results of homologous genomic segments in Arabidopsis thaliana to those obtained by using both a progressive alignment method and an earlier graph-based implementation. Especially for datasets that contain strongly diverged segments, the proposed method achieves a substantially higher alignment accuracy, and proves to be sufficiently fast for large datasets including a few dozens of eukaryotic genomes. http://bioinformatics.psb.ugent.be/software. The algorithm is implemented as a part of the i-ADHoRe 3.0 package.

Fast-switching chiral nematic liquid-crystal mode with polymer-sustained twisted vertical alignment.

PubMed

Chang, Kai-Han; Joshi, Vinay; Chien, Liang-Chy

2017-04-01

We demonstrate a fast-switching liquid-crystal mode with polymer-sustained twisted vertical alignment. By optimizing the polymerization condition, a polymer microstructure with controlled orientation is produced. The polymer microstructure not only synergistically suppresses the optical bounce during field-induced homeotropic-twist transition but also shortens the response time significantly. Theoretical analyses validate that the ground state free energy density is modified by the aligning field of the polymer microstructure, which affects the driving voltage of the device. The outcomes of this paper will enable the development of fast-switching and achromatic electro-optical and photonic devices.

Fast-switching chiral nematic liquid-crystal mode with polymer-sustained twisted vertical alignment

NASA Astrophysics Data System (ADS)

Chang, Kai-Han; Joshi, Vinay; Chien, Liang-Chy

2017-04-01

We demonstrate a fast-switching liquid-crystal mode with polymer-sustained twisted vertical alignment. By optimizing the polymerization condition, a polymer microstructure with controlled orientation is produced. The polymer microstructure not only synergistically suppresses the optical bounce during field-induced homeotropic-twist transition but also shortens the response time significantly. Theoretical analyses validate that the ground state free energy density is modified by the aligning field of the polymer microstructure, which affects the driving voltage of the device. The outcomes of this paper will enable the development of fast-switching and achromatic electro-optical and photonic devices.

FPGA-based protein sequence alignment : A review

NASA Astrophysics Data System (ADS)

Isa, Mohd. Nazrin Md.; Muhsen, Ku Noor Dhaniah Ku; Saiful Nurdin, Dayana; Ahmad, Muhammad Imran; Anuar Zainol Murad, Sohiful; Nizam Mohyar, Shaiful; Harun, Azizi; Hussin, Razaidi

2017-11-01

Sequence alignment have been optimized using several techniques in order to accelerate the computation time to obtain the optimal score by implementing DP-based algorithm into hardware such as FPGA-based platform. During hardware implementation, there will be performance challenges such as the frequent memory access and highly data dependent in computation process. Therefore, investigation in processing element (PE) configuration where involves more on memory access in load or access the data (substitution matrix, query sequence character) and the PE configuration time will be the main focus in this paper. There are various approaches to enhance the PE configuration performance that have been done in previous works such as by using serial configuration chain and parallel configuration chain i.e. the configuration data will be loaded into each PEs sequentially and simultaneously respectively. Some researchers have proven that the performance using parallel configuration chain has optimized both the configuration time and area.

Investigation of compaction and permeability during the out-of-autoclave and vacuum-bag-only manufacturing of a laminate composite with aligned carbon nanofibers

NASA Astrophysics Data System (ADS)

Mann, Erin

Both industry and commercial entities are in the process of using more lightweight composites. Fillers, such as fibers, nanofibers and other nanoconstituents in polymer matrix composites have been proven to enhance the properties of composites and are still being studied in order to optimize the benefits. Further optimization can be studied during the manufacturing process. The air permeability during the out-of-autoclave-vacuum-bag-only (OOA-VBO) cure method is an important property to understand during the optimization of manufacturing processes. Changes in the manufacturing process can improve or decrease composite quality depending on the ability of the composite to evacuate gases such as air and moisture during curing. Therefore, in this study, the axial permeability of a prepreg stack was experimentally studied. Three types of samples were studied: control (no carbon nanofiber (CNF) modification), unaligned CNF modified and aligned CNF modified samples.

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

PubMed Central

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

2015-01-01

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

Feature-based Alignment of Volumetric Multi-modal Images

PubMed Central

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

2014-01-01

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

Hartmann wavefront sensors and their application at FLASH.

PubMed

Keitel, Barbara; Plönjes, Elke; Kreis, Svea; Kuhlmann, Marion; Tiedtke, Kai; Mey, Tobias; Schäfer, Bernd; Mann, Klaus

2016-01-01

Different types of Hartmann wavefront sensors are presented which are usable for a variety of applications in the soft X-ray spectral region at FLASH, the free-electron laser (FEL) in Hamburg. As a typical application, online measurements of photon beam parameters during mirror alignment are reported on. A compact Hartmann sensor, operating in the wavelength range from 4 to 38 nm, was used to determine the wavefront quality as well as aberrations of individual FEL pulses during the alignment procedure. Beam characterization and alignment of the focusing optics of the FLASH beamline BL3 were performed with λ(13.5 nm)/116 accuracy for wavefront r.m.s. (w(rms)) repeatability, resulting in a reduction of w(rms) by 33% during alignment.

The Relationship between Distributed Leadership and Teachers' Academic Optimism

ERIC Educational Resources Information Center

Mascall, Blair; Leithwood, Kenneth; Straus, Tiiu; Sacks, Robin

2008-01-01

Purpose: The goal of this study was to examine the relationship between four patterns of distributed leadership and a modified version of a variable Hoy et al. have labeled "teachers' academic optimism." The distributed leadership patterns reflect the extent to which the performance of leadership functions is consciously aligned across…

Proposing an Optimal Learning Architecture for the Digital Enterprise.

ERIC Educational Resources Information Center

O'Driscoll, Tony

2003-01-01

Discusses the strategic role of learning in information age organizations; analyzes parallels between the application of technology to business and the application of technology to learning; and proposes a learning architecture that aligns with the knowledge-based view of the firm and optimizes the application of technology to achieve proficiency…

Stepwise detection of recombination breakpoints in sequence alignments.

PubMed

Graham, Jinko; McNeney, Brad; Seillier-Moiseiwitsch, Françoise

2005-03-01

We propose a stepwise approach to identify recombination breakpoints in a sequence alignment. The approach can be applied to any recombination detection method that uses a permutation test and provides estimates of breakpoints. We illustrate the approach by analyses of a simulated dataset and alignments of real data from HIV-1 and human chromosome 7. The presented simulation results compare the statistical properties of one-step and two-step procedures. More breakpoints are found with a two-step procedure than with a single application of a given method, particularly for higher recombination rates. At higher recombination rates, the additional breakpoints were located at the cost of only a slight increase in the number of falsely declared breakpoints. However, a large proportion of breakpoints still go undetected. A makefile and C source code for phylogenetic profiling and the maximum chi2 method, tested with the gcc compiler on Linux and WindowsXP, are available at http://stat-db.stat.sfu.ca/stepwise/ jgraham@stat.sfu.ca.

ARYANA: Aligning Reads by Yet Another Approach

PubMed Central

2014-01-01

Motivation Although there are many different algorithms and software tools for aligning sequencing reads, fast gapped sequence search is far from solved. Strong interest in fast alignment is best reflected in the $106 prize for the Innocentive competition on aligning a collection of reads to a given database of reference genomes. In addition, de novo assembly of next-generation sequencing long reads requires fast overlap-layout-concensus algorithms which depend on fast and accurate alignment. Contribution We introduce ARYANA, a fast gapped read aligner, developed on the base of BWA indexing infrastructure with a completely new alignment engine that makes it significantly faster than three other aligners: Bowtie2, BWA and SeqAlto, with comparable generality and accuracy. Instead of the time-consuming backtracking procedures for handling mismatches, ARYANA comes with the seed-and-extend algorithmic framework and a significantly improved efficiency by integrating novel algorithmic techniques including dynamic seed selection, bidirectional seed extension, reset-free hash tables, and gap-filling dynamic programming. As the read length increases ARYANA's superiority in terms of speed and alignment rate becomes more evident. This is in perfect harmony with the read length trend as the sequencing technologies evolve. The algorithmic platform of ARYANA makes it easy to develop mission-specific aligners for other applications using ARYANA engine. Availability ARYANA with complete source code can be obtained from http://github.com/aryana-aligner PMID:25252881

ARYANA: Aligning Reads by Yet Another Approach.

PubMed

Gholami, Milad; Arbabi, Aryan; Sharifi-Zarchi, Ali; Chitsaz, Hamidreza; Sadeghi, Mehdi

2014-01-01

Although there are many different algorithms and software tools for aligning sequencing reads, fast gapped sequence search is far from solved. Strong interest in fast alignment is best reflected in the $10(6) prize for the Innocentive competition on aligning a collection of reads to a given database of reference genomes. In addition, de novo assembly of next-generation sequencing long reads requires fast overlap-layout-concensus algorithms which depend on fast and accurate alignment. We introduce ARYANA, a fast gapped read aligner, developed on the base of BWA indexing infrastructure with a completely new alignment engine that makes it significantly faster than three other aligners: Bowtie2, BWA and SeqAlto, with comparable generality and accuracy. Instead of the time-consuming backtracking procedures for handling mismatches, ARYANA comes with the seed-and-extend algorithmic framework and a significantly improved efficiency by integrating novel algorithmic techniques including dynamic seed selection, bidirectional seed extension, reset-free hash tables, and gap-filling dynamic programming. As the read length increases ARYANA's superiority in terms of speed and alignment rate becomes more evident. This is in perfect harmony with the read length trend as the sequencing technologies evolve. The algorithmic platform of ARYANA makes it easy to develop mission-specific aligners for other applications using ARYANA engine. ARYANA with complete source code can be obtained from http://github.com/aryana-aligner.

Synthesis of Bipartite Tetracysteine PNA Probes for DNA In Situ Fluorescent Labeling.

PubMed

Fang, Ge-Min; Seitz, Oliver

2017-12-24

"Label-free" fluorescent probes that avoid additional steps or building blocks for conjugation of fluorescent dyes with oligonucleotides can significantly reduce the time and cost of parallel bioanalysis of a large number of nucleic acid samples. A method for the synthesis of "label-free" bicysteine-modified PNA probes using solid-phase synthesis and procedures for sequence-specific DNA in situ fluorescent labeling is described here. The concept is based on the adjacent alignment of two bicysteine-modified peptide nucleic acids on a DNA target to form a structurally optimized bipartite tetracysteine motif, which induces a sequence-specific fluorogenic reaction with commercially available biarsenic dyes, even in complex media such as cell lysate. This unit will help researchers to quickly synthesize bipartite tetracysteine PNA probes and carry out low-cost DNA in situ fluorescent labeling experiments. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Information-theoretical noninvasive damage detection in bridge structures

NASA Astrophysics Data System (ADS)

Sudu Ambegedara, Amila; Sun, Jie; Janoyan, Kerop; Bollt, Erik

2016-11-01

Damage detection of mechanical structures such as bridges is an important research problem in civil engineering. Using spatially distributed sensor time series data collected from a recent experiment on a local bridge in Upper State New York, we study noninvasive damage detection using information-theoretical methods. Several findings are in order. First, the time series data, which represent accelerations measured at the sensors, more closely follow Laplace distribution than normal distribution, allowing us to develop parameter estimators for various information-theoretic measures such as entropy and mutual information. Second, as damage is introduced by the removal of bolts of the first diaphragm connection, the interaction between spatially nearby sensors as measured by mutual information becomes weaker, suggesting that the bridge is "loosened." Finally, using a proposed optimal mutual information interaction procedure to prune away indirect interactions, we found that the primary direction of interaction or influence aligns with the traffic direction on the bridge even after damaging the bridge.

FEAST: sensitive local alignment with multiple rates of evolution.

PubMed

Hudek, Alexander K; Brown, Daniel G

2011-01-01

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

Image-guided laser projection for port placement in minimally invasive surgery.

PubMed

Marmurek, Jonathan; Wedlake, Chris; Pardasani, Utsav; Eagleson, Roy; Peters, Terry

2006-01-01

We present an application of an augmented reality laser projection system in which procedure-specific optimal incision sites, computed from pre-operative image acquisition, are superimposed on a patient to guide port placement in minimally invasive surgery. Tests were conducted to evaluate the fidelity of computed and measured port configurations, and to validate the accuracy with which a surgical tool-tip can be placed at an identified virtual target. A high resolution volumetric image of a thorax phantom was acquired using helical computed tomography imaging. Oriented within the thorax, a phantom organ with marked targets was visualized in a virtual environment. A graphical interface enabled marking the locations of target anatomy, and calculation of a grid of potential port locations along the intercostal rib lines. Optimal configurations of port positions and tool orientations were determined by an objective measure reflecting image-based indices of surgical dexterity, hand-eye alignment, and collision detection. Intra-operative registration of the computed virtual model and the phantom anatomy was performed using an optical tracking system. Initial trials demonstrated that computed and projected port placement provided direct access to target anatomy with an accuracy of 2 mm.

An analysis of the surface-normal coupling efficiency of a metal grating coupler embedded in a Scotch tape optical waveguide

NASA Astrophysics Data System (ADS)

Barrios, Carlos Angulo; Canalejas-Tejero, Víctor

2017-01-01

The coupling efficiency at normal incidence of recently demonstrated aluminum grating couplers integrated in flexible Scotch tape waveguides has been analyzed theoretically and experimentally. Finite difference time domain (FDTD) and rigorously coupled wave analysis (RCWA) methods have been used to optimize the dimensions (duty cycle and metal thickness) of Scotch tape-embedded 1D Al gratings for maximum coupling at 635 nm wavelength. Good dimension and tape refractive index tolerances are predicted. FDTD simulations reveal the incident beam width and impinging position (alignment) values that avoid rediffraction and thus maximize the coupling efficiency. A 1D Al diffraction grating integrated into a Scotch tape optical waveguide has been fabricated and characterized. The fabrication process, based on pattern transfer, has been optimized to allow complete Al grating transfer onto the Scotch tape waveguide. A maximum coupling efficiency of 20% for TM-polarized normal incidence has been measured, which is in good agreement with the theoretical predictions. The measured coupling efficiency is further increased up to 28% for TM polarization under oblique incidence. Temperature dependence measurements have been also achieved and related to the simulations results and fabrication procedure.

"Performance Of A Wafer Stepper With Automatic Intra-Die Registration Correction."

NASA Astrophysics Data System (ADS)

van den Brink, M. A.; Wittekoek, S.; Linders, H. F. D.; van Hout, F. J.; George, R. A.

1987-01-01

An evaluation of a wafer stepper with the new improved Philips/ASM-L phase grating alignment system is reported. It is shown that an accurate alignment system needs an accurate X-Y-0 wafer stage and an accurate reticle Z stage to realize optimum overlay accuracy. This follows from a discussion of the overlay budget and an alignment procedure model. The accurate wafer stage permits high overlay accuracy using global alignment only, thus eliminating the throughput penalty of align-by-field schemes. The accurate reticle Z stage enables an intra-die magnification control with respect to the wafer scale. Various overlay data are reported, which have been measured with the automatic metrology program of the stepper. It is demonstrated that the new dual alignment system (with the external spatial filter) has improved the ability to align to weakly reflecting layers. The results are supported by a Fourier analysis of the alignment signal. Resolution data are given for the PAS 2500 projection lenses, which show that the high overlay accuracy of the system is properly matched with submicron linewidth control. The results of a recently introduced 20mm i-line lens with a numerical aperture of 0.4 (Zeiss 10-78-58) are included.

Laparoscopic Suturing as a Barrier to Broader Adoption of Laparoscopic Surgery

PubMed Central

Ghosh, Sudip; Niklewski, Paul; Roy, Sanjoy

2017-01-01

Background: Laparoscopic surgery is increasingly replacing the open procedure because of its many patient-related benefits that are well aligned with policies and programs that seek to optimize health system performance. However, widespread adoption of laparoscopic surgery has been slow, in part, because of the complexity of laparoscopic suturing. The objective of this study was to review the clinical and economic impacts of laparoscopic suturing in key procedures and to assess its role as a barrier to the broader adoption of laparoscopic surgery. Database: A medical literature search of MEDLINE, EMBASE, and BIOSIS from January 2010 through June 2016 identified 47 relevant articles. Conclusion: Laparoscopic suturing and intracorporeal knot tying may result in extended surgical time, complications, and surgeon errors, while improving patient quality of life through improved cosmesis, diet toleration, and better bowel movements. Despite advancement in surgical techniques and the availability of newer surgical tools, the complexity of laparoscopic suturing continues to be a barrier to greater adoption of MIS. The results of the study underscore the need for development of proficiency in laparoscopic suturing, which may help improve patient outcomes and reduce healthcare costs. PMID:28694682

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Design of a self-aligned, wide temperature range (300 mK-300 K) atomic force microscope/magnetic force microscope with 10 nm magnetic force microscope resolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karcı, Özgür; Department of Nanotechnology and Nanomedicine, Hacettepe University, Beytepe, 06800 Ankara; Dede, Münir

We describe the design of a wide temperature range (300 mK-300 K) atomic force microscope/magnetic force microscope with a self-aligned fibre-cantilever mechanism. An alignment chip with alignment groves and a special mechanical design are used to eliminate tedious and time consuming fibre-cantilever alignment procedure for the entire temperature range. A low noise, Michelson fibre interferometer was integrated into the system for measuring deflection of the cantilever. The spectral noise density of the system was measured to be ~12 fm/√Hz at 4.2 K at 3 mW incident optical power. Abrikosov vortices in BSCCO(2212) single crystal sample and a high density hardmore » disk sample were imaged at 10 nm resolution to demonstrate the performance of the system.« less

Accurate multi-robot targeting for keyhole neurosurgery based on external sensor monitoring.

PubMed

Comparetti, Mirko Daniele; Vaccarella, Alberto; Dyagilev, Ilya; Shoham, Moshe; Ferrigno, Giancarlo; De Momi, Elena

2012-05-01

Robotics has recently been introduced in surgery to improve intervention accuracy, to reduce invasiveness and to allow new surgical procedures. In this framework, the ROBOCAST system is an optically surveyed multi-robot chain aimed at enhancing the accuracy of surgical probe insertion during keyhole neurosurgery procedures. The system encompasses three robots, connected as a multiple kinematic chain (serial and parallel), totalling 13 degrees of freedom, and it is used to automatically align the probe onto a desired planned trajectory. The probe is then inserted in the brain, towards the planned target, by means of a haptic interface. This paper presents a new iterative targeting approach to be used in surgical robotic navigation, where the multi-robot chain is used to align the surgical probe to the planned pose, and an external sensor is used to decrease the alignment errors. The iterative targeting was tested in an operating room environment using a skull phantom, and the targets were selected on magnetic resonance images. The proposed targeting procedure allows about 0.3 mm to be obtained as the residual median Euclidean distance between the planned and the desired targets, thus satisfying the surgical accuracy requirements (1 mm), due to the resolution of the diffused medical images. The performances proved to be independent of the robot optical sensor calibration accuracy.

Fusion of range camera and photogrammetry: a systematic procedure for improving 3-D models metric accuracy.

PubMed

Guidi, G; Beraldin, J A; Ciofi, S; Atzeni, C

2003-01-01

The generation of three-dimensional (3-D) digital models produced by optical technologies in some cases involves metric errors. This happens when small high-resolution 3-D images are assembled together in order to model a large object. In some applications, as for example 3-D modeling of Cultural Heritage, the problem of metric accuracy is a major issue and no methods are currently available for enhancing it. The authors present a procedure by which the metric reliability of the 3-D model, obtained through iterative alignments of many range maps, can be guaranteed to a known acceptable level. The goal is the integration of the 3-D range camera system with a close range digital photogrammetry technique. The basic idea is to generate a global coordinate system determined by the digital photogrammetric procedure, measuring the spatial coordinates of optical targets placed around the object to be modeled. Such coordinates, set as reference points, allow the proper rigid motion of few key range maps, including a portion of the targets, in the global reference system defined by photogrammetry. The other 3-D images are normally aligned around these locked images with usual iterative algorithms. Experimental results on an anthropomorphic test object, comparing the conventional and the proposed alignment method, are finally reported.

Accuracy of Patient Specific Cutting Blocks in Total Knee Arthroplasty

PubMed Central

Helmy, Naeder; Kühnel, Stefanie P.

2014-01-01

Background. Long-term survival of total knee arthroplasty (TKA) is mainly determined by optimal positioning of the components and prosthesis alignment. Implant positioning can be optimized by computer assisted surgery (CAS). Patient specific cutting blocks (PSCB) seem to have the potential to improve component alignment compared to the conventional technique and to be comparable to CAS. Methods. 113 knees were selected for PSI and included in this study. Pre- and postoperative mechanical axis, represented by the hip-knee-angle (HKA), the proximal tibial angle (PTA), the distal femoral angle (DFA), and the tibial slope (TS) were measured and the deviation from expected ideal values was calculated. Results. With a margin of error of ±3°, success rates were 81.4% for HKA, 92.0% for TPA, and 94.7% for DFA. With the margin of error for alignments extended to ±4°, we obtained a success rate of 92.9% for the HKA, 98.2% for the PTA, and 99.1% for the DFA. The TS showed postoperative results of 2.86 ± 2.02° (mean change 1.76 ± 2.85°). Conclusion. PSCBs for TKA seem to restore the overall leg alignment. Our data suggest that each individual component can be implanted accurately and the results are comparable to the ones in CAS. PMID:25254210

Subcritical transition scenarios via linear and nonlinear localized optimal perturbations in plane Poiseuille flow

NASA Astrophysics Data System (ADS)

Farano, Mirko; Cherubini, Stefania; Robinet, Jean-Christophe; De Palma, Pietro

2016-12-01

Subcritical transition in plane Poiseuille flow is investigated by means of a Lagrange-multiplier direct-adjoint optimization procedure with the aim of finding localized three-dimensional perturbations optimally growing in a given time interval (target time). Space localization of these optimal perturbations (OPs) is achieved by choosing as objective function either a p-norm (with p\\gg 1) of the perturbation energy density in a linear framework; or the classical (1-norm) perturbation energy, including nonlinear effects. This work aims at analyzing the structure of linear and nonlinear localized OPs for Poiseuille flow, and comparing their transition thresholds and scenarios. The nonlinear optimization approach provides three types of solutions: a weakly nonlinear, a hairpin-like and a highly nonlinear optimal perturbation, depending on the value of the initial energy and the target time. The former shows localization only in the wall-normal direction, whereas the latter appears much more localized and breaks the spanwise symmetry found at lower target times. Both solutions show spanwise inclined vortices and large values of the streamwise component of velocity already at the initial time. On the other hand, p-norm optimal perturbations, although being strongly localized in space, keep a shape similar to linear 1-norm optimal perturbations, showing streamwise-aligned vortices characterized by low values of the streamwise velocity component. When used for initializing direct numerical simulations, in most of the cases nonlinear OPs provide the most efficient route to transition in terms of time to transition and initial energy, even when they are less localized in space than the p-norm OP. The p-norm OP follows a transition path similar to the oblique transition scenario, with slightly oscillating streaks which saturate and eventually experience secondary instability. On the other hand, the nonlinear OP rapidly forms large-amplitude bent streaks and skips the phases of streak saturation, providing a contemporary growth of all of the velocity components due to strong nonlinear coupling.

Improving the magnetoelectric performance of Metglas/PZT laminates by annealing in a magnetic field.

PubMed

Freeman, E; Harper, J; Goel, N; Gilbert, I; Unguris, J; Schiff, S J; Tadigadapa, S

2017-01-01

A comprehensive investigation of magnetostriction optimization in Metglas 2605SA1 ribbons is performed to enhance magnetoelectric performance. We explore a range of annealing conditions to relieve remnant stress and align the magnetic domains in the Metglas, while minimizing unwanted crystallization. The magnetostriction coefficient, magnetoelectric coefficient, and magnetic domain alignment are correlated to optimize magnetoelectric performance. We report on direct magnetostriction observed by in-plane Doppler vibrometer and domain imagining using scanning electron microscopy with polarization analysis for a range of annealing conditions. We find that annealing in an oxygen-free environment at 400 °C for 30 min yields an optimal magnetoelectric coefficient, magnetostriction and magnetostriction coefficient. The optimized ribbons had a magnetostriction of 50.6 ± 0.2 μ m m -1 and magnetoelectric coefficient of 79.3 ± 1.5 μ m m -1 mT -1 . The optimized Metglas 2605SA1 ribbons and PZT-5A (d 31 mode) sensor achieves a magnetic noise floor of approximately 600 pT Hz -1/2 at 100 Hz and a magnetoelectric coefficient of 6.1 ± 0.03 MV m -1 T -1 .

Improving the magnetoelectric performance of Metglas/PZT laminates by annealing in a magnetic field

NASA Astrophysics Data System (ADS)

Freeman, E.; Harper, J.; Goel, N.; Gilbert, I.; Unguris, J.; Schiff, S. J.; Tadigadapa, S.

2017-08-01

A comprehensive investigation of magnetostriction optimization in Metglas 2605SA1 ribbons is performed to enhance magnetoelectric performance. We explore a range of annealing conditions to relieve remnant stress and align the magnetic domains in the Metglas, while minimizing unwanted crystallization. The magnetostriction coefficient, magnetoelectric coefficient, and magnetic domain alignment are correlated to optimize magnetoelectric performance. We report on direct magnetostriction observed by in-plane Doppler vibrometer and domain imagining using scanning electron microscopy with polarization analysis for a range of annealing conditions. We find that annealing in an oxygen-free environment at 400 {}\\circ {{C}} for 30 min yields an optimal magnetoelectric coefficient, magnetostriction and magnetostriction coefficient. The optimized ribbons had a magnetostriction of 50.6 ± 0.2 μ {{m}} {{{m}}}-1 and magnetoelectric coefficient of 79.3 ± 1.5 µm m-1 mT-1. The optimized Metglas 2605SA1 ribbons and PZT-5A (d31 mode) sensor achieves a magnetic noise floor of approximately 600 pT {{{H}}{{z}}}-1/2 at 100 Hz and a magnetoelectric coefficient of 6.1 ± 0.03 MV m-1 T-1.

Feed-forward alignment correction for advanced overlay process control using a standalone alignment station "Litho Booster"

NASA Astrophysics Data System (ADS)

Yahiro, Takehisa; Sawamura, Junpei; Dosho, Tomonori; Shiba, Yuji; Ando, Satoshi; Ishikawa, Jun; Morita, Masahiro; Shibazaki, Yuichi

2018-03-01

One of the main components of an On-Product Overlay (OPO) error budget is the process induced wafer error. This necessitates wafer-to-wafer correction in order to optimize overlay accuracy. This paper introduces the Litho Booster (LB), standalone alignment station as a solution to improving OPO. LB can execute high speed alignment measurements without throughput (THP) loss. LB can be installed in any lithography process control loop as a metrology tool, and is then able to provide feed-forward (FF) corrections to the scanners. In this paper, the detailed LB design is described and basic LB performance and OPO improvement is demonstrated. Litho Booster's extendibility and applicability as a solution for next generation manufacturing accuracy and productivity challenges are also outlined

Aligner optimization increases accuracy and decreases compute times in multi-species sequence data.

PubMed

Robinson, Kelly M; Hawkins, Aziah S; Santana-Cruz, Ivette; Adkins, Ricky S; Shetty, Amol C; Nagaraj, Sushma; Sadzewicz, Lisa; Tallon, Luke J; Rasko, David A; Fraser, Claire M; Mahurkar, Anup; Silva, Joana C; Dunning Hotopp, Julie C

2017-09-01

As sequencing technologies have evolved, the tools to analyze these sequences have made similar advances. However, for multi-species samples, we observed important and adverse differences in alignment specificity and computation time for bwa- mem (Burrows-Wheeler aligner-maximum exact matches) relative to bwa-aln. Therefore, we sought to optimize bwa-mem for alignment of data from multi-species samples in order to reduce alignment time and increase the specificity of alignments. In the multi-species cases examined, there was one majority member (i.e. Plasmodium falciparum or Brugia malayi ) and one minority member (i.e. human or the Wolbachia endosymbiont w Bm) of the sequence data. Increasing bwa-mem seed length from the default value reduced the number of read pairs from the majority sequence member that incorrectly aligned to the reference genome of the minority sequence member. Combining both source genomes into a single reference genome increased the specificity of mapping, while also reducing the central processing unit (CPU) time. In Plasmodium , at a seed length of 18 nt, 24.1 % of reads mapped to the human genome using 1.7±0.1 CPU hours, while 83.6 % of reads mapped to the Plasmodium genome using 0.2±0.0 CPU hours (total: 107.7 % reads mapping; in 1.9±0.1 CPU hours). In contrast, 97.1 % of the reads mapped to a combined Plasmodium- human reference in only 0.7±0.0 CPU hours. Overall, the results suggest that combining all references into a single reference database and using a 23 nt seed length reduces the computational time, while maximizing specificity. Similar results were found for simulated sequence reads from a mock metagenomic data set. We found similar improvements to computation time in a publicly available human-only data set.

Articulated distraction.

PubMed

Hosny, Gamal Ahmed

2011-07-01

Articular hip distraction can be applied either by using a monolateral articulated distractor or a circular fixator. The fixator should be aligned such that its axis is aligned with the transverse axis of the hip joint. Following distraction, the range of motion is maintained with regular physiotherapy. It is a useful salvage procedure in older children with hip stiffness, when other methods of containment are not applicable. Copyright © 2011 Elsevier Inc. All rights reserved.

Microfocusing at the PG1 beamline at FLASH

DOE PAGES

Dziarzhytski, Siarhei; Gerasimova, Natalia; Goderich, Rene; ...

2016-01-01

The Kirkpatrick–Baez (KB) refocusing mirror system installed at the PG1 branch of the plane-grating monochromator beamline at the soft X-ray/XUV free-electron laser in Hamburg (FLASH) is designed to provide tight aberration-free focusing down to 4 µm × 6 µm full width at half-maximum (FWHM) on the sample. Such a focal spot size is mandatory to achieve ultimate resolution and to guarantee best performance of the vacuum-ultraviolet (VUV) off-axis parabolic double-monochromator Raman spectrometer permanently installed at the PG1 beamline as an experimental end-station. The vertical beam size on the sample of the Raman spectrometer, which operates without entrance slit, defines andmore » limits the energy resolution of the instrument which has an unprecedented design value of 2 meV for photon energies below 70 eV and about 15 meV for higher energies up to 200 eV. In order to reach the designed focal spot size of 4 µm FWHM (vertically) and to hold the highest spectrometer resolution, special fully motorized in-vacuum manipulators for the KB mirror holders have been developed and the optics have been aligned employing wavefront-sensing techniques as well as ablative imprints analysis. Lastly, aberrations like astigmatism were minimized. In this article the design and layout of the KB mirror manipulators, the alignment procedure as well as microfocus optimization results are presented.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dziarzhytski, Siarhei; Gerasimova, Natalia; Goderich, Rene

The Kirkpatrick–Baez (KB) refocusing mirror system installed at the PG1 branch of the plane-grating monochromator beamline at the soft X-ray/XUV free-electron laser in Hamburg (FLASH) is designed to provide tight aberration-free focusing down to 4 µm × 6 µm full width at half-maximum (FWHM) on the sample. Such a focal spot size is mandatory to achieve ultimate resolution and to guarantee best performance of the vacuum-ultraviolet (VUV) off-axis parabolic double-monochromator Raman spectrometer permanently installed at the PG1 beamline as an experimental end-station. The vertical beam size on the sample of the Raman spectrometer, which operates without entrance slit, defines andmore » limits the energy resolution of the instrument which has an unprecedented design value of 2 meV for photon energies below 70 eV and about 15 meV for higher energies up to 200 eV. In order to reach the designed focal spot size of 4 µm FWHM (vertically) and to hold the highest spectrometer resolution, special fully motorized in-vacuum manipulators for the KB mirror holders have been developed and the optics have been aligned employing wavefront-sensing techniques as well as ablative imprints analysis. Lastly, aberrations like astigmatism were minimized. In this article the design and layout of the KB mirror manipulators, the alignment procedure as well as microfocus optimization results are presented.« less

Advanced Dispersed Fringe Sensing Algorithm for Coarse Phasing Segmented Mirror Telescopes

NASA Technical Reports Server (NTRS)

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

2013-01-01

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

FRankenstein becomes a cyborg: the automatic recombination and realignment of fold recognition models in CASP6.

PubMed

Kosinski, Jan; Gajda, Michal J; Cymerman, Iwona A; Kurowski, Michal A; Pawlowski, Marcin; Boniecki, Michal; Obarska, Agnieszka; Papaj, Grzegorz; Sroczynska-Obuchowicz, Paulina; Tkaczuk, Karolina L; Sniezynska, Paulina; Sasin, Joanna M; Augustyn, Anna; Bujnicki, Janusz M; Feder, Marcin

2005-01-01

In the course of CASP6, we generated models for all targets using a new version of the "FRankenstein's monster approach." Previously (in CASP5) we were able to build many very accurate full-atom models by selection and recombination of well-folded fragments obtained from crude fold recognition (FR) results, followed by optimization of the sequence-structure fit and assessment of alternative alignments on the structural level. This procedure was however very arduous, as most of the steps required extensive visual and manual input from the human modeler. Now, we have automated the most tedious steps, such as superposition of alternative models, extraction of best-scoring fragments, and construction of a hybrid "monster" structure, as well as generation of alternative alignments in the regions that remain poorly scored in the refined hybrid model. We have also included the ROSETTA method to construct those parts of the target for which no reasonable structures were generated by FR methods (such as long insertions and terminal extensions). The analysis of successes and failures of the current version of the FRankenstein approach in modeling of CASP6 targets reveals that the considerably streamlined and automated method performs almost as well as the initial, mostly manual version, which suggests that it may be a useful tool for accurate protein structure prediction even in the hands of nonexperts. 2005 Wiley-Liss, Inc.

Feasibility study of patient motion monitoring by using tactile array sensors

NASA Astrophysics Data System (ADS)

Kim, Tae-Ho; Kang, Seong-Hee; Kim, Dong-Su; Cho, Min-Seok; Kim, Kyeong-Hyeon; Suh, Tae-Suk; Kim, Siyong

2015-07-01

An ideal alignment method based on the external anatomical surface of the patient should consider the entire region of interest. However, optical-camera-based systems cannot blindly monitor such areas as the patient's back, for example. Furthermore, collecting enough information to correct the associated deformation error is impossible. The study aim is to propose a new patient alignment method using tactile array sensors that can measure the distributed pressure profiles along the contact surface. The TactArray system includes one sensor, a signal-conditioning device (USB drive/interface electronics, power supply, and cables), and a PC. The tactile array sensor was placed between the patient's back and the treatment couch, and the deformations at different location on the patient's back were evaluated. Three healthy male volunteers were enrolled in this study, and pressure profile distributions (PPDs) were obtained with and without immobilization. After the initial pretreatment setup using the laser alignment system, the PPD of the patient's back was acquired. The results were obtained at four different times and included a reference PPD dataset. The contact area and the center-of-pressure value were also acquired based on the PPD data for a more elaborate quantitative data analysis. To evaluate the clinical feasibility of using the proposed alignment method for reducing the deformation error, we implemented a real-time self-correction procedure. Despite the initial alignment, we confirmed that PPD variations existed in both cases of the volunteer studies (with and without the use of the immobilization tool). Additionally, we confirmed that the contact area and the center of pressure varied in both cases, and those variations were observed in all three volunteers. With the proposed alignment method and the real-time selfcorrection procedure, the deformation error was significantly reduced. The proposed alignment method can be used to account for the limitation of the camera-based system and to improve the accuracy of the external surface-based patient setup.

Optimal False Discovery Rate Control for Dependent Data

PubMed Central

Xie, Jichun; Cai, T. Tony; Maris, John; Li, Hongzhe

2013-01-01

This paper considers the problem of optimal false discovery rate control when the test statistics are dependent. An optimal joint oracle procedure, which minimizes the false non-discovery rate subject to a constraint on the false discovery rate is developed. A data-driven marginal plug-in procedure is then proposed to approximate the optimal joint procedure for multivariate normal data. It is shown that the marginal procedure is asymptotically optimal for multivariate normal data with a short-range dependent covariance structure. Numerical results show that the marginal procedure controls false discovery rate and leads to a smaller false non-discovery rate than several commonly used p-value based false discovery rate controlling methods. The procedure is illustrated by an application to a genome-wide association study of neuroblastoma and it identifies a few more genetic variants that are potentially associated with neuroblastoma than several p-value-based false discovery rate controlling procedures. PMID:23378870

Keystroke Analysis: Reflections on Procedures and Measures

ERIC Educational Resources Information Center

Baaijen, Veerle M.; Galbraith, David; de Glopper, Kees

2012-01-01

Although keystroke logging promises to provide a valuable tool for writing research, it can often be difficult to relate logs to underlying processes. This article describes the procedures and measures that the authors developed to analyze a sample of 80 keystroke logs, with a view to achieving a better alignment between keystroke-logging measures…

Detailed Test Plan Redundant Sensor Strapdown IMU Evaluation Program

NASA Technical Reports Server (NTRS)

Hartwell, T.; Miyatake, Y.; Wedekind, D. E.

1971-01-01

The test plan for a redundant sensor strapdown inertial measuring unit evaluation program is presented. The subjects discussed are: (1) test philosophy and limitations, (2) test sequence, (3) equipment specifications, (4) general operating procedures, (5) calibration procedures, (6) alignment test phase, and (7) navigation test phase. The data and analysis requirements are analyzed.

Evolutionary trade-offs and the structure of polymorphisms.

PubMed

Sheftel, Hila; Szekely, Pablo; Mayo, Avi; Sella, Guy; Alon, Uri

2018-05-26

Populations of organisms show genetic differences called polymorphisms. Understanding the effects of polymorphisms is important for biology and medicine. Here, we ask which polymorphisms occur at high frequency when organisms evolve under trade-offs between multiple tasks. Multiple tasks present a problem, because it is not possible to be optimal at all tasks simultaneously and hence compromises are necessary. Recent work indicates that trade-offs lead to a simple geometry of phenotypes in the space of traits: phenotypes fall on the Pareto front, which is shaped as a polytope: a line, triangle, tetrahedron etc. The vertices of these polytopes are the optimal phenotypes for a single task. Up to now, work on this Pareto approach has not considered its genetic underpinnings. Here, we address this by asking how the polymorphism structure of a population is affected by evolution under trade-offs. We simulate a multi-task selection scenario, in which the population evolves to the Pareto front: the line segment between two archetypes or the triangle between three archetypes. We find that polymorphisms that become prevalent in the population have pleiotropic phenotypic effects that align with the Pareto front. Similarly, epistatic effects between prevalent polymorphisms are parallel to the front. Alignment with the front occurs also for asexual mating. Alignment is reduced when drift or linkage is strong, and is replaced by a more complex structure in which many perpendicular allele effects cancel out. Aligned polymorphism structure allows mating to produce offspring that stand a good chance of being optimal multi-taskers in at least one of the locales available to the species.This article is part of the theme issue 'Self-organization in cell biology'. © 2018 The Author(s).

3D QSAR studies on protein tyrosine phosphatase 1B inhibitors: comparison of the quality and predictivity among 3D QSAR models obtained from different conformer-based alignments.

PubMed

Pandey, Gyanendra; Saxena, Anil K

2006-01-01

A set of 65 flexible peptidomimetic competitive inhibitors (52 in the training set and 13 in the test set) of protein tyrosine phosphatase 1B (PTP1B) has been used to compare the quality and predictive power of 3D quantitative structure-activity relationship (QSAR) comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models for the three most commonly used conformer-based alignments, namely, cocrystallized conformer-based alignment (CCBA), docked conformer-based alignment (DCBA), and global minima energy conformer-based alignment (GMCBA). These three conformers of 5-[(2S)-2-({(2S)-2-[(tert-butoxycarbonyl)amino]-3-phenylpropanoyl}amino)3-oxo-3-pentylamino)propyl]-2-(carboxymethoxy)benzoic acid (compound number 66) were obtained from the X-ray structure of its cocrystallized complex with PTP1B (PDB ID: 1JF7), its docking studies, and its global minima by simulated annealing. Among the 3D QSAR models developed using the above three alignments, the CCBA provided the optimal predictive CoMFA model for the training set with cross-validated r2 (q2)=0.708, non-cross-validated r2=0.902, standard error of estimate (s)=0.165, and F=202.553 and the optimal CoMSIA model with q2=0.440, r2=0.799, s=0.192, and F=117.782. These models also showed the best test set prediction for the 13 compounds with predictive r2 values of 0.706 and 0.683, respectively. Though the QSAR models derived using the other two alignments also produced statistically acceptable models in the order DCBA>GMCBA in terms of the values of q2, r2, and predictive r2, they were inferior to the corresponding models derived using CCBA. Thus, the order of preference for the alignment selection for 3D QSAR model development may be CCBA>DCBA>GMCBA, and the information obtained from the CoMFA and CoMSIA contour maps may be useful in designing specific PTP1B inhibitors.

The PILOT optical alignment for its first flight

NASA Astrophysics Data System (ADS)

Mot, B.; Longval, Y.; Bernard, J.-Ph.; Ade, P.; André, Y.; Aumont, J.; Bautista, L.; Bray, N.; deBernardis, P.; Boulade, O.; Bousquet, F.; Bouzit, M.; Buttice, V.; Caillat, A.; Chaigneau, M.; Coudournac, C.; Crane, B.; 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.; Mangilli, A.; 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.; Saccoccio, M.; Salatino, M.; Savini, G.; Stever, S.; Simonella, O.; Tapie, P.; Tauber, J.; Tibbs, C.; Torre, J.-P.; Tucker, C.

2017-12-01

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 and 550 µm with an angular resolution of about two arc-min. PILOT optics is composed of an off-axis Gregorian telescope and a refractive re-imager system. All these optical elements, except the primary mirror, are in a cryostat cooled to 3K. We used optical and 3D measurements combined with thermo-elastic modeling to perform the optical alignment. This paper describes the system analysis, the alignment procedure, and finally the performances obtained during the first flight in September 2015

Aligning with physicians to regionalize services.

PubMed

Fink, John

2014-11-01

When effectively designed and implemented, regionalization allows a health system to coordinate care, eliminate redundancies, reduce costs, optimize resource utilization, and improve outcomes. The preferred model to manage service lines regionally will depend on each facility's capabilities and the willingness of physicians to accept changes in clinical delivery. Health systems can overcome physicians' objections to regionalization by implementing a hospital-physician alignment structure that gives a measure of shared control in the management of the organization.

Tolerancing the alignment of large-core optical fibers, fiber bundles and light guides using a Fourier approach.

PubMed

Sawyer, Travis W; Petersburg, Ryan; Bohndiek, Sarah E

2017-04-20

Optical fiber technology is found in a wide variety of applications to flexibly relay light between two points, enabling information transfer across long distances and allowing access to hard-to-reach areas. Large-core optical fibers and light guides find frequent use in illumination and spectroscopic applications, for example, endoscopy and high-resolution astronomical spectroscopy. Proper alignment is critical for maximizing throughput in optical fiber coupling systems; however, there currently are no formal approaches to tolerancing the alignment of a light-guide coupling system. Here, we propose a Fourier alignment sensitivity (FAS) algorithm to determine the optimal tolerances on the alignment of a light guide by computing the alignment sensitivity. The algorithm shows excellent agreement with both simulated and experimentally measured values and improves on the computation time of equivalent ray-tracing simulations by two orders of magnitude. We then apply FAS to tolerance and fabricate a coupling system, which is shown to meet specifications, thus validating FAS as a tolerancing technique. These results indicate that FAS is a flexible and rapid means to quantify the alignment sensitivity of a light guide, widely informing the design and tolerancing of coupling systems.

Tolerancing the alignment of large-core optical fibers, fiber bundles and light guides using a Fourier approach

PubMed Central

Sawyer, Travis W.; Petersburg, Ryan; Bohndiek, Sarah E.

2017-01-01

Optical fiber technology is found in a wide variety of applications to flexibly relay light between two points, enabling information transfer across long distances and allowing access to hard-to-reach areas. Large-core optical fibers and light guides find frequent use in illumination and spectroscopic applications; for example, endoscopy and high-resolution astronomical spectroscopy. Proper alignment is critical for maximizing throughput in optical fiber coupling systems, however, there currently are no formal approaches to tolerancing the alignment of a light guide coupling system. Here, we propose a Fourier Alignment Sensitivity (FAS) algorithm to determine the optimal tolerances on the alignment of a light guide by computing the alignment sensitivity. The algorithm shows excellent agreement with both simulated and experimentally measured values and improves on the computation time of equivalent ray tracing simulations by two orders of magnitude. We then apply FAS to tolerance and fabricate a coupling system, which is shown to meet specifications, thus validating FAS as a tolerancing technique. These results indicate that FAS is a flexible and rapid means to quantify the alignment sensitivity of a light guide, widely informing the design and tolerancing of coupling systems. PMID:28430250

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

PubMed

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

2017-08-01

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

BAYESIAN PROTEIN STRUCTURE ALIGNMENT.

PubMed

Rodriguez, Abel; Schmidler, Scott C

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.

Optimization of electrospun TSF nanofiber alignment and diameter to promote growth and migration of mesenchymal stem cells

NASA Astrophysics Data System (ADS)

Qu, Jing; Zhou, Dandan; Xu, Xiaojing; Zhang, Feng; He, Lihong; Ye, Rong; Zhu, Ziyu; Zuo, Baoqi; Zhang, Huanxiang

2012-11-01

Silk fibroin scaffolds are a naturally derived biocompatible matrix with the potential for reconstructive surgical applications. In this study, tussah silk fibroin (TSF) nanofiber with different diameters (400 nm, 800 nm and 1200 nm) and alignment (random and aligned) were prepared by electrospinning, then the growth and migration of mesenchymal stem cells (MSCs) on these materials were further evaluated. CD90 immunofluorescence staining showed that fiber alignment exhibited a strong influence on the morphology of MSCs, indicating that the alignment of the scaffolds could determine the distribution of cells. Moreover, smaller diameter and aligned TSF scaffolds are more favorable to the growth of MSCs as compared with 800 nm and 1200 nm random TSF scaffolds. In addition, the increased migration speed and efficiency of MSCs induced by three-D TSF were verified, highlighting the guiding roles of TSF to the migrated MSCs. More importantly, 400 nm aligned TSF scaffolds dramatically improved cell migratory speed and further induced the most efficient migration of MSCs as compared with larger diameter TSF scaffolds. In conclusion, the data demonstrate that smaller diameter and aligned electrospun TSF represent valuable scaffolds for supporting and promoting MSCs growth and migration, thus raising the possibility of manipulating TSF scaffolds to enhance homing and therapeutic potential of MSCs in cellular therapy.

Development of Multiobjective Optimization Techniques for Sonic Boom Minimization

NASA Technical Reports Server (NTRS)

Chattopadhyay, Aditi; Rajadas, John Narayan; Pagaldipti, Naryanan S.

1996-01-01

A discrete, semi-analytical sensitivity analysis procedure has been developed for calculating aerodynamic design sensitivities. The sensitivities of the flow variables and the grid coordinates are numerically calculated using direct differentiation of the respective discretized governing equations. The sensitivity analysis techniques are adapted within a parabolized Navier Stokes equations solver. Aerodynamic design sensitivities for high speed wing-body configurations are calculated using the semi-analytical sensitivity analysis procedures. Representative results obtained compare well with those obtained using the finite difference approach and establish the computational efficiency and accuracy of the semi-analytical procedures. Multidisciplinary design optimization procedures have been developed for aerospace applications namely, gas turbine blades and high speed wing-body configurations. In complex applications, the coupled optimization problems are decomposed into sublevels using multilevel decomposition techniques. In cases with multiple objective functions, formal multiobjective formulation such as the Kreisselmeier-Steinhauser function approach and the modified global criteria approach have been used. Nonlinear programming techniques for continuous design variables and a hybrid optimization technique, based on a simulated annealing algorithm, for discrete design variables have been used for solving the optimization problems. The optimization procedure for gas turbine blades improves the aerodynamic and heat transfer characteristics of the blades. The two-dimensional, blade-to-blade aerodynamic analysis is performed using a panel code. The blade heat transfer analysis is performed using an in-house developed finite element procedure. The optimization procedure yields blade shapes with significantly improved velocity and temperature distributions. The multidisciplinary design optimization procedures for high speed wing-body configurations simultaneously improve the aerodynamic, the sonic boom and the structural characteristics of the aircraft. The flow solution is obtained using a comprehensive parabolized Navier Stokes solver. Sonic boom analysis is performed using an extrapolation procedure. The aircraft wing load carrying member is modeled as either an isotropic or a composite box beam. The isotropic box beam is analyzed using thin wall theory. The composite box beam is analyzed using a finite element procedure. The developed optimization procedures yield significant improvements in all the performance criteria and provide interesting design trade-offs. The semi-analytical sensitivity analysis techniques offer significant computational savings and allow the use of comprehensive analysis procedures within design optimization studies.

A molecular design principle of lyotropic liquid-crystalline conjugated polymers with directed alignment capability for plastic electronics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Bong-Gi; Jeong, Eun Jeong; Chung, Jong Won

Conjugated polymers with a one-dimensional p-orbital overlap exhibit optoelectronic anisotropy. Their unique anisotropic properties can be fully realized in device applications only when the conjugated chains are aligned. Here, we report a molecular design principle of conjugated polymers to achieve concentration-regulated chain planarization, self-assembly, liquid-crystal-like good mobility and non-interdigitated side chains. As a consequence of these intra- and intermolecular attributes, chain alignment along an applied flow field occurs. This liquid-crystalline conjugated polymer was realized by incorporating intramolecular sulphur–fluorine interactions and bulky side chains linked to a tetrahedral carbon having a large form factor. By optimizing the polymer concentration and themore » flow field, we could achieve a high dichroic ratio of 16.67 in emission from conducting conjugated polymer films. Two-dimensional grazing-incidence X-ray diffraction was performed to analyse a well-defined conjugated polymer alignment. Thin-film transistors built on highly aligned conjugated polymer films showed more than three orders of magnitude faster carrier mobility along the conjugated polymer alignment direction than the perpendicular direction.« less

Joint Multi-Leaf Segmentation, Alignment, and Tracking for Fluorescence Plant Videos.

PubMed

Yin, Xi; Liu, Xiaoming; Chen, Jin; Kramer, David M

2018-06-01

This paper proposes a novel framework for fluorescence plant video processing. The plant research community is interested in the leaf-level photosynthetic analysis within a plant. A prerequisite for such analysis is to segment all leaves, estimate their structures, and track them over time. We identify this as a joint multi-leaf segmentation, alignment, and tracking problem. First, leaf segmentation and alignment are applied on the last frame of a plant video to find a number of well-aligned leaf candidates. Second, leaf tracking is applied on the remaining frames with leaf candidate transformation from the previous frame. We form two optimization problems with shared terms in their objective functions for leaf alignment and tracking respectively. A quantitative evaluation framework is formulated to evaluate the performance of our algorithm with four metrics. Two models are learned to predict the alignment accuracy and detect tracking failure respectively in order to provide guidance for subsequent plant biology analysis. The limitation of our algorithm is also studied. Experimental results show the effectiveness, efficiency, and robustness of the proposed method.

A low-complexity add-on score for protein remote homology search with COMER.

PubMed

Margelevicius, Mindaugas

2018-06-15

Protein sequence alignment forms the basis for comparative modeling, the most reliable approach to protein structure prediction, among many other applications. Alignment between sequence families, or profile-profile alignment, represents one of the most, if not the most, sensitive means for homology detection but still necessitates improvement. We aim at improving the quality of profile-profile alignments and the sensitivity induced by them by refining profile-profile substitution scores. We have developed a new score that represents an additional component of profile-profile substitution scores. A comprehensive evaluation shows that the new add-on score statistically significantly improves both the sensitivity and the alignment quality of the COMER method. We discuss why the score leads to the improvement and its almost optimal computational complexity that makes it easily implementable in any profile-profile alignment method. An implementation of the add-on score in the open-source COMER software and data are available at https://sourceforge.net/projects/comer. The COMER software is also available on Github at https://github.com/minmarg/comer and as a Docker image (minmar/comer). Supplementary data are available at Bioinformatics online.

Transcription Factor Map Alignment of Promoter Regions

PubMed Central

Blanco, Enrique; Messeguer, Xavier; Smith, Temple F; Guigó, Roderic

2006-01-01

We address the problem of comparing and characterizing the promoter regions of genes with similar expression patterns. This remains a challenging problem in sequence analysis, because often the promoter regions of co-expressed genes do not show discernible sequence conservation. In our approach, thus, we have not directly compared the nucleotide sequence of promoters. Instead, we have obtained predictions of transcription factor binding sites, annotated the predicted sites with the labels of the corresponding binding factors, and aligned the resulting sequences of labels—to which we refer here as transcription factor maps (TF-maps). To obtain the global pairwise alignment of two TF-maps, we have adapted an algorithm initially developed to align restriction enzyme maps. We have optimized the parameters of the algorithm in a small, but well-curated, collection of human–mouse orthologous gene pairs. Results in this dataset, as well as in an independent much larger dataset from the CISRED database, indicate that TF-map alignments are able to uncover conserved regulatory elements, which cannot be detected by the typical sequence alignments. PMID:16733547

A Randomized Controlled Trial Evaluating the See, Tilt, Align, and Rotate (STAR) Maneuver on Skill Acquisition for Simulated Ultrasound-Guided Interventional Procedures.

PubMed

Lam, Nicholas C K; Fishburn, Steven J; Hammer, Angie R; Petersen, Timothy R; Gerstein, Neal S; Mariano, Edward R

2015-06-01

Achieving the best view of the needle and target anatomy when performing ultrasound-guided interventional procedures requires technical skill, which novices may find difficult to learn. We hypothesized that teaching novice performers to use 4 sequential steps (see, tilt, align, and rotate [STAR] method) to identify the needle under ultrasound guidance is more efficient than training with the commonly described probe movements of align, rotate, and tilt (ART). This study compared 2 instructional methods for transducer manipulation including alignment of a probe and needle by novices during a simulated ultrasound-guided nerve block. Right-handed volunteers between the ages of 18 and 55 years who had no previous ultrasound experience were recruited and randomized to 1 of 2 groups; one group was trained to troubleshoot misalignment with the ART method, and the other was trained with the new STAR maneuver. Participants performed the task, consisting of directing a needle in plane to 3 targets in a standardized gelatin phantom 3 times. The performance assessor and data analyst were blinded to group assignment. Thirty-five participants were recruited. The STAR group was able to complete the task more quickly (P < .001) and visualized the needle in a greater proportion of the procedure time (P = .004) compared to the ART group. All STAR participants were able to complete the task, whereas 41% of ART participants abandoned the task (P = .003). Novices are able to complete a simulated ultrasound-guided nerve block more quickly and efficiently when trained with the 4-step STAR maneuver compared to the ART method. © 2015 by the American Institute of Ultrasound in Medicine.

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.

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

RNA-SeQC: RNA-seq metrics for quality control and process optimization.

PubMed

DeLuca, David S; Levin, Joshua Z; Sivachenko, Andrey; Fennell, Timothy; Nazaire, Marc-Danie; Williams, Chris; Reich, Michael; Winckler, Wendy; Getz, Gad

2012-06-01

RNA-seq, the application of next-generation sequencing to RNA, provides transcriptome-wide characterization of cellular activity. Assessment of sequencing performance and library quality is critical to the interpretation of RNA-seq data, yet few tools exist to address this issue. We introduce RNA-SeQC, a program which provides key measures of data quality. These metrics include yield, alignment and duplication rates; GC bias, rRNA content, regions of alignment (exon, intron and intragenic), continuity of coverage, 3'/5' bias and count of detectable transcripts, among others. The software provides multi-sample evaluation of library construction protocols, input materials and other experimental parameters. The modularity of the software enables pipeline integration and the routine monitoring of key measures of data quality such as the number of alignable reads, duplication rates and rRNA contamination. RNA-SeQC allows investigators to make informed decisions about sample inclusion in downstream analysis. In summary, RNA-SeQC provides quality control measures critical to experiment design, process optimization and downstream computational analysis. See www.genepattern.org to run online, or www.broadinstitute.org/rna-seqc/ for a command line tool.

Surgical accuracy with the mini-subvastus total knee arthroplasty a computer tomography scan analysis of postoperative implant alignment.

PubMed

Schroer, William C; Diesfeld, Paul J; Reedy, Mary E; Lemarr, Angela R

2008-06-01

A total of 50 total knee arthroplasty (TKA) patients, 25 traditional and 25 minimally invasive surgical (MIS), underwent computed tomography scans to determine if a loss of accuracy in implant alignment occurred when a surgeon switched from a traditional medial parapatellar arthrotomy to a mini-subvastus surgical technique. Surgical accuracy was determined by comparing the computed tomography measured implant alignment with the surgical alignment goals. There was no loss in accuracy in the implantation of the tibial component with the mini-subvastus technique. The mean variance for the tibial coronal alignment was 1.03 degrees for the traditional TKA and 1.00 degrees for the MIS TKA (P = .183). Similarly, there was no difference in the mean variance for the posterior tibial slope (P = .054). Femoral coronal alignment was less accurate with the MIS procedure, mean variance of 1.04 degrees and 1.71 degrees for the traditional and MIS TKA, respectively (P = .045). Instrumentation and surgical technique concerns that led to this loss in accuracy were determined.

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

Navigating neurites utilize cellular topography of Schwann cell somas and processes for optimal guidance

PubMed Central

Lopez-Fagundo, Cristina; Mitchel, Jennifer A.; Ramchal, Talisha D.; Dingle, Yu-Ting L.; Hoffman-Kim, Diane

2013-01-01

The path created by aligned Schwann cells (SCs) after nerve injury underlies peripheral nerve regeneration. We developed geometric bioinspired substrates to extract key information needed for axon guidance by deconstructing the topographical cues presented by SCs. We have previously reported materials that directly replicate SC topography with micro- and nanoscale resolution, but a detailed explanation of the means of directed axon extension on SC topography has not yet been described. Here, using neurite tracing and time-lapse microscopy, we analyzed the SC features that influence axon guidance. Novel poly(dimethylsiloxane) materials, fabricated via photolithography, incorporated bioinspired topographical components with the shapes and sizes of aligned SCs, namely somas and processes, where the length of the processes were varied but the soma geometry and dimensions were kept constant. Rat dorsal root ganglia neurites aligned to all materials presenting bioinspired topography after a 5 days in culture and to bioinspired materials presenting soma and process features after only 17 hours in culture. Key findings of this study were: Neurite response to underlying bioinspired topographical features was time dependent, where at 5 days, neurites aligned most strongly to materials presenting combinations of soma and process features, with higher than average density of either process or soma features; but at 17 hours they aligned more strongly to materials presenting average densities of soma and process features and to materials presenting process features only. These studies elucidate the influence of SC topography on axon guidance in a time-dependent setting and have implications for the optimization of nerve regeneration strategies. PMID:23557939

Simultaneous dual-color fluorescence microscope: a characterization study.

PubMed

Li, Zheng; Chen, Xiaodong; Ren, Liqiang; Song, Jie; Li, Yuhua; Zheng, Bin; Liu, Hong

2013-01-01

High spatial resolution and geometric accuracy is crucial for chromosomal analysis of clinical cytogenetic applications. High resolution and rapid simultaneous acquisition of multiple fluorescent wavelengths can be achieved by utilizing concurrent imaging with multiple detectors. However, such class of microscopic systems functions differently from traditional fluorescence microscopes. To develop a practical characterization framework to assess and optimize the performance of a high resolution and dual-color fluorescence microscope designed for clinical chromosomal analysis. A dual-band microscopic imaging system utilizes a dichroic mirror, two sets of specially selected optical filters, and two detectors to simultaneously acquire two fluorescent wavelengths. The system's geometric distortion, linearity, the modulation transfer function, and the dual detectors' alignment were characterized. Experiment results show that the geometric distortion at lens periphery is less than 1%. Both fluorescent channels show linear signal responses, but there exists discrepancy between the two due to the detectors' non-uniform response ratio to different wavelengths. In terms of the spatial resolution, the two contrast transfer function curves trend agreeably with the spatial frequency. The alignment measurement allows quantitatively assessing the cameras' alignment. A result image of adjusted alignment is demonstrated to show the reduced discrepancy by using the alignment measurement method. In this paper, we present a system characterization study and its methods for a specially designed imaging system for clinical cytogenetic applications. The presented characterization methods are not only unique to this dual-color imaging system but also applicable to evaluation and optimization of other similar multi-color microscopic image systems for improving their clinical utilities for future cytogenetic applications.

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

NASA Astrophysics Data System (ADS)

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

2015-03-01

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

Alignment Test Results of the JWST Pathfinder Telescope Mirrors in the Cryogenic Environment

NASA Technical Reports Server (NTRS)

Whitman, Tony L.; Wells, Conrad; Hadaway, James; Knight, J. Scott; Lunt, Sharon

2016-01-01

After integration of the Optical Telescope Element (OTE) to the Integrated Science Instrument Module (ISIM) to become the OTIS, the James Webb Space Telescope OTIS is tested at NASAs Johnson Space Center (JSC) in the cryogenic vacuum Chamber A for alignment and optical performance. The alignment of the mirrors comprises a sequence of steps as follows: The mirrors are coarsely aligned using photogrammetry cameras with reflective targets attached to the sides of the mirrors. Then a multi-wavelength interferometer is aligned to the 18-segment primary mirror using cameras at the center of curvature to align reflected light from the segments and using fiducials at the edge of the primary mirror. Once the interferometer is aligned, the 18 primary mirror segments are then adjusted to optimize wavefront error of the aggregate mirror. This process phases the piston and tilt positions of all the mirror segments. An optical fiber placed at the Cassegrain focus of the telescope then emits light towards the secondary mirror to create a collimated beam emitting from the primary mirror. Portions of the collimated beam are retro-reflected from flat mirrors at the top of the chamber to pass through the telescope to the SI detector. The image on the detector is used for fine alignment of the secondary mirror and a check of the primary mirror alignment using many of the same analysis techniques used in the on-orbit alignment. The entire process was practiced and evaluated in 2015 at cryogenic temperature with the Pathfinder telescope.

An optimized color transformation for the analysis of digital images of hematoxylin & eosin stained slides.

PubMed

Zarella, Mark D; Breen, David E; Plagov, Andrei; Garcia, Fernando U

2015-01-01

Hematoxylin and eosin (H&E) staining is ubiquitous in pathology practice and research. As digital pathology has evolved, the reliance of quantitative methods that make use of H&E images has similarly expanded. For example, cell counting and nuclear morphometry rely on the accurate demarcation of nuclei from other structures and each other. One of the major obstacles to quantitative analysis of H&E images is the high degree of variability observed between different samples and different laboratories. In an effort to characterize this variability, as well as to provide a substrate that can potentially mitigate this factor in quantitative image analysis, we developed a technique to project H&E images into an optimized space more appropriate for many image analysis procedures. We used a decision tree-based support vector machine learning algorithm to classify 44 H&E stained whole slide images of resected breast tumors according to the histological structures that are present. This procedure takes an H&E image as an input and produces a classification map of the image that predicts the likelihood of a pixel belonging to any one of a set of user-defined structures (e.g., cytoplasm, stroma). By reducing these maps into their constituent pixels in color space, an optimal reference vector is obtained for each structure, which identifies the color attributes that maximally distinguish one structure from other elements in the image. We show that tissue structures can be identified using this semi-automated technique. By comparing structure centroids across different images, we obtained a quantitative depiction of H&E variability for each structure. This measurement can potentially be utilized in the laboratory to help calibrate daily staining or identify troublesome slides. Moreover, by aligning reference vectors derived from this technique, images can be transformed in a way that standardizes their color properties and makes them more amenable to image processing.

Vertically aligned carbon nanotubes as anode and air-cathode in single chamber microbial fuel cells

NASA Astrophysics Data System (ADS)

Amade, R.; Moreno, H. A.; Hussain, S.; Vila-Costa, M.; Bertran, E.

2016-10-01

Electrode optimization in microbial fuel cells is a key issue to improve the power output and cell performance. Vertically aligned carbon nanotubes (VACNTs) grown on low cost stainless-steel mesh present an attractive approach to increase the cell performance while avoiding the use of expensive Pt-based materials. In comparison with non-aligned carbon nanotubes (NACNTs), VACNTs increase the oxygen reduction reaction taking place at the cathode by a factor of two. In addition, vertical alignment also increases the power density up to 2.5 times with respect to NACNTs. VACNTs grown at the anode can further improve the cell performance by increasing the electrode surface area and thus the electron transfer between bacteria and the electrode. The maximum power density obtained using VACNTs was 14 mW/m2 and 160 mV output voltage.

Alignment-free detection of horizontal gene transfer between closely related bacterial genomes.

PubMed

Domazet-Lošo, Mirjana; Haubold, Bernhard

2011-09-01

Bacterial epidemics are often caused by strains that have acquired their increased virulence through horizontal gene transfer. Due to this association with disease, the detection of horizontal gene transfer continues to receive attention from microbiologists and bioinformaticians alike. Most software for detecting transfer events is based on alignments of sets of genes or of entire genomes. But despite great advances in the design of algorithms and computer programs, genome alignment remains computationally challenging. We have therefore developed an alignment-free algorithm for rapidly detecting horizontal gene transfer between closely related bacterial genomes. Our implementation of this algorithm is called alfy for "ALignment Free local homologY" and is freely available from http://guanine.evolbio.mpg.de/alfy/. In this comment we demonstrate the application of alfy to the genomes of Staphylococcus aureus. We also argue that-contrary to popular belief and in spite of increasing computer speed-algorithmic optimization is becoming more, not less, important if genome data continues to accumulate at the present rate.

Ultrahigh density alignment of carbon nanotube arrays by dielectrophoresis.

PubMed

Shekhar, Shashank; Stokes, Paul; Khondaker, Saiful I

2011-03-22

We report ultrahigh density assembly of aligned single-walled carbon nanotube (SWNT) two-dimensional arrays via AC dielectrophoresis using high-quality surfactant-free and stable SWNT solutions. After optimization of frequency and trapping time, we can reproducibly control the linear density of the SWNT between prefabricated electrodes from 0.5 SWNT/μm to more than 30 SWNT/μm by tuning the concentration of the nanotubes in the solution. Our maximum density of 30 SWNT/μm is the highest for aligned arrays via any solution processing technique reported so far. Further increase of SWNT concentration results in a dense array with multiple layers. We discuss how the orientation and density of the nanotubes vary with concentrations and channel lengths. Electrical measurement data show that the densely packed aligned arrays have low sheet resistances. Selective removal of metallic SWNTs via controlled electrical breakdown produced field-effect transistors with high current on-off ratio. Ultrahigh density alignment reported here will have important implications in fabricating high-quality devices for digital and analog electronics.

A Domain Decomposition Parallelization of the Fast Marching Method

NASA Technical Reports Server (NTRS)

Herrmann, M.

2003-01-01

In this paper, the first domain decomposition parallelization of the Fast Marching Method for level sets has been presented. Parallel speedup has been demonstrated in both the optimal and non-optimal domain decomposition case. The parallel performance of the proposed method is strongly dependent on load balancing separately the number of nodes on each side of the interface. A load imbalance of nodes on either side of the domain leads to an increase in communication and rollback operations. Furthermore, the amount of inter-domain communication can be reduced by aligning the inter-domain boundaries with the interface normal vectors. In the case of optimal load balancing and aligned inter-domain boundaries, the proposed parallel FMM algorithm is highly efficient, reaching efficiency factors of up to 0.98. Future work will focus on the extension of the proposed parallel algorithm to higher order accuracy. Also, to further enhance parallel performance, the coupling of the domain decomposition parallelization to the G(sub 0)-based parallelization will be investigated.

Computational study of engine external aerodynamics as a part of multidisciplinary optimization procedure

NASA Astrophysics Data System (ADS)

Savelyev, Andrey; Anisimov, Kirill; Kazhan, Egor; Kursakov, Innocentiy; Lysenkov, Alexandr

2016-10-01

The paper is devoted to the development of methodology to optimize external aerodynamics of the engine. Optimization procedure is based on numerical solution of the Reynolds-averaged Navier-Stokes equations. As a method of optimization the surrogate based method is used. As a test problem optimal shape design of turbofan nacelle is considered. The results of the first stage, which investigates classic airplane configuration with engine located under the wing, are presented. Described optimization procedure is considered in the context of multidisciplinary optimization of the 3rd generation, developed in the project AGILE.

Practical, computer-aided registration of multiple, three-dimensional, magnetic-resonance observations of the human brain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Diegert, C.; Sanders, J.A.; Orrison, W.W. Jr.

1992-12-31

Researchers working with MR observations generally agree that far more information is available in a volume (3D) observation than is considered for diagnosis. The key to the new alignment method is in basing it on available information on surfaces. Using the skin surface is effective a robust algorithm can reliably extract this surface from almost any scan of the head, and a human operator`s exquisite sensitivity to facial features is allows him to manually align skin surfaces with precision. Following the definitions, we report on a preliminary experiment where we align three MR observations taken during a single MR examination,more » each weighting arterial, venous, and tissue features. When accurately aligned, a neurosurgeon can use these features as anatomical landmarks for planning and executing interventional procedures.« less

Simulator for beam-based LHC collimator alignment

NASA Astrophysics Data System (ADS)

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

2014-02-01

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

The Impact of Imaging Modality on the Measurement of Coronal Plane Alignment After Total Knee Arthroplasty.

PubMed

Nam, Denis; Vajapey, Sravya; Nunley, Ryan M; Barrack, Robert L

2016-10-01

The optimal coronal alignment after total knee arthroplasty (TKA) has become an area of increased debate. Sources of variability among investigations include the radiographic technique used for both preoperative surgical planning and postoperative alignment assessments. This study's purpose was to assess the impact of the imaging modality used on the measurement of coronal plane alignment after TKA. A consecutive series of patients undergoing TKA using the same cruciate-retaining prosthesis were included for analysis. Postoperatively, all patients received both a rotationally controlled, scout computed tomography scan and a hip-knee-ankle (HKA) image using the EOS Imaging system (EOS Inc., Paris, France). Two, independent observers measured the HKA angle, and femoral and tibial component alignment from each image. After classifying overall and component alignment as neutral, varus, or valgus, 40.6% (65 of 160) of knees had a discordant alignment classification for HKA, 28.1% (45 of 160) for femoral component alignment, and 26.9% (43 of 160) for tibial component alignment between their computed tomography and EOS images. Overall, 24.4% (39 of 160) of patients had a HKA difference of ≥3° between the 2 images, whereas 18.8% (30 of 160) and 20.0% (32 of 160) of patients had a femoral and tibial component alignment difference of ≥2°, respectively. Significant differences are present when comparing 2 measurement techniques of mechanical alignment after TKA. The impact of imaging modality on postoperative assessments must be accounted for and be consistent when comparing the results of different investigations. Copyright © 2016 Elsevier Inc. All rights reserved.

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.

Transition of vertically aligned liquid crystal driven by fan-shaped electric field

NASA Astrophysics Data System (ADS)

Tsung, J. W.; Ting, T. L.; Chen, C. Y.; Liang, W. L.; Lai, C. W.; Lin, T. H.; Hsu, W. H.

2017-09-01

Interdigital electrodes are implemented in many commercial and novel liquid crystal devices to align molecules. Although many empirical principles and patents apply to electrode design, only a few numerical simulations of alignment have been conducted. Why and how the molecules align in an ordered manner has never been adequately explained. Hence, this investigation addresses the Fréedericksz transition of vertically aligned liquid crystal that is driven by fishbone electrodes, and thereafter identifies the mechanism of liquid crystal alignment. Theoretical calculations suggest that the periodic deformation that is caused by the fan-shaped fringe field minimizes the free energy in the liquid crystal cell, and the optimal alignment can be obtained when the cell parameters satisfy the relation p /2 d =√{k11/k33 } , where p is the spatial period of the strips of the electrode; d denotes the cell gap; and k11 and k33 are the splay and bend elastic constants of the liquid crystal, respectively. Polymer-stabilized vertical alignment test cells with various p values and spacings between the electrodes were fabricated, and the process of liquid crystal alignment was observed under an optical microscope. The degree of alignment was evaluated by measuring the transmittance of the test cell. The experimental results were consistent with the theoretical predictions. The principle of design, p /2 d =√{k11/k33 } , greatly improves the uniformity and stability of the aligned liquid crystal. The methods that are presented here can be further applied to cholesteric liquid crystal and other self-assembled soft materials.

Automated assembly of VECSEL components

NASA Astrophysics Data System (ADS)

Brecher, C.; Pyschny, N.; Haag, S.; Mueller, T.

2013-02-01

Due to the architectural advantage of an external cavity architecture that enables the integration of additional elements into the cavity (e.g. for mode control, frequency conversion, wavelength tuning or passive mode-locking) VECSELs are a rapidly developing laser technology. Nevertheless they often have to compete with direct (edge) emitting laser diodes which can have significant cost advantages thanks to their rather simple structure and production processes. One way to compensate the economical disadvantages of VECSELs is to optimize each component in terms of quality and costs and to apply more efficient (batch) production processes. In this context, the paper presents recent process developments for the automated assembly of VECSELs using a new type of desktop assembly station with an ultra-precise micromanipulator. The core concept is to create a dedicated process development environment from which implemented processes can be transferred fluently to production equipment. By now two types of processes have been put into operation on the desktop assembly station: 1.) passive alignment of the pump optics implementing a camera-based alignment process, where the pump spot geometry and position on the semiconductor chip is analyzed and evaluated; 2.) active alignment of the end mirror based on output power measurements and optimization algorithms. In addition to the core concept and corresponding hardware and software developments, detailed results of both processes are presented explaining measurement setups as well as alignment strategies and results.

A Robust Method to Generate Mechanically Anisotropic Vascular Smooth Muscle Cell Sheets for Vascular Tissue Engineering.

PubMed

Backman, Daniel E; LeSavage, Bauer L; Shah, Shivem B; Wong, Joyce Y

2017-06-01

In arterial tissue engineering, mimicking native structure and mechanical properties is essential because compliance mismatch can lead to graft failure and further disease. With bottom-up tissue engineering approaches, designing tissue components with proper microscale mechanical properties is crucial to achieve the necessary macroscale properties in the final implant. This study develops a thermoresponsive cell culture platform for growing aligned vascular smooth muscle cell (VSMC) sheets by photografting N-isopropylacrylamide (NIPAAm) onto micropatterned poly(dimethysiloxane) (PDMS). The grafting process is experimentally and computationally optimized to produce PNIPAAm-PDMS substrates optimal for VSMC attachment. To allow long-term VSMC sheet culture and increase the rate of VSMC sheet formation, PNIPAAm-PDMS surfaces were further modified with 3-aminopropyltriethoxysilane yielding a robust, thermoresponsive cell culture platform for culturing VSMC sheets. VSMC cell sheets cultured on patterned thermoresponsive substrates exhibit cellular and collagen alignment in the direction of the micropattern. Mechanical characterization of patterned, single-layer VSMC sheets reveals increased stiffness in the aligned direction compared to the perpendicular direction whereas nonpatterned cell sheets exhibit no directional dependence. Structural and mechanical anisotropy of aligned, single-layer VSMC sheets makes this platform an attractive microstructural building block for engineering a vascular graft to match the in vivo mechanical properties of native arterial tissue. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

49 CFR 572.74 - Thorax assembly and test procedure.

Code of Federal Regulations, 2010 CFR

2010-10-01

... by a test probe conforming to § 572.77(a) to 20 ±0.3 fps according to the test procedure in paragraph... longitudinal center line of the test probe so that it coincides with the designated impact point, and align the test probe so that at impact, the probe's longitudinal center line coincides (within 2 degrees) with...

49 CFR 572.74 - Thorax assembly and test procedure.

Code of Federal Regulations, 2012 CFR

2012-10-01

... by a test probe conforming to § 572.77(a) to 20 ±0.3 fps according to the test procedure in paragraph... longitudinal center line of the test probe so that it coincides with the designated impact point, and align the test probe so that at impact, the probe's longitudinal center line coincides (within 2 degrees) with...

49 CFR 572.74 - Thorax assembly and test procedure.

Code of Federal Regulations, 2014 CFR

2014-10-01

... by a test probe conforming to § 572.77(a) to 20 ±0.3 fps according to the test procedure in paragraph... longitudinal center line of the test probe so that it coincides with the designated impact point, and align the test probe so that at impact, the probe's longitudinal center line coincides (within 2 degrees) with...

49 CFR 572.74 - Thorax assembly and test procedure.

Code of Federal Regulations, 2013 CFR

2013-10-01

... by a test probe conforming to § 572.77(a) to 20 ±0.3 fps according to the test procedure in paragraph... longitudinal center line of the test probe so that it coincides with the designated impact point, and align the test probe so that at impact, the probe's longitudinal center line coincides (within 2 degrees) with...

49 CFR 572.74 - Thorax assembly and test procedure.

Code of Federal Regulations, 2011 CFR

2011-10-01

... by a test probe conforming to § 572.77(a) to 20 ±0.3 fps according to the test procedure in paragraph... longitudinal center line of the test probe so that it coincides with the designated impact point, and align the test probe so that at impact, the probe's longitudinal center line coincides (within 2 degrees) with...

Propagation of high-energy laser beams through the earth's atmosphere II; Proceedings of the Meeting, Los Angeles, CA, Jan. 21-23, 1991

NASA Technical Reports Server (NTRS)

Ulrich, Peter B. (Editor); Wilson, Leroy E. (Editor)

1991-01-01

Consideration is given to turbulence at the inner scale, modeling turbulent transport in laser beam propagation, variable wind direction effects on thermal blooming correction, realistic wind effects on turbulence and thermal blooming compensation, wide bandwidth spectral measurements of atmospheric tilt turbulence, remote alignment of adaptive optical systems with far-field optimization, focusing infrared laser beams on targets in space without using adaptive optics, and a simplex optimization method for adaptive optics system alignment. Consideration is also given to ground-to-space multiline propagation at 1.3 micron, a path integral approach to thermal blooming, functional reconstruction predictions of uplink whole beam Strehl ratios in the presence of thermal blooming, and stability analysis of semidiscrete schemes for thermal blooming computation.

High-resolution comparative modeling with RosettaCM.

PubMed

Song, Yifan; DiMaio, Frank; Wang, Ray Yu-Ruei; Kim, David; Miles, Chris; Brunette, Tj; Thompson, James; Baker, David

2013-10-08

We describe an improved method for comparative modeling, RosettaCM, which optimizes a physically realistic all-atom energy function over the conformational space defined by homologous structures. Given a set of sequence alignments, RosettaCM assembles topologies by recombining aligned segments in Cartesian space and building unaligned regions de novo in torsion space. The junctions between segments are regularized using a loop closure method combining fragment superposition with gradient-based minimization. The energies of the resulting models are optimized by all-atom refinement, and the most representative low-energy model is selected. The CASP10 experiment suggests that RosettaCM yields models with more accurate side-chain and backbone conformations than other methods when the sequence identity to the templates is greater than ∼15%. Copyright © 2013 Elsevier Ltd. All rights reserved.

Advanced Accelerators for Medical Applications

NASA Astrophysics Data System (ADS)

Uesaka, Mitsuru; Koyama, Kazuyoshi

We review advanced accelerators for medical applications with respect to the following key technologies: (i) higher RF electron linear accelerator (hereafter “linac”); (ii) optimization of alignment for the proton linac, cyclotron and synchrotron; (iii) superconducting magnet; (iv) laser technology. Advanced accelerators for medical applications are categorized into two groups. The first group consists of compact medical linacs with high RF, cyclotrons and synchrotrons downsized by optimization of alignment and superconducting magnets. The second group comprises laser-based acceleration systems aimed of medical applications in the future. Laser plasma electron/ion accelerating systems for cancer therapy and laser dielectric accelerating systems for radiation biology are mentioned. Since the second group has important potential for a compact system, the current status of the established energy and intensity and of the required stability are given.

Advanced Accelerators for Medical Applications

NASA Astrophysics Data System (ADS)

Uesaka, Mitsuru; Koyama, Kazuyoshi

We review advanced accelerators for medical applications with respect to the following key technologies: (i) higher RF electron linear accelerator (hereafter "linac"); (ii) optimization of alignment for the proton linac, cyclotron and synchrotron; (iii) superconducting magnet; (iv) laser technology. Advanced accelerators for medical applications are categorized into two groups. The first group consists of compact medical linacs with high RF, cyclotrons and synchrotrons downsized by optimization of alignment and superconducting magnets. The second group comprises laserbased acceleration systems aimed of medical applications in the future. Laser plasma electron/ion accelerating systems for cancer therapy and laser dielectric accelerating systems for radiation biology are mentioned. Since the second group has important potential for a compact system, the current status of the established energy and intensity and of the required stability are given.

14 CFR 65.37 - Skill requirements: Operating positions.

Code of Federal Regulations, 2011 CFR

2011-01-01

..., prescribed instrument approach, and departure procedures. (9) Radar alignment and technical operation. (10) The application of the prescribed radar and nonradar separation standard, as appropriate. [Doc. No...

14 CFR 65.37 - Skill requirements: Operating positions.

Code of Federal Regulations, 2010 CFR

2010-01-01

..., prescribed instrument approach, and departure procedures. (9) Radar alignment and technical operation. (10) The application of the prescribed radar and nonradar separation standard, as appropriate. [Doc. No...

14 CFR 65.37 - Skill requirements: Operating positions.

Code of Federal Regulations, 2014 CFR

2014-01-01

..., prescribed instrument approach, and departure procedures. (9) Radar alignment and technical operation. (10) The application of the prescribed radar and nonradar separation standard, as appropriate. [Doc. No...

14 CFR 65.37 - Skill requirements: Operating positions.

Code of Federal Regulations, 2012 CFR

2012-01-01

..., prescribed instrument approach, and departure procedures. (9) Radar alignment and technical operation. (10) The application of the prescribed radar and nonradar separation standard, as appropriate. [Doc. No...

14 CFR 65.37 - Skill requirements: Operating positions.

Code of Federal Regulations, 2013 CFR

2013-01-01

..., prescribed instrument approach, and departure procedures. (9) Radar alignment and technical operation. (10) The application of the prescribed radar and nonradar separation standard, as appropriate. [Doc. No...

Apollo 13 Guidance, Navigation, and Control Challenges

NASA Technical Reports Server (NTRS)

Goodman, John L.

2009-01-01

Combustion and rupture of a liquid oxygen tank during the Apollo 13 mission provides lessons and insights for future spacecraft designers and operations personnel who may never, during their careers, have participated in saving a vehicle and crew during a spacecraft emergency. Guidance, Navigation, and Control (GNC) challenges were the reestablishment of attitude control after the oxygen tank incident, re-establishment of a free return trajectory, resolution of a ground tracking conflict between the LM and the Saturn V S-IVB stage, Inertial Measurement Unit (IMU) alignments, maneuvering to burn attitudes, attitude control during burns, and performing manual GNC tasks with most vehicle systems powered down. Debris illuminated by the Sun and gaseous venting from the Service Module (SM) complicated crew attempts to identify stars and prevented execution of nominal IMU alignment procedures. Sightings on the Sun, Moon, and Earth were used instead. Near continuous communications with Mission Control enabled the crew to quickly perform time critical procedures. Overcoming these challenges required the modification of existing contingency procedures.

Acceleration of short and long DNA read mapping without loss of accuracy using suffix array.

PubMed

Tárraga, Joaquín; Arnau, Vicente; Martínez, Héctor; Moreno, Raul; Cazorla, Diego; Salavert-Torres, José; Blanquer-Espert, Ignacio; Dopazo, Joaquín; Medina, Ignacio

2014-12-01

HPG Aligner applies suffix arrays for DNA read mapping. This implementation produces a highly sensitive and extremely fast mapping of DNA reads that scales up almost linearly with read length. The approach presented here is faster (over 20× for long reads) and more sensitive (over 98% in a wide range of read lengths) than the current state-of-the-art mappers. HPG Aligner is not only an optimal alternative for current sequencers but also the only solution available to cope with longer reads and growing throughputs produced by forthcoming sequencing technologies. https://github.com/opencb/hpg-aligner. © The Author 2014. Published by Oxford University Press.

The ABCD matrix for parabolic reflectors and its application to astigmatism free four-mirror cavities

NASA Astrophysics Data System (ADS)

Dupraz, K.; Cassou, K.; Martens, A.; Zomer, F.

2015-10-01

The ABCD matrix for parabolic reflectors is derived for any incident angles. It is used in numerical studies of four-mirror cavities composed of two flat and two parabolic mirrors. Constraints related to laser beam injection efficiency, optical stability, cavity-mode, beam-waist size and high stacking power are satisfied. A dedicated alignment procedure leading to stigmatic cavity-modes is employed to overcome issues related to the optical alignment of parabolic reflectors.

Radiotherapy setup displacements in breast cancer patients: 3D surface imaging experience.

PubMed

Cravo Sá, Ana; Fermento, Ana; Neves, Dalila; Ferreira, Sara; Silva, Teresa; Marques Coelho, Carina; Vaandering, Aude; Roma, Ana; Quaresma, Sérgio; Bonnarens, Emmanuel

2018-01-01

In this study, we intend to compare two different setup procedures for female breast cancer patients. Imaging in radiotherapy provides a precise localization of the tumour, increasing the accuracy of the treatment delivery in breast cancer. Twenty breast cancer patients who underwent whole breast radiotherapy (WBRT) were selected for this study. Patients were divided into two groups of ten. Group one (G1) was positioned by tattoos and then the patient positioning was adjusted with the aid of AlignRT (Vision RT, London, UK). In group two (G2), patients were positioned only by tattoos. For both groups, the first 15 fractions were analyzed, a daily kilovoltage (kV) cone beam computed tomography (CBCT) image was made and then the rotational and translational displacements and, posteriorly, the systematic ( Σ ) and random ( σ ) errors were analyzed. The comparison of CBCT displacements for the two groups showed a statistically significant difference in the translational left-right (LR) direction ( ρ  = 0.03), considering that the procedure with AlignRT system has smaller lateral displacements. The results of systematic ( Σ ) and random ( σ ) errors showed that for translational displacements the group positioned only by tattoos (G2) demonstrated higher values of errors when compared with the group positioned with the aid of AlignRT (G1). AlignRT could help the positioning of breast cancer patients; however, it should be used with another imaging method.

A laid-back trip through the Hennigian Forests

PubMed Central

2017-01-01

Background This paper is a comment on the idea of matrix-free Cladistics. Demonstration of this idea’s efficiency is a major goal of the study. Within the proposed framework, the ordinary (phenetic) matrix is necessary only as “source” of Hennigian trees, not as a primary subject of the analysis. Switching from the matrix-based thinking to the matrix-free Cladistic approach clearly reveals that optimizations of the character-state changes are related not to the real processes, but to the form of the data representation. Methods We focused our study on the binary data. We wrote the simple ruby-based script FORESTER version 1.0 that helps represent a binary matrix as an array of the rooted trees (as a “Hennigian forest”). The binary representations of the genomic (DNA) data have been made by script 1001. The Average Consensus method as well as the standard Maximum Parsimony (MP) approach has been used to analyze the data. Principle findings The binary matrix may be easily re-written as a set of rooted trees (maximal relationships). The latter might be analyzed by the Average Consensus method. Paradoxically, this method, if applied to the Hennigian forests, in principle can help to identify clades despite the absence of the direct evidence from the primary data. Our approach may handle the clock- or non clock-like matrices, as well as the hypothetical, molecular or morphological data. Discussion Our proposal clearly differs from the numerous phenetic alignment-free techniques of the construction of the phylogenetic trees. Dealing with the relations, not with the actual “data” also distinguishes our approach from all optimization-based methods, if the optimization is defined as a way to reconstruct the sequences of the character-state changes on a tree, either the standard alignment-based techniques or the “direct” alignment-free procedure. We are not viewing our recent framework as an alternative to the three-taxon statement analysis (3TA), but there are two major differences between our recent proposal and the 3TA, as originally designed and implemented: (1) the 3TA deals with the three-taxon statements or minimal relationships. According to the logic of 3TA, the set of the minimal trees must be established as a binary matrix and used as an input for the parsimony program. In this paper, we operate directly with maximal relationships written just as trees, not as binary matrices, while also using the Average Consensus method instead of the MP analysis. The solely ‘reversal’-based groups can always be found by our method without the separate scoring of the putative reversals before analyses. PMID:28740753

Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions.

PubMed

Krissinel, E; Henrick, K

2004-12-01

The present paper describes the SSM algorithm of protein structure comparison in three dimensions, which includes an original procedure of matching graphs built on the protein's secondary-structure elements, followed by an iterative three-dimensional alignment of protein backbone Calpha atoms. The SSM results are compared with those obtained from other protein comparison servers, and the advantages and disadvantages of different scores that are used for structure recognition are discussed. A new score, balancing the r.m.s.d. and alignment length Nalign, is proposed. It is found that different servers agree reasonably well on the new score, while showing considerable differences in r.m.s.d. and Nalign.

The Influence Of Component Alignment On The Life Of Total Knee Prostheses

NASA Astrophysics Data System (ADS)

Bugariu, Delia; Bereteu, Liviu

2012-12-01

An arthritic knee affects the patient's life by causing pain and limiting movement. If the cartilage and the bone surfaces are severely affected, the natural joint is replaced with an artificial joint. The procedure is called total knee arthroplasty (TKA). Lately, the numbers of implanted total knee prostheses grow steadily. An important factor in TKA is the perfect alignment of the total knee prosthesis (TKP) components. Component misalignment can lead to the prosthesis loss by producing wear particles. The paper proposes a study on mechanical behaviors of a TKP based on numerical analysis, using ANSYS software. The numerical analysis is based on both the normal and the changed angle of the components alignment.

Markov random field based automatic image alignment for electron tomography.

PubMed

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

2008-03-01

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

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

PubMed

Yang, Zhengfan; Penczek, Pawel A

2008-08-01

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

Cryo-EM Image Alignment Based on Nonuniform Fast Fourier Transform

PubMed Central

Yang, Zhengfan; Penczek, Pawel A.

2008-01-01

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

Self-aligned block technology: a step toward further scaling

NASA Astrophysics Data System (ADS)

Lazzarino, Frédéric; Mohanty, Nihar; Feurprier, Yannick; Huli, Lior; Luong, Vinh; Demand, Marc; Decoster, Stefan; Vega Gonzalez, Victor; Ryckaert, Julien; Kim, Ryan Ryoung Han; Mallik, Arindam; Leray, Philippe; Wilson, Chris; Boemmels, Jürgen; Kumar, Kaushik; Nafus, Kathleen; deVilliers, Anton; Smith, Jeffrey; Fonseca, Carlos; Bannister, Julie; Scheer, Steven; Tokei, Zsolt; Piumi, Daniele; Barla, Kathy

2017-04-01

In this work, we present and compare two integration approaches to enable self-alignment of the block suitable for the 5- nm technology node. The first approach is exploring the insertion of a spin-on metal-based material to memorize the first block and act as an etch stop layer in the overall integration. The second approach is evaluating the self-aligned block technology employing widely used organic materials and well-known processes. The concept and the motivation are discussed considering the effects on design and mask count as well as the impact on process complexity and EPE budget. We show the integration schemes and discuss the requirements to enable self-alignment. We present the details of materials and processes selection to allow optimal selective etches and we demonstrate the proof of concept using a 16- nm half-pitch BEOL vehicle. Finally, a study on technology insertion and cost estimation is presented.

An efficient direct method for image registration of flat objects

NASA Astrophysics Data System (ADS)

Nikolaev, Dmitry; Tihonkih, Dmitrii; Makovetskii, Artyom; Voronin, Sergei

2017-09-01

Image alignment of rigid surfaces is a rapidly developing area of research and has many practical applications. Alignment methods can be roughly divided into two types: feature-based methods and direct methods. Known SURF and SIFT algorithms are examples of the feature-based methods. Direct methods refer to those that exploit the pixel intensities without resorting to image features and image-based deformations are general direct method to align images of deformable objects in 3D space. Nevertheless, it is not good for the registration of images of 3D rigid objects since the underlying structure cannot be directly evaluated. In the article, we propose a model that is suitable for image alignment of rigid flat objects under various illumination models. The brightness consistency assumptions used for reconstruction of optimal geometrical transformation. Computer simulation results are provided to illustrate the performance of the proposed algorithm for computing of an accordance between pixels of two images.

DMD-based multi-object spectrograph on Galileo telescope

NASA Astrophysics Data System (ADS)

Zamkotsian, Frederic; Spano, Paolo; Lanzoni, Patrick; Bon, William; Riva, Marco; Nicastro, Luciano; Molinari, Emilio; Di Marcantonio, Paolo; Zerbi, Filippo; Valenziano, Luca

2013-03-01

Next-generation infrared astronomical instrumentation for ground-based and space telescopes could be based on MOEMS programmable slit masks for multi-object spectroscopy (MOS). This astronomical technique is used extensively to investigate the formation and evolution of galaxies. We propose to develop a 2048x1080 DMD-based MOS instrument to be mounted on the Galileo telescope and called BATMAN. A two-arm instrument has been designed for providing in parallel imaging and spectroscopic capabilities. The two arms with F/4 on the DMD are mounted on a common bench, and an upper bench supports the detectors thanks to two independent hexapods. Very good optical quality on the DMD and the detectors will be reached. ROBIN, a BATMAN demonstrator, has been designed, realized and integrated. It permits to determine the instrument integration procedure, including optics and mechanics integration, alignment procedure and optical quality. First images have been obtained and measured. A DMD pattern manager has been developed in order to generate any slit mask according to the list of objects to be observed; spectra have been generated and measured. Observation strategies will be studied and demonstrated for the scientific optimization strategy over the whole FOV. BATMAN on the sky is of prime importance for characterizing the actual performance of this new family of MOS instruments, as well as investigating the operational procedures on astronomical objects. This instrument will be placed on the Telescopio Nazionale Galileo at the beginning of next year, in 2014.

Minimalist breast conserving surgical approaches for inferiorly sited cancers.

PubMed

Tan, Mona P

2017-08-01

Contemporary data suggests that breast conservation treatment (BCT) may confer a survival advantage when compared to mastectomy. Hence, it would be logical to adopt strategies which increase eligibility of successful BCT without compromising oncologic principles or cosmetic outcome. With respect to achieving good aesthetics, inferiorly sited breast cancers pose a particular technical challenge. A vast array of techniques, collectively referred to as oncoplastic breast surgery (OBS) have been developed to minimise post treatment distortion. The purported advantages of these approaches are the acquisition of wider margins and reduced re-excision rates. However, to date, there is a lack of data demonstrating significant reduction in local recurrence and overall survival when compared with less extensive procedures. In this review, "minimalist" procedures are described where strict oncologic criteria of clear margins are fulfilled and acceptable cosmesis are simultaneously achieved. These techniques offer less tissue loss, less extensive parenchymal mobilisation and shorter operating times without compromising margin status and aesthetics. They involve the combination of innovative incision designs and certain parenchymal resection patterns. Incision designs include the boomerang, golf-tee, anchor and arrowhead incisions which have been previously described but not widely used. Parenchymal resection patterns follow the "sick lobe hypothesis". These techniques, termed "reductionist", or "minimalist" comprising approaches where breast conserving surgery is condensed to its irreducible elements, offer alternatives which align with contemporary objectives of surgery where optimal survival outcomes are achieved through individualised procedures resulting in reduced iatrogenic impact. This logically allows scope for de-escalation of surgical therapy for breast cancer.

Alignment test results of the JWST Pathfinder Telescope mirrors in the cryogenic environment

NASA Astrophysics Data System (ADS)

Whitman, Tony L.; Wells, Conrad; Hadaway, James B.; Knight, J. Scott; Lunt, Sharon

2016-07-01

After integration of the Optical Telescope Element (OTE) to the Integrated Science Instrument Module (ISIM) to become the OTIS, the James Webb Space Telescope OTIS is tested at NASA's Johnson Space Center (JSC) in the cryogenic vacuum Chamber A for alignment and optical performance. The alignment of the mirrors comprises a sequence of steps as follows: The mirrors are coarsely aligned using photogrammetry cameras with reflective targets attached to the sides of the mirrors. Then a multi-wavelength interferometer is aligned to the 18-segment primary mirror using cameras at the center of curvature to align reflected light from the segments and using fiducials at the edge of the primary mirror. Once the interferometer is aligned, the 18 primary mirror segments are then adjusted to optimize wavefront error of the aggregate mirror. This process phases the piston and tilt positions of all the mirror segments. An optical fiber placed at the Cassegrain focus of the telescope then emits light towards the secondary mirror to create a collimated beam emitting from the primary mirror. Portions of the collimated beam are retro-reflected from flat mirrors at the top of the chamber to pass through the telescope to the Science Instrument (SI) detector. The image on the detector is used for fine alignment of the secondary mirror and a check of the primary mirror alignment using many of the same analysis techniques used in the on-orbit alignment. The entire process was practiced and evaluated in 2015 at cryogenic temperature with the Pathfinder telescope.

Mitigation of environmental impacts due to ghat road formation in Palamalai Hills, South India, by optimizing cut and fill volumes using GPS and GIS techniques.

PubMed

Arulmozhi, R; Subramani, T; Sukumar, S

2015-01-01

Formation of new roads generally brings about adverse impact on the environment, and in the case of hill roads, the impact is diverse and effective measures are required to mitigate it. The common problems in hill road formation are tree cutting, destruction of canopies, change in land use pattern, soil erosion, slope instability, induced landslides, invasion of foreign species, and so on. Removal of trees and vegetations causes rapid soil erosion, landslides, and invasion of foreign species posing danger to the survival of weak native species. Dumping of surplus earth materials on the valley side poses a significant threat to the environment as it would cause induced landslides. Using the cut earth for filling in road formation and dumping, the surplus cut earth in safe locations will reduce environmental degradation considerably. Conventionally, hill road alignments are finalized using traditional survey methods using ghat tracer, compass, and leveling surveys which require enormous complicated field and office works. Any revision to reduce the quantum of earthwork is difficult in this method due to its complex nature. In the present study at Palamalai Hills, South India, an alignment for a length of 7.95 km was prepared by traditional methods using ghat tracer and total station instruments for survey works. The earthwork quantities were ascertained from the longitudinal profile of the alignment. A GPS survey was also conducted along the alignment to examine its utility in alignment modification. To modify the stretches, where the earthwork cutting and filling are above normal and unbalanced and result in surplus earth, repeated GPS surveys were conducted along different paths to optimize the earthwork. The earthwork quantities of the original alignment were analyzed, and its correlation with environmental effect and the usefulness of the GPS survey in this task are presented in this paper.

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

PubMed

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

2013-04-19

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

Neural-network-directed alignment of optical systems using the laser-beam spatial filter as an example

NASA Technical Reports Server (NTRS)

Decker, Arthur J.; Krasowski, Michael J.; Weiland, Kenneth E.

1993-01-01

This report describes an effort at NASA Lewis Research Center to use artificial neural networks to automate the alignment and control of optical measurement systems. Specifically, it addresses the use of commercially available neural network software and hardware to direct alignments of the common laser-beam-smoothing spatial filter. The report presents a general approach for designing alignment records and combining these into training sets to teach optical alignment functions to neural networks and discusses the use of these training sets to train several types of neural networks. Neural network configurations used include the adaptive resonance network, the back-propagation-trained network, and the counter-propagation network. This work shows that neural networks can be used to produce robust sequencers. These sequencers can learn by example to execute the step-by-step procedures of optical alignment and also can learn adaptively to correct for environmentally induced misalignment. The long-range objective is to use neural networks to automate the alignment and operation of optical measurement systems in remote, harsh, or dangerous aerospace environments. This work also shows that when neural networks are trained by a human operator, training sets should be recorded, training should be executed, and testing should be done in a manner that does not depend on intellectual judgments of the human operator.

Optimal design of aperiodic, vertical silicon nanowire structures for photovoltaics.

PubMed

Lin, Chenxi; Povinelli, Michelle L

2011-09-12

We design a partially aperiodic, vertically-aligned silicon nanowire array that maximizes photovoltaic absorption. The optimal structure is obtained using a random walk algorithm with transfer matrix method based electromagnetic forward solver. The optimal, aperiodic structure exhibits a 2.35 times enhancement in ultimate efficiency compared to its periodic counterpart. The spectral behavior mimics that of a periodic array with larger lattice constant. For our system, we find that randomly-selected, aperiodic structures invariably outperform the periodic array.

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.

LABVIEW graphical user interface for precision multichannel alignment of Raman lidar at Jet Propulsion Laboratory, Table Mountain Facility.

PubMed

Aspey, R A; McDermid, I S; Leblanc, T; Howe, J W; Walsh, T D

2008-09-01

The Jet Propulsion Laboratory operates lidar systems at Table Mountain Facility (TMF), California (34.4 degrees N, 117.7 degrees W) and Mauna Loa Observatory, Hawaii (19.5 degrees N, 155.6 degrees W) under the framework of the Network for the Detection of Atmospheric Composition Change. To complement these systems a new Raman lidar has been developed at TMF with particular attention given to optimizing water vapor profile measurements up to the tropopause and lower stratosphere. The lidar has been designed for accuracies of 5% up to 12 km in the free troposphere and a detection capability of <5 ppmv. One important feature of the lidar is a precision alignment system using range resolved data from eight Licel transient recorders, allowing fully configurable alignment via a LABVIEW/C++ graphical user interface (GUI). This allows the lidar to be aligned on any channel while simultaneously displaying signals from other channels at configurable altitude/bin combinations. The general lidar instrumental setup and the details of the alignment control system, data acquisition, and GUI alignment software are described. Preliminary validation results using radiosonde and lidar intercomparisons are briefly presented.

49 CFR 572.176 - Knees and knee impact test procedure.

Code of Federal Regulations, 2012 CFR

2012-10-01

... procedure in subsection (c) of this section: (1) The peak resistance force as measured with the test probe.... (3) Align the test probe so that throughout its stroke and at contact with the knee it is within 2... contact between the impactor and the knee. (5) The test probe velocity at the time of contact shall be 2.1...

49 CFR 572.176 - Knees and knee impact test procedure.

Code of Federal Regulations, 2014 CFR

2014-10-01

... procedure in subsection (c) of this section: (1) The peak resistance force as measured with the test probe.... (3) Align the test probe so that throughout its stroke and at contact with the knee it is within 2... contact between the impactor and the knee. (5) The test probe velocity at the time of contact shall be 2.1...

49 CFR 572.176 - Knees and knee impact test procedure.

Code of Federal Regulations, 2013 CFR

2013-10-01

... procedure in subsection (c) of this section: (1) The peak resistance force as measured with the test probe.... (3) Align the test probe so that throughout its stroke and at contact with the knee it is within 2... contact between the impactor and the knee. (5) The test probe velocity at the time of contact shall be 2.1...

Accuracy in breast shape alignment with 3D surface fitting algorithms.

PubMed

Riboldi, Marco; Gierga, David P; Chen, George T Y; Baroni, Guido

2009-04-01

Surface imaging is in use in radiotherapy clinical practice for patient setup optimization and monitoring. Breast alignment is accomplished by searching for a tentative spatial correspondence between the reference and daily surface shape models. In this study, the authors quantify whole breast shape alignment by relying on texture features digitized on 3D surface models. Texture feature localization was validated through repeated measurements in a silicone breast phantom, mounted on a high precision mechanical stage. Clinical investigations on breast shape alignment included 133 fractions in 18 patients treated with accelerated partial breast irradiation. The breast shape was detected with a 3D video based surface imaging system so that breathing was compensated. An in-house algorithm for breast alignment, based on surface fitting constrained by nipple matching (constrained surface fitting), was applied. Results were compared with a commercial software where no constraints are utilized (unconstrained surface fitting). Texture feature localization was validated within 2 mm in each anatomical direction. Clinical data show that unconstrained surface fitting achieves adequate accuracy in most cases, though nipple mismatch is considerably higher than residual surface distances (3.9 mm vs 0.6 mm on average). Outliers beyond 1 cm can be experienced as the result of a degenerate surface fit, where unconstrained surface fitting is not sufficient to establish spatial correspondence. In the constrained surface fitting algorithm, average surface mismatch within 1 mm was obtained when nipple position was forced to match in the [1.5; 5] mm range. In conclusion, optimal results can be obtained by trading off the desired overall surface congruence vs matching of selected landmarks (constraint). Constrained surface fitting is put forward to represent an improvement in setup accuracy for those applications where whole breast positional reproducibility is an issue.

Procedures for shape optimization of gas turbine disks

NASA Technical Reports Server (NTRS)

Cheu, Tsu-Chien

1989-01-01

Two procedures, the feasible direction method and sequential linear programming, for shape optimization of gas turbine disks are presented. The objective of these procedures is to obtain optimal designs of turbine disks with geometric and stress constraints. The coordinates of the selected points on the disk contours are used as the design variables. Structural weight, stress and their derivatives with respect to the design variables are calculated by an efficient finite element method for design senitivity analysis. Numerical examples of the optimal designs of a disk subjected to thermo-mechanical loadings are presented to illustrate and compare the effectiveness of these two procedures.

The contribution of medializing calcaneal osteotomy on hindfoot alignment in the reconstruction of the stage II adult acquired flatfoot deformity.

PubMed

Chan, Jeremy Y; Williams, Benjamin R; Nair, Pallavi; Young, Elizabeth; Sofka, Carolyn; Deland, Jonathan T; Ellis, Scott J

2013-02-01

Successful correction of hindfoot alignment in adult acquired flatfoot deformity (AAFD) is likely influenced by the degree of medializing calcaneal osteotomy (MCO) performed, but it is not known if other reconstruction procedures significantly contribute as well. The purpose of this study was to evaluate the correlation between common preoperative and postoperative variables and hindfoot alignment. Thirty patients with stage II AAFD undergoing flatfoot reconstruction were followed prospectively. Preoperative and postoperative radiographs were reviewed to assess for correction in hindfoot alignment as measured by the change in hindfoot moment arm. Nineteen variables were analyzed, including age, gender, height, weight, body mass index (BMI), medial cuneiform-fifth metatarsal height, anteroposterior (AP) talonavicular coverage, AP talus-first metatarsal, lateral talus-first metatarsal and calcaneal pitch angles as well as intraoperative use of the MCO, lateral column lengthening (LCL), Cotton osteotomy, first tarsometatarsal fusion, flexor digitorum longus transfer, spring ligament reconstruction, and gastrocnemius recession or Achilles lengthening. Mean age was 57.3 years (range, 22-77). Final radiographs were obtained at a mean of 47 weeks (range, 25-78) postoperatively. Seven variables were found to significantly affect hindfoot moment arm. These were gender (P < .05), the amount of MCO performed (P < .001), LCL (P < .01), first tarsometatarsal fusion (P < .01), spring ligament reconstruction (P < .01), medial cuneiform-fifth metatarsal height (P < .001), and calcaneal pitch angle (P < .05). Multivariate regression analysis revealed that MCO was the only significant predictor of hindfoot moment arm. The final regression model for MCO showed a good fit (R(2) = .93, P < .001). Correction of hindfoot valgus alignment obtained in flatfoot reconstruction is primarily determined by the MCO procedure and can be modeled linearly. We believe that the hindfoot alignment view can serve as a valuable preoperative measurement to help surgeons adjust the proper amount of correction intraoperatively. Level IV, prospective case series.

Technique tip: use of anterior cruciate ligament jig for hindfoot fusion by calcanio-talo-tibial nail.

PubMed

Haque, Syed; Sarkar, Jay

2012-08-01

The use of intramedullary nail fixation for tibio-talo-calcaneal fusion is gaining popularity. There is chance of failure of procedure following faulty operative technique specially alignment. The article describes a useful application of tibial tunnel jig in inserting the calcanio-talo-tibial guide wire. There is precision of few millimeters in the exit point of guide wire on talus. The authors believe that this helps in better positioning of nail and hence better alignment and better operative outcome.

Fast and accurate reference-free alignment of subtomograms.

PubMed

Chen, Yuxiang; Pfeffer, Stefan; Hrabe, Thomas; Schuller, Jan Michael; Förster, Friedrich

2013-06-01

In cryoelectron tomography alignment and averaging of subtomograms, each dnepicting the same macromolecule, improves the resolution compared to the individual subtomogram. Major challenges of subtomogram alignment are noise enhancement due to overfitting, the bias of an initial reference in the iterative alignment process, and the computational cost of processing increasingly large amounts of data. Here, we propose an efficient and accurate alignment algorithm via a generalized convolution theorem, which allows computation of a constrained correlation function using spherical harmonics. This formulation increases computational speed of rotational matching dramatically compared to rotation search in Cartesian space without sacrificing accuracy in contrast to other spherical harmonic based approaches. Using this sampling method, a reference-free alignment procedure is proposed to tackle reference bias and overfitting, which also includes contrast transfer function correction by Wiener filtering. Application of the method to simulated data allowed us to obtain resolutions near the ground truth. For two experimental datasets, ribosomes from yeast lysate and purified 20S proteasomes, we achieved reconstructions of approximately 20Å and 16Å, respectively. The software is ready-to-use and made public to the community. Copyright © 2013 Elsevier Inc. All rights reserved.

Enhanced piezoresponse of highly aligned electrospun poly(vinylidene fluoride) nanofibers

NASA Astrophysics Data System (ADS)

Kang, Sung Bum; Won, Sang Hyuk; Im, Min Ji; Kim, Chan Ul; Park, Won Il; Baik, Jeong Min; Choi, Kyoung Jin

2017-09-01

Well-ordered nanostructure arrays with controlled densities can potentially improve material properties; however, their fabrication typically involves the use of complicated processing techniques. In this work, we demonstrate a uniaxial alignment procedure for fabricating poly(vinylidene fluoride) (PVDF) electrospun nanofibers (NFs) by introducing collectors with additional steps. The mechanism of the observed NF alignment, which occurs due to the concentration of lateral electric field lines around collector steps, has been elucidated via finite-difference time-domain simulations. The membranes composed of well-aligned PVDF NFs are characterized by a higher content of the PVDF β-phase, as compared to those manufactured from randomly orientated fibers. The piezoelectric energy harvester, which was fabricated by transferring well-aligned PVDF NFs onto flexible substrates with Ag electrodes attached to both sides, exhibited a 2-fold increase in the output voltage and a 3-fold increase in the output current as compared to the corresponding values obtained for the device manufactured from randomly oriented NFs. The enhanced piezoresponse observed for the aligned PVDF NFs is due to their higher β-phase content, denser structure, smaller effective radius of curvature during bending, greater applied strain, and higher fraction of contributing NFs.

Robust through-the-wall radar image classification using a target-model alignment procedure.

PubMed

Smith, Graeme E; Mobasseri, Bijan G

2012-02-01

A through-the-wall radar image (TWRI) bears little resemblance to the equivalent optical image, making it difficult to interpret. To maximize the intelligence that may be obtained, it is desirable to automate the classification of targets in the image to support human operators. This paper presents a technique for classifying stationary targets based on the high-range resolution profile (HRRP) extracted from 3-D TWRIs. The dependence of the image on the target location is discussed using a system point spread function (PSF) approach. It is shown that the position dependence will cause a classifier to fail, unless the image to be classified is aligned to a classifier-training location. A target image alignment technique based on deconvolution of the image with the system PSF is proposed. Comparison of the aligned target images with measured images shows the alignment process introducing normalized mean squared error (NMSE) ≤ 9%. The HRRP extracted from aligned target images are classified using a naive Bayesian classifier supported by principal component analysis. The classifier is tested using a real TWRI of canonical targets behind a concrete wall and shown to obtain correct classification rates ≥ 97%. © 2011 IEEE

Computational design and engineering of polymeric orthodontic aligners.

PubMed

Barone, S; Paoli, A; Razionale, A V; Savignano, R

2016-10-05

Transparent and removable aligners represent an effective solution to correct various orthodontic malocclusions through minimally invasive procedures. An aligner-based treatment requires patients to sequentially wear dentition-mating shells obtained by thermoforming polymeric disks on reference dental models. An aligner is shaped introducing a geometrical mismatch with respect to the actual tooth positions to induce a loading system, which moves the target teeth toward the correct positions. The common practice is based on selecting the aligner features (material, thickness, and auxiliary elements) by only considering clinician's subjective assessments. In this article, a computational design and engineering methodology has been developed to reconstruct anatomical tissues, to model parametric aligner shapes, to simulate orthodontic movements, and to enhance the aligner design. The proposed approach integrates computer-aided technologies, from tomographic imaging to optical scanning, from parametric modeling to finite element analyses, within a 3-dimensional digital framework. The anatomical modeling provides anatomies, including teeth (roots and crowns), jaw bones, and periodontal ligaments, which are the references for the down streaming parametric aligner shaping. The biomechanical interactions between anatomical models and aligner geometries are virtually reproduced using a finite element analysis software. The methodology allows numerical simulations of patient-specific conditions and the comparative analyses of different aligner configurations. In this article, the digital framework has been used to study the influence of various auxiliary elements on the loading system delivered to a maxillary and a mandibular central incisor during an orthodontic tipping movement. Numerical simulations have shown a high dependency of the orthodontic tooth movement on the auxiliary element configuration, which should then be accurately selected to maximize the aligner's effectiveness. Copyright © 2016 John Wiley & Sons, Ltd.

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

PubMed

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

2018-02-01

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

Self-pressurizing Stirling engine

DOEpatents

Bennett, Charles L.

2010-10-12

A solar thermal powered aircraft powered by heat energy from the sun. A heat engine, such as a Stirling engine, is carried by the aircraft body for producing power for a propulsion mechanism, such as a propeller. The heat engine has a thermal battery in thermal contact with it so that heat is supplied from the thermal battery. A solar concentrator, such as reflective parabolic trough, is movably connected to an optically transparent section of the aircraft body for receiving and concentrating solar energy from within the aircraft. Concentrated solar energy is collected by a heat collection and transport conduit, and heat transported to the thermal battery. A solar tracker includes a heliostat for determining optimal alignment with the sun, and a drive motor actuating the solar concentrator into optimal alignment with the sun based on a determination by the heliostat.

Solar thermal aircraft

DOEpatents

Bennett, Charles L.

2007-09-18

A solar thermal powered aircraft powered by heat energy from the sun. A heat engine, such as a Stirling engine, is carried by the aircraft body for producing power for a propulsion mechanism, such as a propeller. The heat engine has a thermal battery in thermal contact with it so that heat is supplied from the thermal battery. A solar concentrator, such as reflective parabolic trough, is movably connected to an optically transparent section of the aircraft body for receiving and concentrating solar energy from within the aircraft. Concentrated solar energy is collected by a heat collection and transport conduit, and heat transported to the thermal battery. A solar tracker includes a heliostat for determining optimal alignment with the sun, and a drive motor actuating the solar concentrator into optimal alignment with the sun based on a determination by the heliostat.

Optical design and optical properties of a VUV spectrographic imager for ICON mission

NASA Astrophysics Data System (ADS)

Loicq, Jerome; Kintziger, Christian; Mazzoli, Alexandra; Miller, Tim; Chou, Cathy; Frey, Harald U.; Immel, Thomas J.; Mende, Stephen B.

2016-07-01

In the frame of the ICON (Ionospheric Connection Explorer) mission of NASA led by UC Berkeley, CSL and SSL Berkeley have designed in cooperation a new Far UV spectro-imager. The instrument is based on a Czerny-Turner spectrograph coupled with two back imagers. The whole field of view covers [+/- 12° vertical, +/- 9° horizontal]. The instrument is surmounted by a rotating mirror to adjust the horizontal field of view pointing by +/- 30°. To meet the scientific imaging and spectral requirements the instrument has been optimized. The optimization philosophy and related analysis are presented in the present paper. PSF, distortion map and spectral properties are described. A tolerance study and alignment cases were performed to prove the instrument can be built and aligned. Finally straylight and out of band properties are discussed.

Eye muscle repair

MedlinePlus

... and physical exam before the procedure Orthoptic measurements (eye movement measurements) Always tell your child's health care provider: ... D, Plummer LS, Stass-Isern M. Disorders of eye movement and alignment. In: Kliegman RM, Stanton BF, St. ...

High-throughput flow alignment of barcoded hydrogel microparticles†

PubMed Central

Chapin, Stephen C.; Pregibon, Daniel C.

2010-01-01

Suspension (particle-based) arrays offer several advantages over conventional planar arrays in the detection and quantification of biomolecules, including the use of smaller sample volumes, more favorable probe-target binding kinetics, and rapid probe-set modification. We present a microfluidic system for the rapid alignment of multifunctional hydrogel microparticles designed to bear one or several biomolecule probe regions, as well as a graphical code to identify the embedded probes. Using high-speed imaging, we have developed and optimized a flow-through system that (1) allows for a high particle throughput, (2) ensures proper particle alignment for decoding and target quantification, and (3) can be reliably operated continuously without clogging. A tapered channel flanked by side focusing streams is used to orient the flexible, tablet-shaped particles into a well-ordered flow in the center of the channel. The effects of channel geometry, particle geometry, particle composition, particle loading density, and barcode design are explored to determine the best combination for eventual use in biological assays. Particles in the optimized system move at velocities of ~50 cm s−1 and with throughputs of ~40 particles s−1. Simple physical models and CFD simulations have been used to investigate flow behavior in the device. PMID:19823726

200 MeV Proton Radiography Studies with a Hand Phantom Using a Prototype Proton CT Scanner

PubMed Central

Plautz, Tia; Bashkirov, V.; Feng, V.; Hurley, F.; Johnson, R.P.; Leary, C.; Macafee, S.; Plumb, A.; Rykalin, V.; Sadrozinski, H.F.-W.; Schubert, K.; Schulte, R.; Schultze, B.; Steinberg, D.; Witt, M.; Zatserklyaniy, A.

2014-01-01

Proton radiography has applications in patient alignment and verification procedures for proton beam radiation therapy. In this paper, we report an experiment which used 200 MeV protons to generate proton energy-loss and scattering radiographs of a hand phantom. The experiment used the first-generation proton CT scanner prototype, which was installed on the research beam line of the clinical proton synchrotron at Loma Linda University Medical Center (LLUMC). It was found that while both radiographs displayed anatomical details of the hand phantom, the energy-loss radiograph had a noticeably higher resolution. Nonetheless, scattering radiography may yield more contrast between soft and bone tissue than energy-loss radiography, however, this requires further study. This study contributes to the optimization of the performance of the next-generation of clinical proton CT scanners. Furthermore, it demonstrates the potential of proton imaging (proton radiography and CT), which is now within reach of becoming available as a new, potentially low-dose medical imaging modality. PMID:24710156

Enhanced Multiobjective Optimization Technique for Comprehensive Aerospace Design. Part A

NASA Technical Reports Server (NTRS)

Chattopadhyay, Aditi; Rajadas, John N.

1997-01-01

A multidisciplinary design optimization procedure which couples formal multiobjectives based techniques and complex analysis procedures (such as computational fluid dynamics (CFD) codes) developed. The procedure has been demonstrated on a specific high speed flow application involving aerodynamics and acoustics (sonic boom minimization). In order to account for multiple design objectives arising from complex performance requirements, multiobjective formulation techniques are used to formulate the optimization problem. Techniques to enhance the existing Kreisselmeier-Steinhauser (K-S) function multiobjective formulation approach have been developed. The K-S function procedure used in the proposed work transforms a constrained multiple objective functions problem into an unconstrained problem which then is solved using the Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithm. Weight factors are introduced during the transformation process to each objective function. This enhanced procedure will provide the designer the capability to emphasize specific design objectives during the optimization process. The demonstration of the procedure utilizes a computational Fluid dynamics (CFD) code which solves the three-dimensional parabolized Navier-Stokes (PNS) equations for the flow field along with an appropriate sonic boom evaluation procedure thus introducing both aerodynamic performance as well as sonic boom as the design objectives to be optimized simultaneously. Sensitivity analysis is performed using a discrete differentiation approach. An approximation technique has been used within the optimizer to improve the overall computational efficiency of the procedure in order to make it suitable for design applications in an industrial setting.

Challenges of healthcare administration: optimizing quality and value at an affordable cost in pediatric cardiology.

PubMed

Cohen, Mitchell I; Frias, Patricio A

2018-01-01

The purpose of this review is to explore the paradigm shift in healthcare delivery that will need to take place over the next few years away from an emphasis on supply-driven health care to better quality transparent-driven health care whose focus is on the consumer's best interest. The current healthcare system is fragmented and costs continue to rise. The best way to contain costs is to improve quality to the consumer, the patient. Physicians and hospitals need to align in a team-based approach that allows physicians to understand current costs and how to strive toward a focus on healthcare outcomes. Pediatric cardiology is a unique discipline that cares for patients with complex congenital conditions that will span their lifetime and also involves not just cardiology but surgery, intensive care, anesthesia, nursing, and a host of inpatient and ambulatory services. Understanding what matters to the patient and his/her family and presenting quality outcomes in a transparent fashion will gradually allow a shift to take place away from physician visits, tests ordered, and procedures performed. This can only be achieved with physicians, given the appropriate tools to understand costs, value, and outcomes and models where the hospitals and physicians are aligned. The transformation to a value-based healthcare system is beginning and pediatric cardiologists need to be educated, given the appropriate resources, receive appropriate feedback, and patients need to be part of the solution so that care providers can understand what matters most to them.

An error analysis perspective for patient alignment systems.

PubMed

Figl, Michael; Kaar, Marcus; Hoffman, Rainer; Kratochwil, Alfred; Hummel, Johann

2013-09-01

This paper analyses the effects of error sources which can be found in patient alignment systems. As an example, an ultrasound (US) repositioning system and its transformation chain are assessed. The findings of this concept can also be applied to any navigation system. In a first step, all error sources were identified and where applicable, corresponding target registration errors were computed. By applying error propagation calculations on these commonly used registration/calibration and tracking errors, we were able to analyse the components of the overall error. Furthermore, we defined a special situation where the whole registration chain reduces to the error caused by the tracking system. Additionally, we used a phantom to evaluate the errors arising from the image-to-image registration procedure, depending on the image metric used. We have also discussed how this analysis can be applied to other positioning systems such as Cone Beam CT-based systems or Brainlab's ExacTrac. The estimates found by our error propagation analysis are in good agreement with the numbers found in the phantom study but significantly smaller than results from patient evaluations. We probably underestimated human influences such as the US scan head positioning by the operator and tissue deformation. Rotational errors of the tracking system can multiply these errors, depending on the relative position of tracker and probe. We were able to analyse the components of the overall error of a typical patient positioning system. We consider this to be a contribution to the optimization of the positioning accuracy for computer guidance systems.

Aligning Arrays of Lenses and Single-Mode Optical Fibers

NASA Technical Reports Server (NTRS)

Liu, Duncan

2004-01-01

A procedure now under development is intended to enable the precise alignment of sheet arrays of microscopic lenses with the end faces of a coherent bundle of as many as 1,000 single-mode optical fibers packed closely in a regular array (see Figure 1). In the original application that prompted this development, the precise assembly of lenses and optical fibers serves as a single-mode spatial filter for a visible-light nulling interferometer. The precision of alignment must be sufficient to limit any remaining wavefront error to a root-mean-square value of less than 1/10 of a wavelength of light. This wavefront-error limit translates to requirements to (1) ensure uniformity of both the lens and fiber arrays, (2) ensure that the lateral distance from the central axis of each lens and the corresponding optical fiber is no more than a fraction of a micron, (3) angularly align the lens-sheet planes and the fiber-bundle end faces to within a few arc seconds, and (4) axially align the lenses and the fiber-bundle end faces to within tens of microns of the focal distance. Figure 2 depicts the apparatus used in the alignment procedure. The beam of light from a Zygo (or equivalent) interferometer is first compressed by a ratio of 20:1 so that upon its return to the interferometer, the beam will be magnified enough to enable measurement of wavefront quality. The apparatus includes relay lenses that enable imaging of the arrays of microscopic lenses in a charge-coupled-device (CCD) camera that is part of the interferometer. One of the arrays of microscopic lenses is mounted on a 6-axis stage, in proximity to the front face of the bundle of optical fibers. The bundle is mounted on a separate stage. A mirror is attached to the back face of the bundle of optical fibers for retroreflection of light. When a microscopic lens and a fiber are aligned with each other, the affected portion of the light is reflected back by the mirror, recollimated by the microscopic lens, transmitted through the relay lenses and the beam compressor/expander, then split so that half goes to a detector and half to the interferometer. The output of the detector is used as a feedback control signal for the six-axis stage to effect alignment.

Performance optimization of helicopter rotor blades

NASA Technical Reports Server (NTRS)

Walsh, Joanne L.

1991-01-01

As part of a center-wide activity at NASA Langley Research Center to develop multidisciplinary design procedures by accounting for discipline interactions, a performance design optimization procedure is developed. The procedure optimizes the aerodynamic performance of rotor blades by selecting the point of taper initiation, root chord, taper ratio, and maximum twist which minimize hover horsepower while not degrading forward flight performance. The procedure uses HOVT (a strip theory momentum analysis) to compute the horse power required for hover and the comprehensive helicopter analysis program CAMRAD to compute the horsepower required for forward flight and maneuver. The optimization algorithm consists of the general purpose optimization program CONMIN and approximate analyses. Sensitivity analyses consisting of derivatives of the objective function and constraints are carried out by forward finite differences. The procedure is applied to a test problem which is an analytical model of a wind tunnel model of a utility rotor blade.

Complexity Analysis and Algorithms for Optimal Resource Allocation in Wireless Networks

DTIC Science & Technology

2012-09-01

independent orthogonal signaling such as OFDM . The general formulation will exploit the concept of ‘interference alignment’ which is known to provide...substantial rate gain over OFDM signalling for general interference channels. We have successfully analyzed the complexity to characterize the optimal...categories: PaperReceived Gennady Lyubeznik, Zhi-Quan Luo, Meisam Razaviyayn. On the degrees of freedom achievable through interference alignment in a MIMO

Optimizing nursing care by integrating theory-driven evidence-based practice.

PubMed

Pipe, Teri Britt

2007-01-01

An emerging challenge for nursing leadership is how to convey the importance of both evidence-based practice (EBP) and theory-driven care in ensuring patient safety and optimizing outcomes. This article describes a specific example of a leadership strategy based on Rosswurm and Larrabee's model for change to EBP, which was effective in aligning the processes of EBP and theory-driven care.

Least-squares/parabolized Navier-Stokes procedure for optimizing hypersonic wind tunnel nozzles

NASA Technical Reports Server (NTRS)

Korte, John J.; Kumar, Ajay; Singh, D. J.; Grossman, B.

1991-01-01

A new procedure is demonstrated for optimizing hypersonic wind-tunnel-nozzle contours. The procedure couples a CFD computer code to an optimization algorithm, and is applied to both conical and contoured hypersonic nozzles for the purpose of determining an optimal set of parameters to describe the surface geometry. A design-objective function is specified based on the deviation from the desired test-section flow-field conditions. The objective function is minimized by optimizing the parameters used to describe the nozzle contour based on the solution to a nonlinear least-squares problem. The effect of the changes in the nozzle wall parameters are evaluated by computing the nozzle flow using the parabolized Navier-Stokes equations. The advantage of the new procedure is that it directly takes into account the displacement effect of the boundary layer on the wall contour. The new procedure provides a method for optimizing hypersonic nozzles of high Mach numbers which have been designed by classical procedures, but are shown to produce poor flow quality due to the large boundary layers present in the test section. The procedure is demonstrated by finding the optimum design parameters for a Mach 10 conical nozzle and a Mach 6 and a Mach 15 contoured nozzle.

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

PubMed

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

2017-06-17

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

Conductivity map from scanning tunneling potentiometry.

PubMed

Zhang, Hao; Li, Xianqi; Chen, Yunmei; Durand, Corentin; Li, An-Ping; Zhang, X-G

2016-08-01

We present a novel method for extracting two-dimensional (2D) conductivity profiles from large electrochemical potential datasets acquired by scanning tunneling potentiometry of a 2D conductor. The method consists of a data preprocessing procedure to reduce/eliminate noise and a numerical conductivity reconstruction. The preprocessing procedure employs an inverse consistent image registration method to align the forward and backward scans of the same line for each image line followed by a total variation (TV) based image restoration method to obtain a (nearly) noise-free potential from the aligned scans. The preprocessed potential is then used for numerical conductivity reconstruction, based on a TV model solved by accelerated alternating direction method of multiplier. The method is demonstrated on a measurement of the grain boundary of a monolayer graphene, yielding a nearly 10:1 ratio for the grain boundary resistivity over bulk resistivity.

Characterization of assembled MEMS

NASA Astrophysics Data System (ADS)

Jandric, Zoran; Randall, John N.; Saini, Rahul; Nolan, Michael; Skidmore, George

2004-12-01

Zyvex is developing a low-cost high-precision method for manufacturing MEMS-based three-dimensional structures/assemblies. The assembly process relies on compliant properties of the interconnecting components. The sockets and connectors are designed to benefit from their compliant nature by allowing the mechanical component to self-align, i.e. reposition themselves to their designed, stable position, independent of the initial placement of the part by the external robot. Thus, the self-aligning property guarantees the precision of the assembled structure to be very close to, or the same, as the precision of the lithography process itself. A three-dimensional (3D) structure is achieved by inserting the connectors into the sockets through the use of a passive end-effector. We have developed the automated, high-yield, assembly procedure which permits connectors to be picked up from any location within the same die, or a separate die. This general procedure allows for the possibility to assemble parts of dissimilar materials. We have built many 3D MEMS structures, including several 3D MEMS devices such as a scanning electron microscope (SEM) micro column, mass-spectrometer column, variable optical attenuator. For these 3D MEMS structures we characterize their mechanical strength through finite element simulation, dynamic properties by finite-element analysis and experimentally with UMECH"s MEMS motion analyzer (MMA), alignment accuracy by using an in-house developed dihedral angle measurement laser autocollimator, and impact properties by performing drop tests. The details of the experimental set-ups, the measurement procedures, and the experimental data are presented in this paper.

Characterization of assembled MEMS

NASA Astrophysics Data System (ADS)

Jandric, Zoran; Randall, John N.; Saini, Rahul; Nolan, Michael; Skidmore, George

2005-01-01

Zyvex is developing a low-cost high-precision method for manufacturing MEMS-based three-dimensional structures/assemblies. The assembly process relies on compliant properties of the interconnecting components. The sockets and connectors are designed to benefit from their compliant nature by allowing the mechanical component to self-align, i.e. reposition themselves to their designed, stable position, independent of the initial placement of the part by the external robot. Thus, the self-aligning property guarantees the precision of the assembled structure to be very close to, or the same, as the precision of the lithography process itself. A three-dimensional (3D) structure is achieved by inserting the connectors into the sockets through the use of a passive end-effector. We have developed the automated, high-yield, assembly procedure which permits connectors to be picked up from any location within the same die, or a separate die. This general procedure allows for the possibility to assemble parts of dissimilar materials. We have built many 3D MEMS structures, including several 3D MEMS devices such as a scanning electron microscope (SEM) micro column, mass-spectrometer column, variable optical attenuator. For these 3D MEMS structures we characterize their mechanical strength through finite element simulation, dynamic properties by finite-element analysis and experimentally with UMECH"s MEMS motion analyzer (MMA), alignment accuracy by using an in-house developed dihedral angle measurement laser autocollimator, and impact properties by performing drop tests. The details of the experimental set-ups, the measurement procedures, and the experimental data are presented in this paper.

Porosimetry and packing morphology of vertically-aligned carbon nanotube arrays via impedance spectroscopy.

PubMed

Mutha, Heena K; Lu, Yuan; Stein, Itai; Cho, H Jeremy; Suss, Matthew; Laoui, Tahar; Thompson, Carl; Wardle, Brian; Wang, Evelyn

2016-12-13

Vertically aligned one-dimensional nanostructure arrays are promising in many applications such as electrochemical systems, solar cells, and electronics, taking advantage of high surface area per unit volume, nanometer length scale packing, and alignment leading to high conductivity. However, many devices need to optimize arrays for device performance by selecting an appropriate morphology. Developing a simple, non-invasive tool for understanding the role of pore volume distribution and interspacing would aid in the optimization of nanostructure morphologies in electrodes. In this work, we combined electrochemical impedance spectroscopy (EIS) with capacitance measurements and porous electrode theory to conduct in situ porosimetry of vertically-aligned carbon nanotubes (VA-CNTs) non-destructively. We utilized the EIS measurements with a pore size distribution model to quantify the average and dispersion of inter-CNT spacing (Γ), stochastically, in carpets that were mechanically densified from 1.7 × 10¹⁰ tubes/cm² to 4.5 × 10¹¹ tubes/cm². Our analysis predicts that the inter-CNT spacing ranges from over 100 ± 50 nm in sparse carpets to sub 10 ± 5 nm in packed carpets. Our results suggest that waviness of CNTs leads to variations in the inter-CNT spacing, which can be significant in sparse carpets. This methodology can be used to predict the performance of many nanostructured devices, including supercapacitors, batteries, solar cells, and semiconductor electronics. Copyright 2016 IOP Publishing Ltd.

Judging Surgical Research: How Should We Evaluate Performance and Measure Value?

PubMed Central

Souba, Wiley W.; Wilmore, Douglas W.

2000-01-01

Objective To establish criteria to evaluate performance in surgical research, and to suggest strategies to optimize research in the future. Summary Background Data Research is an integral component of the academic mission, focusing on important clinical problems, accounting for surgical advances, and providing training and mentoring for young surgeons. With constraints on healthcare resources, there is increasing pressure to generate clinical revenues at the expense of the time and effort devoted to surgical research. An approach that would assess the value of research would allow prioritization of projects. Further, alignment of high-priority research projects with clinical goals would optimize research gains and maximize the clinical enterprise. Methods The authors reviewed performance criteria applied to industrial research and modified these criteria to apply to surgical research. They reviewed several programs that align research objectives with clinical goals. Results Performance criteria were categorized along several dimensions: internal measures (quality, productivity, innovation, learning, and development), customer satisfaction, market share, and financial indices (cost and profitability). A “report card” was proposed to allow the assessment of research in an individual department or division. Conclusions The department’s business strategy can no longer be divorced from its research strategy. Alignment between research and clinical goals will maximize the department’s objectives but will create the need to modify existing hierarchical structures and reward systems. Such alignment appears to be the best way to ensure the success of surgical research in the future. PMID:10862192

A simple solution to systematic errors in density determination by X-ray reflectivity: The XRR-density evaluation (XRR-DE) method

NASA Astrophysics Data System (ADS)

Bergese, P.; Bontempi, E.; Depero, L. E.

2006-10-01

X-ray reflectivity (XRR) is a non-destructive, accurate and fast technique for evaluating film density. Indeed, sample-goniometer alignment is a critical experimental factor and the overriding error source in XRR density determination. With commercial single-wavelength X-ray reflectometers, alignment is difficult to control and strongly depends on the operator. In the present work, the contribution of misalignment on density evaluation error is discussed, and a novel procedure (named XRR-density evaluation or XRR-DE method) to minimize the problem will be presented. The method allows to overcome the alignment step through the extrapolation of the correct density value from appropriate non-specular XRR data sets. This procedure is operator independent and suitable for commercial single-wavelength X-ray reflectometers. To test the XRR-DE method, single crystals of TiO 2 and SrTiO 3 were used. In both cases the determined densities differed from the nominal ones less than 5.5%. Thus, the XRR-DE method can be successfully applied to evaluate the density of thin films for which only optical reflectivity is today used. The advantage is that this method can be considered thickness independent.

Optimization for minimum sensitivity to uncertain parameters

NASA Technical Reports Server (NTRS)

Pritchard, Jocelyn I.; Adelman, Howard M.; Sobieszczanski-Sobieski, Jaroslaw

1994-01-01

A procedure to design a structure for minimum sensitivity to uncertainties in problem parameters is described. The approach is to minimize directly the sensitivity derivatives of the optimum design with respect to fixed design parameters using a nested optimization procedure. The procedure is demonstrated for the design of a bimetallic beam for minimum weight with insensitivity to uncertainties in structural properties. The beam is modeled with finite elements based on two dimensional beam analysis. A sequential quadratic programming procedure used as the optimizer supplies the Lagrange multipliers that are used to calculate the optimum sensitivity derivatives. The method was perceived to be successful from comparisons of the optimization results with parametric studies.

Alignment of the CMS Tracker: Latest Results from LHC Run-II

NASA Astrophysics Data System (ADS)

Mittag, Gregor; CMS Collaboration

2017-10-01

The all-silicon design of the tracking system of the CMS experiment provides excellent measurements of charged-particle tracks and an efficient tagging of jets. Conditions of the CMS tracker changed repeatedly during the 2015/2016 shutdown and the 2016 data-taking period. Still the true position and orientation of each of the 15 148 silicon strip and 1440 silicon pixel modules need to be known with high precision for all intervals. The alignment constants also need to be promptly re-adjusted each time the state of the CMS magnet is changed between 0T and 3.8 T. Latest Run-II results of the CMS tracker alignment and resolution performance are presented, which are obtained using several millions of reconstructed tracks from collision and cosmic-ray data of 2016. The geometries and the resulting performance of physics observables are carefully validated. In addition to the offline alignment, an online procedure has been put in place which continuously monitors movements of the pixel high-level structures and triggers updates of the alignment constants if certain thresholds are exceeded.

An optimal thermal evaporation synthesis of c-axis oriented ZnO nanowires with excellent UV sensing and emission characteristics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saha, Tridib, E-mail: tridib.saha@monash.edu; Achath Mohanan, Ajay, E-mail: ajay.mohanan@monash.edu; Swamy, Varghese, E-mail: varghese.swamy@monash.edu

Highlights: • c-Axis alignment of ZnO nanowires was optimized using self-seeding thermal evaporation method. • Influence of purified air on the morphology and optoelectronic properties were studied. • Nanowires grown under optimal conditions exhibit strong UV emission peak in PL spectrum. • Optimized growth condition establish nanowires of excellent UV sensing characteristics - Abstract: Well-aligned (c-axis oriented) ZnO nanowire arrays were successfully synthesized on Si (1 0 0) substrates through an optimized self-seeding thermal evaporation method. An open-ended chemical vapor deposition (CVD) setup was used in the experiment, with argon and purified air as reaction gases. Epitaxial growth of c-axismore » oriented ZnO nanowires was observed for 5 sccm flow rate of purified air, whereas Zn/Zn suboxide layers and multiple polycrystalline layers of ZnO were obtained for absence and excess of purified air, respectively. Ultraviolet (UV) sensing and emission properties of the as-grown ZnO nanostructures were investigated through the current–voltage (I–V) characteristics of the nanowires under UV (λ = 365 nm) illumination of 8 mW/cm{sup 2} and using photoluminescence spectra. Nanowires grown under optimum flow of air emitted four times higher intensity of 380 nm UV light as well as exhibited 34 times higher UV radiation sensitivity compared to that of other nanostructures synthesized in this study.« less

Optimal control theory with continuously distributed target states: An application to NaK

NASA Astrophysics Data System (ADS)

Kaiser, Andreas; May, Volkhard

2006-01-01

Laser pulse control of molecular dynamics is studied theoretically by using optimal control theory. The control theory is extended to target states which are distributed in time as well as in a space of parameters which are responsible for a change of individual molecular properties. This generalized treatment of a control task is first applied to wave packet formation in randomly oriented diatomic systems. Concentrating on an ensemble of NaK molecules which are not aligned the control yield decreases drastically when compared with an aligned ensemble. Second, we demonstrate for NaK the maximization of the probe pulse transient absorption in a pump-probe scheme with an optimized pump pulse. These computations suggest an overall optical control scheme, whereby a flexible technique is suggested to form particular wave packets in the excited state potential energy surface. In particular, it is shown that considerable wave packet localization at the turning points of the first-excited Σ-state potential energy surfaces of NaK may be achieved. The dependency of the control yield on the probe pulse parameters is also discussed.

49 CFR 572.126 - Knees and knee impact test procedure.

Code of Federal Regulations, 2014 CFR

2014-10-01

... procedure in section 572.127(c), the peak resistance force as measured with the test probe mounted... exterior surface. (3) Align the test probe so that throughout its stroke and at contact with the knee it is... probe velocity at the time of contact shall be 2.1 ±0.03 m/s (6.9 # 0.1 ft/s). (6) No suspension...

49 CFR 572.126 - Knees and knee impact test procedure.

Code of Federal Regulations, 2011 CFR

2011-10-01

... procedure in section 572.127(c), the peak resistance force as measured with the test probe mounted... exterior surface. (3) Align the test probe so that throughout its stroke and at contact with the knee it is... probe velocity at the time of contact shall be 2.1 ±0.03 m/s (6.9 # 0.1 ft/s). (6) No suspension...

49 CFR 572.126 - Knees and knee impact test procedure.

Code of Federal Regulations, 2013 CFR

2013-10-01

... procedure in section 572.127(c), the peak resistance force as measured with the test probe mounted... exterior surface. (3) Align the test probe so that throughout its stroke and at contact with the knee it is... probe velocity at the time of contact shall be 2.1 ±0.03 m/s (6.9 # 0.1 ft/s). (6) No suspension...

49 CFR 572.126 - Knees and knee impact test procedure.

Code of Federal Regulations, 2010 CFR

2010-10-01

... procedure in section 572.127(c), the peak resistance force as measured with the test probe mounted... exterior surface. (3) Align the test probe so that throughout its stroke and at contact with the knee it is... probe velocity at the time of contact shall be 2.1 ±0.03 m/s (6.9 # 0.1 ft/s). (6) No suspension...

49 CFR 572.126 - Knees and knee impact test procedure.

Code of Federal Regulations, 2012 CFR

2012-10-01

... procedure in section 572.127(c), the peak resistance force as measured with the test probe mounted... exterior surface. (3) Align the test probe so that throughout its stroke and at contact with the knee it is... probe velocity at the time of contact shall be 2.1 ±0.03 m/s (6.9 # 0.1 ft/s). (6) No suspension...

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.

Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daily, Jeffrey A.

Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. As a result, a faster intra-sequence pairwise alignment implementation is described and benchmarked. Using a 375 residue query sequence a speed of 136 billion cell updates permore » second (GCUPS) was achieved on a dual Intel Xeon E5-2670 12-core processor system, the highest reported for an implementation based on Farrar’s ’striped’ approach. When using only a single thread, parasail was 1.7 times faster than Rognes’s SWIPE. For many score matrices, parasail is faster than BLAST. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. In conclusion, applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.« less

A practical strategy for the accurate measurement of residual dipolar couplings in strongly aligned small molecules

NASA Astrophysics Data System (ADS)

Liu, Yizhou; Cohen, Ryan D.; Martin, Gary E.; Williamson, R. Thomas

2018-06-01

Accurate measurement of residual dipolar couplings (RDCs) requires an appropriate degree of alignment in order to optimize data quality. An overly weak alignment yields very small anisotropic data that are susceptible to measurement errors, whereas an overly strong alignment introduces extensive anisotropic effects that severely degrade spectral quality. The ideal alignment amplitude also depends on the specific pulse sequence used for the coupling measurement. In this work, we introduce a practical strategy for the accurate measurement of one-bond 13C-1H RDCs up to a range of ca. -300 to +300 Hz, corresponding to an alignment that is an order of magnitude stronger than typically employed for small molecule structural elucidation. This strong alignment was generated in the mesophase of the commercially available poly-γ-(benzyl-L-glutamate) polymer. The total coupling was measured by the simple and well-studied heteronuclear two-dimensional J-resolved experiment, which performs well in the presence of strong anisotropic effects. In order to unequivocally determine the sign of the total coupling and resolve ambiguities in assigning total couplings in the CH2 group, coupling measurements were conducted at an isotropic condition plus two anisotropic conditions of different alignment amplitudes. Most RDCs could be readily extracted from these measurements whereas more complicated spectral effects resulting from strong homonuclear coupling could be interpreted either theoretically or by simulation. Importantly, measurement of these very large RDCs actually offers significantly improved data quality and utility for the structure determination of small organic molecules.

Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

DOE PAGES

Daily, Jeffrey A.

2016-02-10

Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. As a result, a faster intra-sequence pairwise alignment implementation is described and benchmarked. Using a 375 residue query sequence a speed of 136 billion cell updates permore » second (GCUPS) was achieved on a dual Intel Xeon E5-2670 12-core processor system, the highest reported for an implementation based on Farrar’s ’striped’ approach. When using only a single thread, parasail was 1.7 times faster than Rognes’s SWIPE. For many score matrices, parasail is faster than BLAST. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. In conclusion, applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.« less

Screening synteny blocks in pairwise genome comparisons through integer programming.

PubMed

Tang, Haibao; Lyons, Eric; Pedersen, Brent; Schnable, James C; Paterson, Andrew H; Freeling, Michael

2011-04-18

It is difficult to accurately interpret chromosomal correspondences such as true orthology and paralogy due to significant divergence of genomes from a common ancestor. Analyses are particularly problematic among lineages that have repeatedly experienced whole genome duplication (WGD) events. To compare multiple "subgenomes" derived from genome duplications, we need to relax the traditional requirements of "one-to-one" syntenic matchings of genomic regions in order to reflect "one-to-many" or more generally "many-to-many" matchings. However this relaxation may result in the identification of synteny blocks that are derived from ancient shared WGDs that are not of interest. For many downstream analyses, we need to eliminate weak, low scoring alignments from pairwise genome comparisons. Our goal is to objectively select subset of synteny blocks whose total scores are maximized while respecting the duplication history of the genomes in comparison. We call this "quota-based" screening of synteny blocks in order to appropriately fill a quota of syntenic relationships within one genome or between two genomes having WGD events. We have formulated the synteny block screening as an optimization problem known as "Binary Integer Programming" (BIP), which is solved using existing linear programming solvers. The computer program QUOTA-ALIGN performs this task by creating a clear objective function that maximizes the compatible set of synteny blocks under given constraints on overlaps and depths (corresponding to the duplication history in respective genomes). Such a procedure is useful for any pairwise synteny alignments, but is most useful in lineages affected by multiple WGDs, like plants or fish lineages. For example, there should be a 1:2 ploidy relationship between genome A and B if genome B had an independent WGD subsequent to the divergence of the two genomes. We show through simulations and real examples using plant genomes in the rosid superorder that the quota-based screening can eliminate ambiguous synteny blocks and focus on specific genomic evolutionary events, like the divergence of lineages (in cross-species comparisons) and the most recent WGD (in self comparisons). The QUOTA-ALIGN algorithm screens a set of synteny blocks to retain only those compatible with a user specified ploidy relationship between two genomes. These blocks, in turn, may be used for additional downstream analyses such as identifying true orthologous regions in interspecific comparisons. There are two major contributions of QUOTA-ALIGN: 1) reducing the block screening task to a BIP problem, which is novel; 2) providing an efficient software pipeline starting from all-against-all BLAST to the screened synteny blocks with dot plot visualizations. Python codes and full documentations are publicly available http://github.com/tanghaibao/quota-alignment. QUOTA-ALIGN program is also integrated as a major component in SynMap http://genomevolution.com/CoGe/SynMap.pl, offering easier access to thousands of genomes for non-programmers. © 2011 Tang et al; licensee BioMed Central Ltd.

The impact of training under different visual-spatial conditions on reverse-alignment laparoscopic skills development.

PubMed

Holznecht, Catherine; Schmidt, Travis; Gould, Jon

2012-01-01

Circumstances may arise during laparoscopic procedures in which alignment of the laparoscope and the instruments is off by 180°, creating a mirror image of the operative field. It has been shown that task performance is degraded under these reverse-alignment conditions, and that the magnitude of performance impairment is directly related to laparoscopic experience and skill. The aim of this study was to determine if reverse-alignment surgical skills could be developed through training. Twenty-two medical students were randomized to train in either reverse- or forward-alignment conditions on a standardized laparoscopic task in a video trainer (peg transfer). Baseline scores were attained for each group under both orientations. Subjects participated in three 1-h training sessions during an 8-week period. Post-training scores were then obtained under both alignment conditions. Pre and post-training scores were compared for users in each study group under both conditions. Post-training assessments in the forward orientation demonstrated that subjects in the forward-training group improved significantly compared to pre-testing, while the performance of subjects in the reverse-training group did not improve. Under reverse-alignment conditions, both groups improved on post-test assessment, with dramatic improvements observed for those in the reverse-training group. Laparoscopic novices can learn to adapt to a sensorimotor discordance in a simulated training environment. While it is possible that skills developed by training under standard forward-alignment conditions can be utilized in situations of extreme visual-spatial discordance, the intentional development of reverse-alignment skills by training under these conditions may prove beneficial to novice surgeons.

Development of a turbomachinery design optimization procedure using a multiple-parameter nonlinear perturbation method

NASA Technical Reports Server (NTRS)

Stahara, S. S.

1984-01-01

An investigation was carried out to complete the preliminary development of a combined perturbation/optimization procedure and associated computational code for designing optimized blade-to-blade profiles of turbomachinery blades. The overall purpose of the procedures developed is to provide demonstration of a rapid nonlinear perturbation method for minimizing the computational requirements associated with parametric design studies of turbomachinery flows. The method combines the multiple parameter nonlinear perturbation method, successfully developed in previous phases of this study, with the NASA TSONIC blade-to-blade turbomachinery flow solver, and the COPES-CONMIN optimization procedure into a user's code for designing optimized blade-to-blade surface profiles of turbomachinery blades. Results of several design applications and a documented version of the code together with a user's manual are provided.

Robust prediction of consensus secondary structures using averaged base pairing probability matrices.

PubMed

Kiryu, Hisanori; Kin, Taishin; Asai, Kiyoshi

2007-02-15

Recent transcriptomic studies have revealed the existence of a considerable number of non-protein-coding RNA transcripts in higher eukaryotic cells. To investigate the functional roles of these transcripts, it is of great interest to find conserved secondary structures from multiple alignments on a genomic scale. Since multiple alignments are often created using alignment programs that neglect the special conservation patterns of RNA secondary structures for computational efficiency, alignment failures can cause potential risks of overlooking conserved stem structures. We investigated the dependence of the accuracy of secondary structure prediction on the quality of alignments. We compared three algorithms that maximize the expected accuracy of secondary structures as well as other frequently used algorithms. We found that one of our algorithms, called McCaskill-MEA, was more robust against alignment failures than others. The McCaskill-MEA method first computes the base pairing probability matrices for all the sequences in the alignment and then obtains the base pairing probability matrix of the alignment by averaging over these matrices. The consensus secondary structure is predicted from this matrix such that the expected accuracy of the prediction is maximized. We show that the McCaskill-MEA method performs better than other methods, particularly when the alignment quality is low and when the alignment consists of many sequences. Our model has a parameter that controls the sensitivity and specificity of predictions. We discussed the uses of that parameter for multi-step screening procedures to search for conserved secondary structures and for assigning confidence values to the predicted base pairs. The C++ source code that implements the McCaskill-MEA algorithm and the test dataset used in this paper are available at http://www.ncrna.org/papers/McCaskillMEA/. Supplementary data are available at Bioinformatics online.

Automated side-chain model building and sequence assignment by template matching.

PubMed

Terwilliger, Thomas C

2003-01-01

An algorithm is described for automated building of side chains in an electron-density map once a main-chain model is built and for alignment of the protein sequence to the map. The procedure is based on a comparison of electron density at the expected side-chain positions with electron-density templates. The templates are constructed from average amino-acid side-chain densities in 574 refined protein structures. For each contiguous segment of main chain, a matrix with entries corresponding to an estimate of the probability that each of the 20 amino acids is located at each position of the main-chain model is obtained. The probability that this segment corresponds to each possible alignment with the sequence of the protein is estimated using a Bayesian approach and high-confidence matches are kept. Once side-chain identities are determined, the most probable rotamer for each side chain is built into the model. The automated procedure has been implemented in the RESOLVE software. Combined with automated main-chain model building, the procedure produces a preliminary model suitable for refinement and extension by an experienced crystallographer.

Multidisciplinary design optimization using multiobjective formulation techniques

NASA Technical Reports Server (NTRS)

Chattopadhyay, Aditi; Pagaldipti, Narayanan S.

1995-01-01

This report addresses the development of a multidisciplinary optimization procedure using an efficient semi-analytical sensitivity analysis technique and multilevel decomposition for the design of aerospace vehicles. A semi-analytical sensitivity analysis procedure is developed for calculating computational grid sensitivities and aerodynamic design sensitivities. Accuracy and efficiency of the sensitivity analysis procedure is established through comparison of the results with those obtained using a finite difference technique. The developed sensitivity analysis technique are then used within a multidisciplinary optimization procedure for designing aerospace vehicles. The optimization problem, with the integration of aerodynamics and structures, is decomposed into two levels. Optimization is performed for improved aerodynamic performance at the first level and improved structural performance at the second level. Aerodynamic analysis is performed by solving the three-dimensional parabolized Navier Stokes equations. A nonlinear programming technique and an approximate analysis procedure are used for optimization. The proceduredeveloped is applied to design the wing of a high speed aircraft. Results obtained show significant improvements in the aircraft aerodynamic and structural performance when compared to a reference or baseline configuration. The use of the semi-analytical sensitivity technique provides significant computational savings.

New Method of Calibrating IRT Models.

ERIC Educational Resources Information Center

Jiang, Hai; Tang, K. Linda

This discussion of new methods for calibrating item response theory (IRT) models looks into new optimization procedures, such as the Genetic Algorithm (GA) to improve on the use of the Newton-Raphson procedure. The advantages of using a global optimization procedure like GA is that this kind of procedure is not easily affected by local optima and…

Heuristics for multiobjective multiple sequence alignment.

PubMed

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

2016-07-15

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

FPFH-based graph matching for 3D point cloud registration

NASA Astrophysics Data System (ADS)

Zhao, Jiapeng; Li, Chen; Tian, Lihua; Zhu, Jihua

2018-04-01

Correspondence detection is a vital step in point cloud registration and it can help getting a reliable initial alignment. In this paper, we put forward an advanced point feature-based graph matching algorithm to solve the initial alignment problem of rigid 3D point cloud registration with partial overlap. Specifically, Fast Point Feature Histograms are used to determine the initial possible correspondences firstly. Next, a new objective function is provided to make the graph matching more suitable for partially overlapping point cloud. The objective function is optimized by the simulated annealing algorithm for final group of correct correspondences. Finally, we present a novel set partitioning method which can transform the NP-hard optimization problem into a O(n3)-solvable one. Experiments on the Stanford and UWA public data sets indicates that our method can obtain better result in terms of both accuracy and time cost compared with other point cloud registration methods.

Rankline-Brayton engine powered solar thermal aircraft

DOEpatents

Bennett, Charles L [Livermore, CA

2012-03-13

A solar thermal powered aircraft powered by heat energy from the sun. A Rankine-Brayton hybrid cycle heat engine is carried by the aircraft body for producing power for a propulsion mechanism, such as a propeller or other mechanism for enabling sustained free flight. The Rankine-Brayton engine has a thermal battery, preferably containing a lithium-hydride and lithium mixture, operably connected to it so that heat is supplied from the thermal battery to a working fluid. A solar concentrator, such as reflective parabolic trough, is movably connected to an optically transparent section of the aircraft body for receiving and concentrating solar energy from within the aircraft. Concentrated solar energy is collected by a heat collection and transport conduit, and heat transported to the thermal battery. A solar tracker includes a heliostat for determining optimal alignment with the sun, and a drive motor actuating the solar concentrator into optimal alignment with the sun based on a determination by the heliostat.

Rankine-Brayton engine powered solar thermal aircraft

DOEpatents

Bennett, Charles L [Livermore, CA

2009-12-29

A solar thermal powered aircraft powered by heat energy from the sun. A Rankine-Brayton hybrid cycle heat engine is carried by the aircraft body for producing power for a propulsion mechanism, such as a propeller or other mechanism for enabling sustained free flight. The Rankine-Brayton engine has a thermal battery, preferably containing a lithium-hydride and lithium mixture, operably connected to it so that heat is supplied from the thermal battery to a working fluid. A solar concentrator, such as reflective parabolic trough, is movably connected to an optically transparent section of the aircraft body for receiving and concentrating solar energy from within the aircraft. Concentrated solar energy is collected by a heat collection and transport conduit, and heat transported to the thermal battery. A solar tracker includes a heliostat for determining optimal alignment with the sun, and a drive motor actuating the solar concentrator into optimal alignment with the sun based on a determination by the heliostat.

Free-viewpoint video of human actors using multiple handheld Kinects.

PubMed

Ye, Genzhi; Liu, Yebin; Deng, Yue; Hasler, Nils; Ji, Xiangyang; Dai, Qionghai; Theobalt, Christian

2013-10-01

We present an algorithm for creating free-viewpoint video of interacting humans using three handheld Kinect cameras. Our method reconstructs deforming surface geometry and temporal varying texture of humans through estimation of human poses and camera poses for every time step of the RGBZ video. Skeletal configurations and camera poses are found by solving a joint energy minimization problem, which optimizes the alignment of RGBZ data from all cameras, as well as the alignment of human shape templates to the Kinect data. The energy function is based on a combination of geometric correspondence finding, implicit scene segmentation, and correspondence finding using image features. Finally, texture recovery is achieved through jointly optimization on spatio-temporal RGB data using matrix completion. As opposed to previous methods, our algorithm succeeds on free-viewpoint video of human actors under general uncontrolled indoor scenes with potentially dynamic background, and it succeeds even if the cameras are moving.

Realizations of highly heterogeneous collagen networks via stochastic reconstruction for micromechanical analysis of tumor cell invasion

NASA Astrophysics Data System (ADS)

Nan, Hanqing; Liang, Long; Chen, Guo; Liu, Liyu; Liu, Ruchuan; Jiao, Yang

2018-03-01

Three-dimensional (3D) collective cell migration in a collagen-based extracellular matrix (ECM) is among one of the most significant topics in developmental biology, cancer progression, tissue regeneration, and immune response. Recent studies have suggested that collagen-fiber mediated force transmission in cellularized ECM plays an important role in stress homeostasis and regulation of collective cellular behaviors. Motivated by the recent in vitro observation that oriented collagen can significantly enhance the penetration of migrating breast cancer cells into dense Matrigel which mimics the intravasation process in vivo [Han et al. Proc. Natl. Acad. Sci. USA 113, 11208 (2016), 10.1073/pnas.1610347113], we devise a procedure for generating realizations of highly heterogeneous 3D collagen networks with prescribed microstructural statistics via stochastic optimization. Specifically, a collagen network is represented via the graph (node-bond) model and the microstructural statistics considered include the cross-link (node) density, valence distribution, fiber (bond) length distribution, as well as fiber orientation distribution. An optimization problem is formulated in which the objective function is defined as the squared difference between a set of target microstructural statistics and the corresponding statistics for the simulated network. Simulated annealing is employed to solve the optimization problem by evolving an initial network via random perturbations to generate realizations of homogeneous networks with randomly oriented fibers, homogeneous networks with aligned fibers, heterogeneous networks with a continuous variation of fiber orientation along a prescribed direction, as well as a binary system containing a collagen region with aligned fibers and a dense Matrigel region with randomly oriented fibers. The generation and propagation of active forces in the simulated networks due to polarized contraction of an embedded ellipsoidal cell and a small group of cells are analyzed by considering a nonlinear fiber model incorporating strain hardening upon large stretching and buckling upon compression. Our analysis shows that oriented fibers can significantly enhance long-range force transmission in the network. Moreover, in the oriented-collagen-Matrigel system, the forces generated by a polarized cell in collagen can penetrate deeply into the Matrigel region. The stressed Matrigel fibers could provide contact guidance for the migrating cell cells, and thus enhance their penetration into Matrigel. This suggests a possible mechanism for the observed enhanced intravasation by oriented collagen.

The direction of stretch-induced cell and stress fiber orientation depends on collagen matrix stress.

PubMed

Tondon, Abhishek; Kaunas, Roland

2014-01-01

Cell structure depends on both matrix strain and stiffness, but their interactive effects are poorly understood. We investigated the interactive roles of matrix properties and stretching patterns on cell structure by uniaxially stretching U2OS cells expressing GFP-actin on silicone rubber sheets supporting either a surface-adsorbed coating or thick hydrogel of type-I collagen. Cells and their actin stress fibers oriented perpendicular to the direction of cyclic stretch on collagen-coated sheets, but oriented parallel to the stretch direction on collagen gels. There was significant alignment parallel to the direction of a steady increase in stretch for cells on collagen gels, while cells on collagen-coated sheets did not align in any direction. The extent of alignment was dependent on both strain rate and duration. Stretch-induced alignment on collagen gels was blocked by the myosin light-chain kinase inhibitor ML7, but not by the Rho-kinase inhibitor Y27632. We propose that active orientation of the actin cytoskeleton perpendicular and parallel to direction of stretch on stiff and soft substrates, respectively, are responses that tend to maintain intracellular tension at an optimal level. Further, our results indicate that cells can align along directions of matrix stress without collagen fibril alignment, indicating that matrix stress can directly regulate cell morphology.

Polymer chain alignment and transistor properties of nanochannel-templated poly(3-hexylthiophene) nanowires

NASA Astrophysics Data System (ADS)

Oh, Seungjun; Hayakawa, Ryoma; Pan, Chengjun; Sugiyasu, Kazunori; Wakayama, Yutaka

2016-08-01

Nanowires of semiconducting poly(3-hexylthiophene) (P3HT) were produced by a nanochannel-template technique. Polymer chain alignment in P3HT nanowires was investigated as a function of nanochannel widths (W) and polymer chain lengths (L). We found that the ratio between chain length and channel width (L/W) was a key parameter as regards promoting polymer chain alignment. Clear dichroism was observed in polarized ultraviolet-visible (UV-Vis) absorption spectra only at a ratio of approximately L/W = 2, indicating that the L/W ratio must be optimized to achieve uniaxial chain alignment in the nanochannel direction. We speculate that an appropriate L/W ratio is effective in confining the geometries and conformations of polymer chains. This discussion was supported by theoretical simulations based on molecular dynamics. That is, the geometry of the polymer chains, including the distance and tilting angles of the chains in relation to the nanochannel surface, was dominant in determining the longitudinal alignment along the nanochannels. Thus prepared highly aligned polymer nanowire is advantageous for electrical carrier transport and has great potential for improving the device performance of field-effect transistors. In fact, a one-order improvement in carrier mobility was observed in a P3HT nanowire transistor.

Leveraging FPGAs for Accelerating Short Read Alignment.

PubMed

Arram, James; Kaplan, Thomas; Luk, Wayne; Jiang, Peiyong

2017-01-01

One of the key challenges facing genomics today is how to efficiently analyze the massive amounts of data produced by next-generation sequencing platforms. With general-purpose computing systems struggling to address this challenge, specialized processors such as the Field-Programmable Gate Array (FPGA) are receiving growing interest. The means by which to leverage this technology for accelerating genomic data analysis is however largely unexplored. In this paper, we present a runtime reconfigurable architecture for accelerating short read alignment using FPGAs. This architecture exploits the reconfigurability of FPGAs to allow the development of fast yet flexible alignment designs. We apply this architecture to develop an alignment design which supports exact and approximate alignment with up to two mismatches. Our design is based on the FM-index, with optimizations to improve the alignment performance. In particular, the n-step FM-index, index oversampling, a seed-and-compare stage, and bi-directional backtracking are included. Our design is implemented and evaluated on a 1U Maxeler MPC-X2000 dataflow node with eight Altera Stratix-V FPGAs. Measurements show that our design is 28 times faster than Bowtie2 running with 16 threads on dual Intel Xeon E5-2640 CPUs, and nine times faster than Soap3-dp running on an NVIDIA Tesla C2070 GPU.

47 CFR 1.2202 - Competitive bidding design options.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Section 1.2202 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL PRACTICE AND PROCEDURE Grants...) Procedures that utilize mathematical computer optimization software, such as integer programming, to evaluate... evaluating bids using a ranking based on specified factors. (B) Procedures that combine computer optimization...

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

NASA Astrophysics Data System (ADS)

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

2012-02-01

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

Interpolation schemes for peptide rearrangements.

PubMed

Bauer, Marianne S; Strodel, Birgit; Fejer, Szilard N; Koslover, Elena F; Wales, David J

2010-02-07

A variety of methods (in total seven) comprising different combinations of internal and Cartesian coordinates are tested for interpolation and alignment in connection attempts for polypeptide rearrangements. We consider Cartesian coordinates, the internal coordinates used in CHARMM, and natural internal coordinates, each of which has been interfaced to the OPTIM code and compared with the corresponding results for united-atom force fields. We show that aligning the methylene hydrogens to preserve the sign of a local dihedral angle, rather than minimizing a distance metric, provides significant improvements with respect to connection times and failures. We also demonstrate the superiority of natural coordinate methods in conjunction with internal alignment. Checking the potential energy of the interpolated structures can act as a criterion for the choice of the interpolation coordinate system, which reduces failures and connection times significantly.

Fully integrated aerodynamic/dynamic optimization of helicopter rotor blades

NASA Technical Reports Server (NTRS)

Walsh, Joanne L.; Lamarsh, William J., II; Adelman, Howard M.

1992-01-01

This paper describes a fully integrated aerodynamic/dynamic optimization procedure for helicopter rotor blades. The procedure combines performance and dynamics analyses with a general purpose optimizer. The procedure minimizes a linear combination of power required (in hover, forward flight, and maneuver) and vibratory hub shear. The design variables include pretwist, taper initiation, taper ratio, root chord, blade stiffnesses, tuning masses, and tuning mass locations. Aerodynamic constraints consist of limits on power required in hover, forward flight and maneuver; airfoil section stall; drag divergence Mach number; minimum tip chord; and trim. Dynamic constraints are on frequencies, minimum autorotational inertia, and maximum blade weight. The procedure is demonstrated for two cases. In the first case the objective function involves power required (in hover, forward flight, and maneuver) and dynamics. The second case involves only hover power and dynamics. The designs from the integrated procedure are compared with designs from a sequential optimization approach in which the blade is first optimized for performance and then for dynamics. In both cases, the integrated approach is superior.

Fully integrated aerodynamic/dynamic optimization of helicopter rotor blades

NASA Technical Reports Server (NTRS)

Walsh, Joanne L.; Lamarsh, William J., II; Adelman, Howard M.

1992-01-01

A fully integrated aerodynamic/dynamic optimization procedure is described for helicopter rotor blades. The procedure combines performance and dynamic analyses with a general purpose optimizer. The procedure minimizes a linear combination of power required (in hover, forward flight, and maneuver) and vibratory hub shear. The design variables include pretwist, taper initiation, taper ratio, root chord, blade stiffnesses, tuning masses, and tuning mass locations. Aerodynamic constraints consist of limits on power required in hover, forward flight and maneuvers; airfoil section stall; drag divergence Mach number; minimum tip chord; and trim. Dynamic constraints are on frequencies, minimum autorotational inertia, and maximum blade weight. The procedure is demonstrated for two cases. In the first case, the objective function involves power required (in hover, forward flight and maneuver) and dynamics. The second case involves only hover power and dynamics. The designs from the integrated procedure are compared with designs from a sequential optimization approach in which the blade is first optimized for performance and then for dynamics. In both cases, the integrated approach is superior.

Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud.

PubMed

Di Tommaso, Paolo; Orobitg, Miquel; Guirado, Fernando; Cores, Fernado; Espinosa, Toni; Notredame, Cedric

2010-08-01

We present the first parallel implementation of the T-Coffee consistency-based multiple aligner. We benchmark it on the Amazon Elastic Cloud (EC2) and show that the parallelization procedure is reasonably effective. We also conclude that for a web server with moderate usage (10K hits/month) the cloud provides a cost-effective alternative to in-house deployment. T-Coffee is a freeware open source package available from http://www.tcoffee.org/homepage.html

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Modeling Training Site Vegetation Coverage Probability with a Random Optimizing Procedure: An Artificial Neural Network Approach.

DTIC Science & Technology

1998-05-01

Coverage Probability with a Random Optimization Procedure: An Artificial Neural Network Approach by Biing T. Guan, George Z. Gertner, and Alan B...Modeling Training Site Vegetation Coverage Probability with a Random Optimizing Procedure: An Artificial Neural Network Approach 6. AUTHOR(S) Biing...coverage based on past coverage. Approach A literature survey was conducted to identify artificial neural network analysis techniques applicable for

Nonextraction Treatment of Severe Crowding with the Aid of Corticotomy-Assisted Orthodontics

PubMed Central

Aljhani, Ali S.; Zawawi, Khalid H.

2012-01-01

This paper illustrates the combined nonextraction orthodontic treatment with the corticotomy technique in an adult patient (age: 25 years and 3 months) with severely crowded arches to accelerate tooth movement and shorten the treatment time. Both her upper lateral incisors were congenitally absent and both upper central incisors' roots were short. Initial fixed orthodontic appliances (bidimensional) were bonded and one week later buccal and lingual corticotomy with alveolar augmentation procedure in the maxilla and mandible was performed. Orthodontic activation to level and align and unravel the crowding was performed every two weeks. The total treatment time was 8 months with no adverse effects observed at the end of active treatment. The addition of the decortication procedure to the conventional orthodontic therapy decreased the duration of treatment significantly. Successful alignment of both arches with ideal overbite and overjet as well as adequate occlusion was achieved. PMID:22848854

A 'digital' technique for manual extraction of data from aerial photography

NASA Technical Reports Server (NTRS)

Istvan, L. B.; Bondy, M. T.

1977-01-01

The interpretation procedure described uses a grid cell approach. In addition, a random point is located in each cell. The procedure required that the cell/point grid be established on a base map, and identical grids be made to precisely match the scale of the photographic frames. The grid is then positioned on the photography by visual alignment to obvious features. Several alignments on one frame are sometimes required to make a precise match of all points to be interpreted. This system inherently corrects for distortions in the photography. Interpretation is then done cell by cell. In order to meet the time constraints, first order interpretation should be maintained. The data is put onto coding forms, along with other appropriate data, if desired. This 'digital' manual interpretation technique has proven to be efficient, and time and cost effective, while meeting strict requirements for data format and accuracy.

The aberration characteristics in a misaligned three-mirror anastigmatic (TMA) system

NASA Astrophysics Data System (ADS)

Wang, Bin; Wu, Fan; Ye, Yutang

2016-09-01

To realize the efficient alignment of the TMA system, the aberrations in a misaligned TMA system had been analyzed theoretically in this paper. Firstly, based on the nodal aberration theory (NAT), the aberration types and characteristics in the misaligned TMA system had been concluded; Secondly, a simulation validation had been carried out to testify the analysis results, the simulation results validates the aberration characteristics; Finally, the alignment procedures were determined according to the aberration characteristics: adjust the axial spacing of the mirrors in terms of Z9 in the center field of TMA system first; and then, adjust the decenters and tilts of the mirrors in terms of Z5 - Z8 in the edge field of TMA system. This method is helpful for the alignment of the TMA telescope.

Analysis of the influence of manufacturing and alignment related errors on an optical tweezer system

NASA Astrophysics Data System (ADS)

Kampmann, R.; Sinzinger, S.

2014-12-01

In this work we present the design process as well as experimental results of an optical system for trapping particles in air. For positioning applications of micro-sized objects onto a glass wafer we developed a highly efficient optical tweezer. The focus of this paper is the iterative design process where we combine classical optics design software with a ray optics based force simulation tool. Thus we can find the best compromise which matches the optical systems restrictions with stable trapping conditions. Furthermore we analyze the influence of manufacturing related tolerances and errors in the alignment process of the optical elements on the optical forces. We present the design procedure for the necessary optical elements as well as experimental results for the aligned system.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruland, Robert

The Visible-Infrared SASE Amplifier (VISA) undulator consists of four 99cm long segments. Each undulator segment is set up on a pulsed-wire bench, to characterize the magnetic properties and to locate the magnetic axis of the FODO array. Subsequently, the location of the magnetic axis, as defined by the wire, is referenced to tooling balls on each magnet segment by means of a straightness interferometer. After installation in the vacuum chamber, the four magnet segments are aligned with respect to themselves and globally to the beam line reference laser. A specially designed alignment fixture is used to mount one straightness interferometermore » each in the horizontal and vertical plane of the beam. The goal of these procedures is to keep the combined rms trajectory error, due to magnetic and alignment errors, to 50{micro}m.« less

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

Photothermal camera port accessory for microscopic thermal diffusivity imaging

NASA Astrophysics Data System (ADS)

Escola, Facundo Zaldívar; Kunik, Darío; Mingolo, Nelly; Martínez, Oscar Eduardo

2016-06-01

The design of a scanning photothermal accessory is presented, which can be attached to the camera port of commercial microscopes to measure thermal diffusivity maps with micrometer resolution. The device is based on the thermal expansion recovery technique, which measures the defocusing of a probe beam due to the curvature induced by the local heat delivered by a focused pump beam. The beam delivery and collecting optics are built using optical fiber technology, resulting in a robust optical system that provides collinear pump and probe beams without any alignment adjustment necessary. The quasiconfocal configuration for the signal collection using the same optical fiber sets very restrictive conditions on the positioning and alignment of the optical components of the scanning unit, and a detailed discussion of the design equations is presented. The alignment procedure is carefully described, resulting in a system so robust and stable that no further alignment is necessary for the day-to-day use, becoming a tool that can be used for routine quality control, operated by a trained technician.

Elevating the role of finance at Mary Lanning Healthcare.

PubMed

Hoffman, Amanda; Spence, Jay

2013-11-01

To effectively partner with hospital operations leaders, healthcare finance leaders should: Streamline and align financial planning and budgeting functions across the organization; Ensure capital planning is regarded as a strategic process; Optimize performance monitoring across management levels.

Early functional outcome after lateral UKA is sensitive to postoperative lower limb alignment.

PubMed

van der List, J P; Chawla, H; Villa, J C; Zuiderbaan, H A; Pearle, A D

2017-03-01

The predictive role of patient-specific characteristics and radiographic parameters on medial unicompartmental knee arthroplasty (UKA) outcomes is well known, but knowledge of these predictors is lacking in lateral UKA. Therefore, purpose of this study was to assess the predictive role of these parameters on short-term functional outcomes of lateral UKA. In this retrospective cohort study, Western Ontario and McMaster Universities Arthritis Index scores were collected at 2-year follow-up (median 2.2 years, range 2.0-4.0 years) in 39 patients who underwent lateral UKA. Patient-specific characteristics included age, BMI and gender, while radiographic parameters included osteoarthritis severity of all three compartments and both preoperative and postoperative hip-knee-ankle alignment. BMI, gender, age and preoperative valgus alignment were not correlated with functional outcomes, while postoperative valgus alignment was correlated with functional outcomes (0.561; p = 0.001). Postoperative valgus of 3°-7° was correlated with better outcomes than more neutral (-2° to 3° valgus) alignment (96.7 vs. 85.6; p = 0.011). Postoperative alignment was a predictor when corrected for patient-specific characteristics (regression coefficient 4.1; p < 0.001) and radiological parameters (regression coefficient 3.8; p = 0.002). Postoperative valgus alignment of 3°-7° was correlated with the best short-term functional outcomes in lateral UKA surgery, while patient-specific parameters and preoperative alignment were not correlated with functional outcomes. Based on these findings, a surgeon should aim for valgus alignment of 3°-7° when performing lateral UKA surgery for optimal functional outcomes. Prognostic study, Level II.

Is multiple-sequence alignment required for accurate inference of phylogeny?

PubMed

Höhl, Michael; Ragan, Mark A

2007-04-01

The process of inferring phylogenetic trees from molecular sequences almost always starts with a multiple alignment of these sequences but can also be based on methods that do not involve multiple sequence alignment. Very little is known about the accuracy with which such alignment-free methods recover the correct phylogeny or about the potential for increasing their accuracy. We conducted a large-scale comparison of ten alignment-free methods, among them one new approach that does not calculate distances and a faster variant of our pattern-based approach; all distance-based alignment-free methods are freely available from http://www.bioinformatics.org.au (as Python package decaf+py). We show that most methods exhibit a higher overall reconstruction accuracy in the presence of high among-site rate variation. Under all conditions that we considered, variants of the pattern-based approach were significantly better than the other alignment-free methods. The new pattern-based variant achieved a speed-up of an order of magnitude in the distance calculation step, accompanied by a small loss of tree reconstruction accuracy. A method of Bayesian inference from k-mers did not improve on classical alignment-free (and distance-based) methods but may still offer other advantages due to its Bayesian nature. We found the optimal word length k of word-based methods to be stable across various data sets, and we provide parameter ranges for two different alphabets. The influence of these alphabets was analyzed to reveal a trade-off in reconstruction accuracy between long and short branches. We have mapped the phylogenetic accuracy for many alignment-free methods, among them several recently introduced ones, and increased our understanding of their behavior in response to biologically important parameters. In all experiments, the pattern-based approach emerged as superior, at the expense of higher resource consumption. Nonetheless, no alignment-free method that we examined recovers the correct phylogeny as accurately as does an approach based on maximum-likelihood distance estimates of multiply aligned sequences.

Atmospheric monitoring in the millimetre and submillimetre bands for cosmological observations: CASPER2

NASA Astrophysics Data System (ADS)

De Petris, M.; De Gregori, S.; Decina, B.; Lamagna, L.; Pardo, J. R.

2013-02-01

Cosmological observations from ground at millimetre and submillimetre wavelengths are affected by atmospheric absorption and consequent emission. The low- and high-frequency (sky-noise) fluctuations of atmospheric performance necessitate careful observational strategies and/or instrumental technical solutions. Measurements of atmospheric emission spectra are necessary for accurate calibration procedures as well as for site-testing statistics. CASPER2, an instrument designed to explore the 90-450 GHz (3-15 cm-1) spectral region, was developed and had its operation verified in the Alps. A Martin-Puplett interferometer (MPI) operates by comparing sky radiation, coming from a field of view (FOV) of 28 arcmin (full width at half-maximum) and collected by a 62-cm-diameter Pressman-Camichel telescope, with a reference source. The signals at the two output ports of the interferometer are detected by two bolometers cooled to 300 mK inside a wet cryostat. Three different but complementary interferometric techniques can be performed with CASPER2: amplitude modulation (AM), fast-scan (FS) and phase modulation (PM). An altazimuthal mount allows sky pointing, possibly co-aligned with the optical axis of the 2.6-m-diameter telescope of MITO (Millimetre and Infrared Testagrigia Observatory, Italy). The optimal time-scale to average acquired spectra is inferred by Allan variance analysis at five fiducial frequencies. We present the motivation for and design of the atmospheric spectrometer CASPER2. The procedure adopted to calibrate the instrument and the preliminary performance of it are described. Instrument capabilities were checked during the summer observational campaign at MITO in 2010 July by measuring atmospheric emission spectra with the three procedures.

BATMAN: a DMD-based multi-object spectrograph on Galileo telescope

NASA Astrophysics Data System (ADS)

Zamkotsian, Frederic; Spano, Paolo; Lanzoni, Patrick; Ramarijaona, Harald; Moschetti, Manuele; Riva, Marco; Bon, William; Nicastro, Luciano; Molinari, Emilio; Cosentino, Rosario; Ghedina, Adriano; Gonzalez, Manuel; Di Marcantonio, Paolo; Coretti, Igor; Cirami, Roberto; Zerbi, Filippo; Valenziano, Luca

2014-07-01

Next-generation infrared astronomical instrumentation for ground-based and space telescopes could be based on MOEMS programmable slit masks for multi-object spectroscopy (MOS). This astronomical technique is used extensively to investigate the formation and evolution of galaxies. We are developing a 2048x1080 Digital-Micromirror-Device-based (DMD) MOS instrument to be mounted on the Galileo telescope and called BATMAN. A two-arm instrument has been designed for providing in parallel imaging and spectroscopic capabilities. The field of view (FOV) is 6.8 arcmin x 3.6 arcmin with a plate scale of 0.2 arcsec per micromirror. The wavelength range is in the visible and the spectral resolution is R=560 for 1 arcsec object (typical slit size). The two arms will have 2k x 4k CCD detectors. ROBIN, a BATMAN demonstrator, has been designed, realized and integrated. It permits to determine the instrument integration procedure, including optics and mechanics integration, alignment procedure and optical quality. First images and spectra have been obtained and measured: typical spot diameters are within 1.5 detector pixels, and spectra generated by one micro-mirror slits are displayed with this optical quality over the whole visible wavelength range. Observation strategies are studied and demonstrated for the scientific optimization strategy over the whole FOV. BATMAN on the sky is of prime importance for characterizing the actual performance of this new family of MOS instruments, as well as investigating the operational procedures on astronomical objects. This instrument will be placed on the Telescopio Nazionale Galileo mid-2015.

Alignment of training curriculum and surgical practice: implications for competency, manpower, and practice modeling.

PubMed

Sømme, S; Bronsert, M; Kempe, A; Morrato, E H; Ziegler, M

2012-02-01

The attractiveness of pediatric surgery (PS) as a specialty includes its primary role in the care of multisystemic disease. We were interested in identifying changes in operative case quality and quantity when comparing PS residents to PS practitioners. The 2006 Accreditation Council for Graduate Medical Education PS resident current procedural terminology (CPT) code database (26,077 resident cases) was merged with the 2006 Kids' Inpatient Database of International Classification of Diseases (ICD)-9 procedure codes (230,504 practitioner cases) and categorized by case type and volumes according to a resident CPT reference file. Cases were categorized into 84 procedure types. A recent estimate of 691 practicing pediatric surgeons was used as denominator to calculate case volume per surgeon. Our analysis focused on the PS index cases and we compared PS residents to subspecialty board certified general pediatric surgeons in practice. We excluded cases that may be performed by general surgeons without PS training. Our data indicate that, on average, 501 cases are performed annually by each PS resident. We identified significant differences in case volume per surgeon between training and practice for most PS index cases.CONCLUSIONS The PS index case quantity declined significantly from training to practice. If a volume to outcome relationship applies to these complex and infrequent PS cases, then to sustain and improve clinical quality post-training will require a new paradigm of continued learning. Additionally, a relook at the optimal manpower and more focused regionalization is warranted. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

Minimalist breast conserving surgical approaches for inferiorly sited cancers

PubMed Central

2017-01-01

Contemporary data suggests that breast conservation treatment (BCT) may confer a survival advantage when compared to mastectomy. Hence, it would be logical to adopt strategies which increase eligibility of successful BCT without compromising oncologic principles or cosmetic outcome. With respect to achieving good aesthetics, inferiorly sited breast cancers pose a particular technical challenge. A vast array of techniques, collectively referred to as oncoplastic breast surgery (OBS) have been developed to minimise post treatment distortion. The purported advantages of these approaches are the acquisition of wider margins and reduced re-excision rates. However, to date, there is a lack of data demonstrating significant reduction in local recurrence and overall survival when compared with less extensive procedures. In this review, “minimalist” procedures are described where strict oncologic criteria of clear margins are fulfilled and acceptable cosmesis are simultaneously achieved. These techniques offer less tissue loss, less extensive parenchymal mobilisation and shorter operating times without compromising margin status and aesthetics. They involve the combination of innovative incision designs and certain parenchymal resection patterns. Incision designs include the boomerang, golf-tee, anchor and arrowhead incisions which have been previously described but not widely used. Parenchymal resection patterns follow the “sick lobe hypothesis”. These techniques, termed “reductionist”, or “minimalist” comprising approaches where breast conserving surgery is condensed to its irreducible elements, offer alternatives which align with contemporary objectives of surgery where optimal survival outcomes are achieved through individualised procedures resulting in reduced iatrogenic impact. This logically allows scope for de-escalation of surgical therapy for breast cancer. PMID:28861382

Improving anatomical mapping of complexly deformed anatomy for external beam radiotherapy and brachytherapy dose accumulation in cervical cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vásquez Osorio, Eliana M., E-mail: e.vasquezosorio@erasmusmc.nl; Kolkman-Deurloo, Inger-Karine K.; Schuring-Pereira, Monica

Purpose: In the treatment of cervical cancer, large anatomical deformations, caused by, e.g., tumor shrinkage, bladder and rectum filling changes, organ sliding, and the presence of the brachytherapy (BT) applicator, prohibit the accumulation of external beam radiotherapy (EBRT) and BT dose distributions. This work proposes a structure-wise registration with vector field integration (SW+VF) to map the largely deformed anatomies between EBRT and BT, paving the way for 3D dose accumulation between EBRT and BT. Methods: T2w-MRIs acquired before EBRT and as a part of the MRI-guided BT procedure for 12 cervical cancer patients, along with the manual delineations of themore » bladder, cervix-uterus, and rectum-sigmoid, were used for this study. A rigid transformation was used to align the bony anatomy in the MRIs. The proposed SW+VF method starts by automatically segmenting features in the area surrounding the delineated organs. Then, each organ and feature pair is registered independently using a feature-based nonrigid registration algorithm developed in-house. Additionally, a background transformation is calculated to account for areas far from all organs and features. In order to obtain one transformation that can be used for dose accumulation, the organ-based, feature-based, and the background transformations are combined into one vector field using a weighted sum, where the contribution of each transformation can be directly controlled by its extent of influence (scope size). The optimal scope sizes for organ-based and feature-based transformations were found by an exhaustive analysis. The anatomical correctness of the mapping was independently validated by measuring the residual distances after transformation for delineated structures inside the cervix-uterus (inner anatomical correctness), and for anatomical landmarks outside the organs in the surrounding region (outer anatomical correctness). The results of the proposed method were compared with the results of the rigid transformation and nonrigid registration of all structures together (AST). Results: The rigid transformation achieved a good global alignment (mean outer anatomical correctness of 4.3 mm) but failed to align the deformed organs (mean inner anatomical correctness of 22.4 mm). Conversely, the AST registration produced a reasonable alignment for the organs (6.3 mm) but not for the surrounding region (16.9 mm). SW+VF registration achieved the best results for both regions (3.5 and 3.4 mm for the inner and outer anatomical correctness, respectively). All differences were significant (p < 0.02, Wilcoxon rank sum test). Additionally, optimization of the scope sizes determined that the method was robust for a large range of scope size values. Conclusions: The novel SW+VF method improved the mapping of large and complex deformations observed between EBRT and BT for cervical cancer patients. Future studies that quantify the mapping error in terms of dose errors are required to test the clinical applicability of dose accumulation by the SW+VF method.« less

How accurately does high tibial osteotomy correct the mechanical axis of an arthritic varus knee? A systematic review.

PubMed

Van den Bempt, Maxim; Van Genechten, Wouter; Claes, Toon; Claes, Steven

2016-12-01

The aim of this study was to give an overview of the accuracy of coronal limb alignment correction after high tibial osteotomy (HTO) for the arthritic varus knee by performing a systematic review of the literature. The databases PubMed, MEDLINE and Cochrane Library were screened for relevant articles. Only prospective clinical studies with the accuracy of alignment correction by performing HTO as primary or secondary objective were included. Fifteen studies were included in this systematic review and were subdivided in 23 cohorts. A total of 966 procedures were considered. Nine cohorts used computer navigation during HTO and the other 14 cohorts used a conventional method. In seven computer navigation cohorts, at least 75% of the study population fell into the accepted "range of accuracy" (AR) as proposed by the different studies, but only six out of 14 conventional cohorts reached this percentage. Four out of eight conventional cohorts that provided data on under- and overcorrection, had a tendency to undercorrection. The accuracy of coronal alignment corrections using conventional HTO falls short. The number of procedures outside the proposed AR is surprising and exposes a critical concern for modern HTO. Computer navigation might improve the accuracy of correction, but its use is not widespread among orthopedic surgeons. Although HTO procedures have been shown to be successful in the treatment of unicompartmental knee arthritis when performed accurately, the results of this review stress the importance of ongoing efforts in order to improve correction accuracy in modern HTO. Copyright © 2016 Elsevier B.V. All rights reserved.

Cluster analysis of commercial samples of Bauhinia spp. using HPLC-UV/PDA and MCR-ALS/PCA without peak alignment procedure.

PubMed

Ardila, Jorge Armando; Funari, Cristiano Soleo; Andrade, André Marques; Cavalheiro, Alberto José; Carneiro, Renato Lajarim

2015-01-01

Bauhinia forficata Link. is recognised by the Brazilian Health Ministry as a treatment of hypoglycemia and diabetes. Analytical methods are useful to assess the plant identity due the similarities found in plants from Bauhinia spp. HPLC-UV/PDA in combination with chemometric tools is an alternative widely used and suitable for authentication of plant material, however, the shifts of retention times for similar compounds in different samples is a problem. To perform comparisons between the authentic medicinal plant (Bauhinia forficata Link.) and samples commercially available in drugstores claiming to be "Bauhinia spp. to treat diabetes" and to evaluate the performance of multivariate curve resolution - alternating least squares (MCR-ALS) associated to principal component analysis (PCA) when compared to pure PCA. HPLC-UV/PDA data obtained from extracts of leaves were evaluated employing a combination of MCR-ALS and PCA, which allowed the use of the full chromatographic and spectrometric information without the need of peak alignment procedures. The use of MCR-ALS/PCA showed better results than the conventional PCA using only one wavelength. Only two of nine commercial samples presented characteristics similar to the authentic Bauhinia forficata spp., considering the full HPLC-UV/PDA data. The combination of MCR-ALS and PCA is very useful when applied to a group of samples where a general alignment procedure could not be applied due to the different chromatographic profiles. This work also demonstrates the need of more strict control from the health authorities regarding herbal products available on the market. Copyright © 2015 John Wiley & Sons, Ltd.

DR-TAMAS: Diffeomorphic Registration for Tensor Accurate alignMent of Anatomical Structures

PubMed Central

Irfanoglu, M. Okan; Nayak, Amritha; Jenkins, Jeffrey; Hutchinson, Elizabeth B.; Sadeghi, Neda; Thomas, Cibu P.; Pierpaoli, Carlo

2016-01-01

In this work, we propose DR-TAMAS (Diffeomorphic Registration for Tensor Accurate alignMent of Anatomical Structures), a novel framework for intersubject registration of Diffusion Tensor Imaging (DTI) data sets. This framework is optimized for brain data and its main goal is to achieve an accurate alignment of all brain structures, including white matter (WM), gray matter (GM), and spaces containing cerebrospinal fluid (CSF). Currently most DTI-based spatial normalization algorithms emphasize alignment of anisotropic structures. While some diffusion-derived metrics, such as diffusion anisotropy and tensor eigenvector orientation, are highly informative for proper alignment of WM, other tensor metrics such as the trace or mean diffusivity (MD) are fundamental for a proper alignment of GM and CSF boundaries. Moreover, it is desirable to include information from structural MRI data, e.g., T1-weighted or T2-weighted images, which are usually available together with the diffusion data. The fundamental property of DR-TAMAS is to achieve global anatomical accuracy by incorporating in its cost function the most informative metrics locally. Another important feature of DR-TAMAS is a symmetric time-varying velocity-based transformation model, which enables it to account for potentially large anatomical variability in healthy subjects and patients. The performance of DR-TAMAS is evaluated with several data sets and compared with other widely-used diffeomorphic image registration techniques employing both full tensor information and/or DTI-derived scalar maps. Our results show that the proposed method has excellent overall performance in the entire brain, while being equivalent to the best existing methods in WM. PMID:26931817

Mercury-Cadmium-Telluride Focal Plane Array Performance Under Non-Standard Operating Conditions

NASA Technical Reports Server (NTRS)

Richardson, Brandon S.; Eastwood, Michael L.; Bruce, Carl F.; Green, Robert O.; Coles, J. B.

2011-01-01

This paper highlights a new technique that allows the Teledyne Scientific & Imaging LLC TCM6604A Mercury-Cadmium-Telluride (MCT) Focal Plane Array (FPA) to operate at room temperature. The Teledyne MCT FPA has been a standard in Imaging Spectroscopy since its creation in the 1980's. This FPA has been used in applications ranging from space instruments such as CRISM, M3 and ARTEMIS to airborne instruments such as MaRS and the Next Generation AVIRIS Instruments1. Precise focal plane alignment is always a challenge for such instruments. The current FPA alignment process results in multiple cold cycles requiring week-long durations, thereby increasing the risk and cost of a project. These alignment cycles are necessary because optimal alignment is approached incrementally and can only be measured with the FPA and Optics at standard operating conditions, requiring a cold instrument. Instruments using this FPA are normally cooled to temperatures below 150K for the MCT FPA to properly function. When the FPA is run at higher temperatures the dark current increases saturating the output. This paper covers the prospect of warm MCT FPA operation from a theoretical and experimental perspective. We discuss the empirical models and physical laws that govern MCT material properties and predict the optimal settings that will result in the best MCT PA performance at 300K. Theoretical results are then calculated for the proposed settings. We finally present the images and data obtained using the actual system with the warm MCT FPA settings. The paper concludes by emphasizing the strong positive correlation between the measured values and the theoretical results.

40 CFR 91.316 - Hydrocarbon analyzer calibration.

Code of Federal Regulations, 2011 CFR

2011-07-01

... periodic optimization of detector response. Prior to introduction into service and at least annually... nitrogen. (2) One of the following procedures is required for FID or HFID optimization: (i) The procedure outlined in Society of Automotive Engineers (SAE) paper No. 770141, “Optimization of Flame Ionization...

Decision making with regard to antiviral intervention during an influenza pandemic.

PubMed

Shim, Eunha; Chapman, Gretchen B; Galvani, Alison P

2010-01-01

Antiviral coverage is defined by the proportion of the population that takes antiviral prophylaxis or treatment. High coverage of an antiviral drug has epidemiological and evolutionary repercussions. Antivirals select for drug resistance within the population, and individuals may experience adverse effects. To determine optimal antiviral coverage in the context of an influenza outbreak, we compared 2 perspectives: 1) the individual level (the Nash perspective), and 2) the population level (utilitarian perspective). We developed an epidemiological game-theoretic model of an influenza pandemic. The data sources were published literature and a national survey. The target population was the US population. The time horizon was 6 months. The perspective was individuals and the population overall. The interventions were antiviral prophylaxis and treatment. The outcome measures were the optimal coverage of antivirals in an influenza pandemic. At current antiviral pricing, the optimal Nash strategy is 0% coverage for prophylaxis and 30% coverage for treatment, whereas the optimal utilitarian strategy is 19% coverage for prophylaxis and 100% coverage for treatment. Subsidizing prophylaxis by $440 and treatment by $85 would bring the Nash and utilitarian strategies into alignment. For both prophylaxis and treatment, the optimal antiviral coverage decreases as pricing of antivirals increases. Our study does not incorporate the possibility of an effective vaccine and lacks probabilistic sensitivity analysis. Our survey also does not completely represent the US population. Because our model assumes a homogeneous population and homogeneous antiviral pricing, it does not incorporate heterogeneity of preference. The optimal antiviral coverage from the population perspective and individual perspectives differs widely for both prophylaxis and treatment strategies. Optimal population and individual strategies for prophylaxis and treatment might be aligned through subsidization.

Decision Making with Regard to Antiviral Intervention during an Influenza Pandemic

PubMed Central

Shim, Eunha; Chapman, Gretchen B.; Galvani, Alison P.

2012-01-01

Background Antiviral coverage is defined by the proportion of the population that takes antiviral prophylaxis or treatment. High coverage of an antiviral drug has epidemiological and evolutionary repercussions. Antivirals select for drug resistance within the population, and individuals may experience adverse effects. To determine optimal antiviral coverage in the context of an influenza outbreak, we compared 2 perspectives: 1) the individual level (the Nash perspective), and 2) the population level (utilitarian perspective). Methods We developed an epidemiological game-theoretic model of an influenza pandemic. The data sources were published literature and a national survey. The target population was the US population. The time horizon was 6 months. The perspective was individuals and the population overall. The interventions were antiviral prophylaxis and treatment. The outcome measures were the optimal coverage of antivirals in an influenza pandemic. Results At current antiviral pricing, the optimal Nash strategy is 0% coverage for prophylaxis and 30% coverage for treatment, whereas the optimal utilitarian strategy is 19% coverage for prophylaxis and 100% coverage for treatment. Subsidizing prophylaxis by $440 and treatment by $85 would bring the Nash and utilitarian strategies into alignment. For both prophylaxis and treatment, the optimal antiviral coverage decreases as pricing of antivirals increases. Our study does not incorporate the possibility of an effective vaccine and lacks probabilistic sensitivity analysis. Our survey also does not completely represent the US population. Because our model assumes a homogeneous population and homogeneous antiviral pricing, it does not incorporate heterogeneity of preference. Conclusions The optimal antiviral coverage from the population perspective and individual perspectives differs widely for both prophylaxis and treatment strategies. Optimal population and individual strategies for prophylaxis and treatment might be aligned through subsidization. PMID:20634545

Study of flutter related computational procedures for minimum weight structural sizing of advanced aircraft

NASA Technical Reports Server (NTRS)

Oconnell, R. F.; Hassig, H. J.; Radovcich, N. A.

1976-01-01

Results of a study of the development of flutter modules applicable to automated structural design of advanced aircraft configurations, such as a supersonic transport, are presented. Automated structural design is restricted to automated sizing of the elements of a given structural model. It includes a flutter optimization procedure; i.e., a procedure for arriving at a structure with minimum mass for satisfying flutter constraints. Methods of solving the flutter equation and computing the generalized aerodynamic force coefficients in the repetitive analysis environment of a flutter optimization procedure are studied, and recommended approaches are presented. Five approaches to flutter optimization are explained in detail and compared. An approach to flutter optimization incorporating some of the methods discussed is presented. Problems related to flutter optimization in a realistic design environment are discussed and an integrated approach to the entire flutter task is presented. Recommendations for further investigations are made. Results of numerical evaluations, applying the five methods of flutter optimization to the same design task, are presented.

Automatic lung nodule matching for the follow-up in temporal chest CT scans

NASA Astrophysics Data System (ADS)

Hong, Helen; Lee, Jeongjin; Shin, Yeong Gil

2006-03-01

We propose a fast and robust registration method for matching lung nodules of temporal chest CT scans. Our method is composed of four stages. First, the lungs are extracted from chest CT scans by the automatic segmentation method. Second, the gross translational mismatch is corrected by the optimal cube registration. This initial registration does not require extracting any anatomical landmarks. Third, initial alignment is step by step refined by the iterative surface registration. To evaluate the distance measure between surface boundary points, a 3D distance map is generated by the narrow-band distance propagation, which drives fast and robust convergence to the optimal location. Fourth, nodule correspondences are established by the pairs with the smallest Euclidean distances. The results of pulmonary nodule alignment of twenty patients are reported on a per-center-of mass point basis using the average Euclidean distance (AED) error between corresponding nodules of initial and follow-up scans. The average AED error of twenty patients is significantly reduced to 4.7mm from 30.0mm by our registration. Experimental results show that our registration method aligns the lung nodules much faster than the conventional ones using a distance measure. Accurate and fast result of our method would be more useful for the radiologist's evaluation of pulmonary nodules on chest CT scans.

Accelerated Profile HMM Searches

PubMed Central

Eddy, Sean R.

2011-01-01

Profile hidden Markov models (profile HMMs) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been hindered by the computational expense of existing software implementations. Here I describe an acceleration heuristic for profile HMMs, the “multiple segment Viterbi” (MSV) algorithm. The MSV algorithm computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment. MSV scores follow the same statistical distribution as gapped optimal local alignment scores, allowing rapid evaluation of significance of an MSV score and thus facilitating its use as a heuristic filter. I also describe a 20-fold acceleration of the standard profile HMM Forward/Backward algorithms using a method I call “sparse rescaling”. These methods are assembled in a pipeline in which high-scoring MSV hits are passed on for reanalysis with the full HMM Forward/Backward algorithm. This accelerated pipeline is implemented in the freely available HMMER3 software package. Performance benchmarks show that the use of the heuristic MSV filter sacrifices negligible sensitivity compared to unaccelerated profile HMM searches. HMMER3 is substantially more sensitive and 100- to 1000-fold faster than HMMER2. HMMER3 is now about as fast as BLAST for protein searches. PMID:22039361

Extrinsic Factors as Component Positions to Bone and Intrinsic Factors Affecting Postoperative Rotational Limb Alignment in Total Knee Arthroplasty.

PubMed

Mochizuki, Tomoharu; Sato, Takashi; Tanifuji, Osamu; Watanabe, Satoshi; Kobayashi, Koichi; Endo, Naoto

2018-02-13

This study aimed to identify the factors affecting postoperative rotational limb alignment of the tibia relative to the femur. We hypothesized that not only component positions but also several intrinsic factors were associated with postoperative rotational limb alignment. This study included 99 knees (90 women and 9 men) with a mean age of 77 ± 6 years. A three-dimensional (3D) assessment system was applied under weight-bearing conditions to biplanar long-leg radiographs using 3D-to-2D image registration technique. The evaluation parameters were (1) component position; (2) preoperative and postoperative coronal, sagittal, and rotational limb alignment; (3) preoperative bony deformity, including femoral torsion, condylar twist angle, and tibial torsion; and (4) preoperative and postoperative range of motion (ROM). In multiple linear regression analysis using a stepwise procedure, postoperative rotational limb alignment was associated with the following: (1) rotation of the component position (tibia: β = 0.371, P < .0001; femur: β = -0.327, P < .0001), (2) preoperative rotational limb alignment (β = 0.253, P = .001), (3) postoperative flexion angle (β = 0.195, P = .007), and (4) tibial torsion (β = 0.193, P = .010). In addition to component positions, the intrinsic factors, such as preoperative rotational limb alignment, ROM, and tibial torsion, affected postoperative rotational limb alignment. On a premise of correct component positions, the intrinsic factors that can be controlled by surgeons should be taken care. In particular, ROM is necessary to be improved within the possible range to acquire better postoperative rotational limb alignment. Copyright © 2018 Elsevier Inc. All rights reserved.

Fast and accurate phylogeny reconstruction using filtered spaced-word matches

PubMed Central

Sohrabi-Jahromi, Salma; Morgenstern, Burkhard

2017-01-01

Abstract Motivation: Word-based or ‘alignment-free’ algorithms are increasingly used for phylogeny reconstruction and genome comparison, since they are much faster than traditional approaches that are based on full sequence alignments. Existing alignment-free programs, however, are less accurate than alignment-based methods. Results: We propose Filtered Spaced Word Matches (FSWM), a fast alignment-free approach to estimate phylogenetic distances between large genomic sequences. For a pre-defined binary pattern of match and don’t-care positions, FSWM rapidly identifies spaced word-matches between input sequences, i.e. gap-free local alignments with matching nucleotides at the match positions and with mismatches allowed at the don’t-care positions. We then estimate the number of nucleotide substitutions per site by considering the nucleotides aligned at the don’t-care positions of the identified spaced-word matches. To reduce the noise from spurious random matches, we use a filtering procedure where we discard all spaced-word matches for which the overall similarity between the aligned segments is below a threshold. We show that our approach can accurately estimate substitution frequencies even for distantly related sequences that cannot be analyzed with existing alignment-free methods; phylogenetic trees constructed with FSWM distances are of high quality. A program run on a pair of eukaryotic genomes of a few hundred Mb each takes a few minutes. Availability and Implementation: The program source code for FSWM including a documentation, as well as the software that we used to generate artificial genome sequences are freely available at http://fswm.gobics.de/ Contact: chris.leimeister@stud.uni-goettingen.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28073754

Fast and accurate phylogeny reconstruction using filtered spaced-word matches.

PubMed

Leimeister, Chris-André; Sohrabi-Jahromi, Salma; Morgenstern, Burkhard

2017-04-01

Word-based or 'alignment-free' algorithms are increasingly used for phylogeny reconstruction and genome comparison, since they are much faster than traditional approaches that are based on full sequence alignments. Existing alignment-free programs, however, are less accurate than alignment-based methods. We propose Filtered Spaced Word Matches (FSWM) , a fast alignment-free approach to estimate phylogenetic distances between large genomic sequences. For a pre-defined binary pattern of match and don't-care positions, FSWM rapidly identifies spaced word-matches between input sequences, i.e. gap-free local alignments with matching nucleotides at the match positions and with mismatches allowed at the don't-care positions. We then estimate the number of nucleotide substitutions per site by considering the nucleotides aligned at the don't-care positions of the identified spaced-word matches. To reduce the noise from spurious random matches, we use a filtering procedure where we discard all spaced-word matches for which the overall similarity between the aligned segments is below a threshold. We show that our approach can accurately estimate substitution frequencies even for distantly related sequences that cannot be analyzed with existing alignment-free methods; phylogenetic trees constructed with FSWM distances are of high quality. A program run on a pair of eukaryotic genomes of a few hundred Mb each takes a few minutes. The program source code for FSWM including a documentation, as well as the software that we used to generate artificial genome sequences are freely available at http://fswm.gobics.de/. chris.leimeister@stud.uni-goettingen.de. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

How Near is a Near-Optimal Solution: Confidence Limits for the Global Optimum.

DTIC Science & Technology

1980-05-01

or near-optimal solutions are the only practical solutions available. This paper identifies and compares some procedures which use independent near...approximate or near-optimal solutions are the only practical solutions available. This paper identifies and compares some procedures which use inde- pendent...The objective of this paper is to indicate some relatively new statistical procedures for obtaining an upper confidence limit on G Each of these

Numerical modeling and optimization of the Iguassu gas centrifuge

NASA Astrophysics Data System (ADS)

Bogovalov, S. V.; Borman, V. D.; Borisevich, V. D.; Tronin, V. N.; Tronin, I. V.

2017-07-01

The full procedure of the numerical calculation of the optimized parameters of the Iguassu gas centrifuge (GC) is under discussion. The procedure consists of a few steps. On the first step the problem of a hydrodynamical flow of the gas in the rotating rotor of the GC is solved numerically. On the second step the problem of diffusion of the binary mixture of isotopes is solved. The separation power of the gas centrifuge is calculated after that. On the last step the time consuming procedure of optimization of the GC is performed providing us the maximum of the separation power. The optimization is based on the BOBYQA method exploring the results of numerical simulations of the hydrodynamics and diffusion of the mixture of isotopes. Fast convergence of calculations is achieved due to exploring of a direct solver at the solution of the hydrodynamical and diffusion parts of the problem. Optimized separative power and optimal internal parameters of the Iguassu GC with 1 m rotor were calculated using the developed approach. Optimization procedure converges in 45 iterations taking 811 minutes.

Experimental Estimation of CLASP Spatial Resolution: Results of the Instrument's Optical Alignment

NASA Technical Reports Server (NTRS)

Giono, Gabrial; Katsukawa, Yukio; Ishikawa, Ryoko; Narukage, Noriyuki; Bando, Takamasa; Kano, Ryohei; Suematsu, Yoshinori; Kobayashi, Ken; Winebarger, Amy; Auchere, Frederic

2015-01-01

The Chromospheric Lyman-Alpha SpectroPolarimeter (CLASP) is a sounding-rocket experiment currently being built at the National Astronomical Observatory of Japan. This instrument aims to probe for the first time the magnetic field strength and orientation in the solar upper-chromosphere and lower-transition region. CLASP will measure the polarization of the Lyman-Alpha line (121.6nm) with an unprecedented accuracy, and derive the magnetic field information through the Hanle effect. Although polarization accuracy and spectral resolution are crucial for the Hanle effect detection, spatial resolution is also important to get reliable context image via the slit-jaw camera. As spatial resolution is directly related with the alignment of optics, it is also a good way of ensuring the alignment of the instrument to meet the scientific requirement. This poster will detail the experiments carried out to align CLASP's optics (telescope and spectrograph), as both part of the instrument were aligned separately. The telescope was aligned in double-pass mode, and a laser interferometer (He-Ne) was used to measure the telescope's wavefront error (WFE). The secondary mirror tilt and position were adjusted to remove comas and defocus aberrations from the WFE. Effect of gravity on the WFE measurement was estimated and the final WFE derived in zero-g condition for CLASP telescope will be presented. In addition, an estimation of the spot shape and size derived from the final WFE will also be shown. The spectrograph was aligned with a custom procedure: because Ly-??light is absorbed by air, the spectrograph's off-axis parabolic mirrors were aligned in Visible Light (VL) using a custom-made VL grating instead of the flight Ly-? grating. Results of the alignment in Visible Light will be shown and the spot shape recorded with CCDs at various position along the slit will be displayed. Results from both alignment experiment will be compared to the design requirement, and will be combined in order to estimate CLASP spatial resolution after its alignment in visible light.

A Multicenter Radiographic Evaluation of the Rates of Preoperative and Postoperative Malalignment in Degenerative Spinal Fusions.

PubMed

Leveque, Jean-Christophe A; Segebarth, Bradley; Schroerlucke, Samuel R; Khanna, Nitin; Pollina, John; Youssef, Jim A; Tohmeh, Antoine G; Uribe, Juan S

2018-07-01

Multicenter, retrospective, institutional-review-board -approved study at 18 institutions in the United States with 24 treating investigators. This study was designed to retrospectively assess the prevalence of spinopelvic malalignment in patients who underwent one- or two-level lumbar fusions for degenerative (nondeformity) indications and to assess the incidence of malalignment after fusion surgery as well as the rate of alignment preservation and/or correction in this population. Spinopelvic malalignment after lumbar fusion has been associated with lower postoperative health-related quality of life and elevated risk of adjacent segment failure. The prevalence of spinopelvic malalignment in short-segment degenerative lumbar fusion procedures from a large sample of patients is heretofore unreported and may lead to an under-appreciation of these factors in surgical planning and ultimate preservation or correction of alignment. Lateral preoperative and postoperative lumbar radiographs were retrospectively acquired from 578 one- or two-level lumbar fusion patients and newly measured for lumbar lordosis (LL), pelvic incidence (PI), and pelvic tilt. Patients were categorized at preop and postop time points as aligned if PI-LL < 10° or malaligned if PI-LL≥10°. Patients were grouped into categories based on their alignment progression from pre- to postoperative, with preserved (aligned to aligned), restored (malaligned to aligned), not corrected (malaligned to malaligned), and worsened (aligned to malaligned) designations. Preoperatively, 173 (30%) patients exhibited malalignment. Postoperatively, 161 (28%) of patients were malaligned. Alignment was preserved in 63%, restored in 9%, not corrected in 21%, and worsened in 7% of patients. This is the first multicenter study to evaluate the preoperative prevalence and postoperative incidence of spinopelvic malalignment in a large series of short-segment degenerative lumbar fusions, finding over 25% of patients out of alignment at both time points, suggesting that alignment preservation/restoration considerations should be incorporated into the decision-making of even degenerative lumbar spinal fusions. 3.

Filament Winding Multifunctional Carbon Nanotube Composites of Various Dimensionality

NASA Astrophysics Data System (ADS)

Wells, Brian David

Carbon nanotubes (CNT) have been long considered an optimal material for composites due to their high strength, high modulus, and electrical/thermal conductivity. These composite materials have the potential to be used in the aerospace, computer, automotive, medical industry as well as many others. The nano dimensions of these structures make controlled alignment and distribution difficult using many production techniques. An area that shows promise for controlled alignment is the formation of CNT yarns. Different approaches have been used to create yarns with various winding angles and diameters. CNTs resemble traditional textile fiber structures due to their one-dimensional dimensions, axial strength and radial flexibility. One difference is, depending on the length, CNTs can have aspect ratios that far exceed those of traditional textile fibers. This can complicate processing techniques and cause agglomeration which prevents optimal structures from being created. However, with specific aspect ratios and spatial distributions a specific type of CNT, vertically aligned spinnable carbon nanotubes (VASCNTs), have interesting properties that allow carbon nanotubes to be drawn from an array in a continuous aligned web. This dissertation examines the feasibility of combining VASCNTs with another textile manufacturing process, filament winding, to create structures with various levels of dimensionality. While yarn formation with CNTs has been largely studied, there has not been significant work studying the use of VASCNTs to create composite materials. The studies that have been produces revolve around mixing CNTs into epoxy or creating uni-directional wound structures. In this dissertation VASCNTs are used to create filament wound materials with various degrees of alignment. These structures include 1 dimensional coatings applied to non-conductive polymer monofilaments, two dimensional multifunctional adhesive films, and three dimensional hybrid-nano composites. The angle of alignment between the individual CNTs relative to the overall structure was used to affect the electrical properties in all of these structures and the mechanical properties of the adhesive films and hybrid-nano composites. Varying the concentration of CNT was also found to have a significant effect on the electrical and mechanical properties. The variable properties that can be created with these production techniques allow users to engineer the structure to match the desired property.

CMSA: a heterogeneous CPU/GPU computing system for multiple similar RNA/DNA sequence alignment.

PubMed

Chen, Xi; Wang, Chen; Tang, Shanjiang; Yu, Ce; Zou, Quan

2017-06-24

The multiple sequence alignment (MSA) is a classic and powerful technique for sequence analysis in bioinformatics. With the rapid growth of biological datasets, MSA parallelization becomes necessary to keep its running time in an acceptable level. Although there are a lot of work on MSA problems, their approaches are either insufficient or contain some implicit assumptions that limit the generality of usage. First, the information of users' sequences, including the sizes of datasets and the lengths of sequences, can be of arbitrary values and are generally unknown before submitted, which are unfortunately ignored by previous work. Second, the center star strategy is suited for aligning similar sequences. But its first stage, center sequence selection, is highly time-consuming and requires further optimization. Moreover, given the heterogeneous CPU/GPU platform, prior studies consider the MSA parallelization on GPU devices only, making the CPUs idle during the computation. Co-run computation, however, can maximize the utilization of the computing resources by enabling the workload computation on both CPU and GPU simultaneously. This paper presents CMSA, a robust and efficient MSA system for large-scale datasets on the heterogeneous CPU/GPU platform. It performs and optimizes multiple sequence alignment automatically for users' submitted sequences without any assumptions. CMSA adopts the co-run computation model so that both CPU and GPU devices are fully utilized. Moreover, CMSA proposes an improved center star strategy that reduces the time complexity of its center sequence selection process from O(mn 2 ) to O(mn). The experimental results show that CMSA achieves an up to 11× speedup and outperforms the state-of-the-art software. CMSA focuses on the multiple similar RNA/DNA sequence alignment and proposes a novel bitmap based algorithm to improve the center star strategy. We can conclude that harvesting the high performance of modern GPU is a promising approach to accelerate multiple sequence alignment. Besides, adopting the co-run computation model can maximize the entire system utilization significantly. The source code is available at https://github.com/wangvsa/CMSA .

RNA-Skim: a rapid method for RNA-Seq quantification at transcript level

PubMed Central

Zhang, Zhaojun; Wang, Wei

2014-01-01

Motivation: RNA-Seq technique has been demonstrated as a revolutionary means for exploring transcriptome because it provides deep coverage and base pair-level resolution. RNA-Seq quantification is proven to be an efficient alternative to Microarray technique in gene expression study, and it is a critical component in RNA-Seq differential expression analysis. Most existing RNA-Seq quantification tools require the alignments of fragments to either a genome or a transcriptome, entailing a time-consuming and intricate alignment step. To improve the performance of RNA-Seq quantification, an alignment-free method, Sailfish, has been recently proposed to quantify transcript abundances using all k-mers in the transcriptome, demonstrating the feasibility of designing an efficient alignment-free method for transcriptome quantification. Even though Sailfish is substantially faster than alternative alignment-dependent methods such as Cufflinks, using all k-mers in the transcriptome quantification impedes the scalability of the method. Results: We propose a novel RNA-Seq quantification method, RNA-Skim, which partitions the transcriptome into disjoint transcript clusters based on sequence similarity, and introduces the notion of sig-mers, which are a special type of k-mers uniquely associated with each cluster. We demonstrate that the sig-mer counts within a cluster are sufficient for estimating transcript abundances with accuracy comparable with any state-of-the-art method. This enables RNA-Skim to perform transcript quantification on each cluster independently, reducing a complex optimization problem into smaller optimization tasks that can be run in parallel. As a result, RNA-Skim uses <4% of the k-mers and <10% of the CPU time required by Sailfish. It is able to finish transcriptome quantification in <10 min per sample by using just a single thread on a commodity computer, which represents >100 speedup over the state-of-the-art alignment-based methods, while delivering comparable or higher accuracy. Availability and implementation: The software is available at http://www.csbio.unc.edu/rs. Contact: weiwang@cs.ucla.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24931995

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

PubMed

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

2015-07-01

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