WorldWideScience

Sample records for accurate molecular alignment

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

    International Nuclear Information System (INIS)

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

    2011-01-01

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

  2. Prediction of molecular alignment of nucleic acids in aligned media

    International Nuclear Information System (INIS)

    Wu Bin; Petersen, Michael; Girard, Frederic; Tessari, Marco; Wijmenga, Sybren S.

    2006-01-01

    We demonstrate - using the data base of all deposited DNA and RNA structures aligned in Pf1-medium and RDC refined - that for nucleic acids in a Pf1-medium the electrostatic alignment tensor can be predicted reliably and accurately via a simple and fast calculation based on the gyration tensor spanned out by the phosphodiester atoms. The rhombicity is well predicted over its full range from 0 to 0.66, while the alignment tensor orientation is predicted correctly for rhombicities up to ca. 0.4, for larger rhombicities it appears to deviate somewhat more than expected based on structural noise and measurement error. This simple analytical approach is based on the Debye-Huckel approximation for the electrostatic interaction potential, valid at distances sufficiently far away from a poly-ionic charged surface, a condition naturally enforced when the charge of alignment medium and solute are of equal sign, as for nucleic acids in a Pf1-phage medium. For the usual salt strengths and nucleic acid sizes, the Debye-Huckel screening length is smaller than the nucleic acid size, but large enough for the collective of Debye-Huckel spheres to encompass the whole molecule. The molecular alignment is then purely electrostatic, but it's functional form is under these conditions similar to that for steric alignment. The proposed analytical expression allows for very fast calculation of the alignment tensor and hence RDCs from the conformation of the nucleic acid molecule. This information provides opportunities for improved structure determination of nucleic acids, including better assessment of dynamics in (multi-domain) nucleic acids and the possibility to incorporate alignment tensor prediction from shape directly into the structure calculation process. The procedures are incorporated into MATLAB scripts, which are available on request

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

    Science.gov (United States)

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

    2009-07-01

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

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

    DEFF Research Database (Denmark)

    Lu, David V; Brown, Randall H; Arumugam, Manimozhiyan

    2009-01-01

    MOTIVATION: The most accurate way to determine the intron-exon structures in a genome is to align spliced cDNA sequences to the genome. Thus, cDNA-to-genome alignment programs are a key component of most annotation pipelines. The scoring system used to choose the best alignment is a primary...... determinant of alignment accuracy, while heuristics that prevent consideration of certain alignments are a primary determinant of runtime and memory usage. Both accuracy and speed are important considerations in choosing an alignment algorithm, but scoring systems have received much less attention than...

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

    Science.gov (United States)

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

    2012-01-01

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

  6. Accurate and robust brain image alignment using boundary-based registration.

    Science.gov (United States)

    Greve, Douglas N; Fischl, Bruce

    2009-10-15

    The fine spatial scales of the structures in the human brain represent an enormous challenge to the successful integration of information from different images for both within- and between-subject analysis. While many algorithms to register image pairs from the same subject exist, visual inspection shows that their accuracy and robustness to be suspect, particularly when there are strong intensity gradients and/or only part of the brain is imaged. This paper introduces a new algorithm called Boundary-Based Registration, or BBR. The novelty of BBR is that it treats the two images very differently. The reference image must be of sufficient resolution and quality to extract surfaces that separate tissue types. The input image is then aligned to the reference by maximizing the intensity gradient across tissue boundaries. Several lower quality images can be aligned through their alignment with the reference. Visual inspection and fMRI results show that BBR is more accurate than correlation ratio or normalized mutual information and is considerably more robust to even strong intensity inhomogeneities. BBR also excels at aligning partial-brain images to whole-brain images, a domain in which existing registration algorithms frequently fail. Even in the limit of registering a single slice, we show the BBR results to be robust and accurate.

  7. Molecular-alignment dependence in the transfer excitation of H2

    International Nuclear Information System (INIS)

    Wang, Y.D.; McGuire, J.H.; Weaver, O.L.; Corchs, S.E.; Rivarola, R.D.

    1993-01-01

    Molecular-alignment effects in the transfer excitation of H 2 by high-velocity heavy ions are studied using a two-step mechanism with amplitudes evaluated from first-order perturbation theory. Two-electron transfer excitation is treated as a result of two independent collision processes (excitation and electron transfer). Cross sections for each one-electron subprocess as well as the combined two-electron process are calculated as functions of the molecular-alignment angle. Within the independent-electron approximation, the dynamic roles of electron excitation and transfer in conjunction with molecular alignment are explored. While both excitation and transfer cross sections may strongly depend on molecular alignment, it is electron transfer that is largely responsible for the molecular-alignment dependence in the transfer excitation process. Interpretation of some experimental observations based on this model will also be discussed

  8. How accurate is anatomic limb alignment in predicting mechanical limb alignment after total knee arthroplasty?

    Science.gov (United States)

    Lee, Seung Ah; Choi, Sang-Hee; Chang, Moon Jong

    2015-10-27

    Anatomic limb alignment often differs from mechanical limb alignment after total knee arthroplasty (TKA). We sought to assess the accuracy, specificity, and sensitivity for each of three commonly used ranges for anatomic limb alignment (3-9°, 5-10° and 2-10°) in predicting an acceptable range (neutral ± 3°) for mechanical limb alignment after TKA. We also assessed whether the accuracy of anatomic limb alignment was affected by anatomic variation. This retrospective study included 314 primary TKAs. The alignment of the limb was measured with both anatomic and mechanical methods of measurement. We also measured anatomic variation, including the femoral bowing angle, tibial bowing angle, and neck-shaft angle of the femur. All angles were measured on the same full-length standing anteroposterior radiographs. The accuracy, specificity, and sensitivity for each range of anatomic limb alignment were calculated and compared using mechanical limb alignment as the reference standard. The associations between the accuracy of anatomic limb alignment and anatomic variation were also determined. The range of 2-10° for anatomic limb alignment showed the highest accuracy, but it was only 73 % (3-9°, 65 %; 5-10°, 67 %). The specificity of the 2-10° range was 81 %, which was higher than that of the other ranges (3-9°, 69 %; 5-10°, 67 %). However, the sensitivity of the 2-10° range to predict varus malalignment was only 16 % (3-9°, 35 %; 5-10°, 68 %). In addition, the sensitivity of the 2-10° range to predict valgus malalignment was only 43 % (3-9°, 71 %; 5-10°, 43 %). The accuracy of anatomical limb alignment was lower for knees with greater femoral (odds ratio = 1.2) and tibial (odds ratio = 1.2) bowing. Anatomic limb alignment did not accurately predict mechanical limb alignment after TKA, and its accuracy was affected by anatomic variation. Thus, alignment after TKA should be assessed by measuring mechanical alignment rather than anatomic

  9. Improved fingercode alignment for accurate and compact fingerprint recognition

    CSIR Research Space (South Africa)

    Brown, Dane

    2016-05-01

    Full Text Available Alignment for Accurate and Compact Fingerprint Recognition Dane Brown∗† and Karen Bradshaw∗ ∗Department of Computer Science Rhodes University Grahamstown, South Africa †Council for Scientific and Industrial Research Modelling and Digital Sciences Pretoria.... The experimental analysis and results are discussed in Section IV. Section V concludes the paper. II. RELATED STUDIES FingerCode [1] uses circular tessellation of filtered finger- print images centered at the reference point, which results in a circular ROI...

  10. Angular momentum alignment in molecular beam scattering

    International Nuclear Information System (INIS)

    Treffers, M.A.

    1985-01-01

    It is shown how the angular momentum alignment in a molecular beam can be determined using laser-induced fluorescence in combination with precession of the angular momenta in a magnetic field. After a general analysis of the method, some results are presented to illustrate the possibilities of the method. Experimental data are presented on the alignment production for Na 2 molecules that made a collision induced angular momentum transition. Magnitude as well as direction of the alignment have been determined for scattering with several scattering partners and for a large number of scattering angles and transitions. The last chapter deals with the total alignment production in a final J-state, i.e. without state selection of the initial rotational state. (orig.)

  11. Flexible, fast and accurate sequence alignment profiling on GPGPU with PaSWAS.

    Directory of Open Access Journals (Sweden)

    Sven Warris

    Full Text Available To obtain large-scale sequence alignments in a fast and flexible way is an important step in the analyses of next generation sequencing data. Applications based on the Smith-Waterman (SW algorithm are often either not fast enough, limited to dedicated tasks or not sufficiently accurate due to statistical issues. Current SW implementations that run on graphics hardware do not report the alignment details necessary for further analysis.With the Parallel SW Alignment Software (PaSWAS it is possible (a to have easy access to the computational power of NVIDIA-based general purpose graphics processing units (GPGPUs to perform high-speed sequence alignments, and (b retrieve relevant information such as score, number of gaps and mismatches. The software reports multiple hits per alignment. The added value of the new SW implementation is demonstrated with two test cases: (1 tag recovery in next generation sequence data and (2 isotype assignment within an immunoglobulin 454 sequence data set. Both cases show the usability and versatility of the new parallel Smith-Waterman implementation.

  12. Flexible, fast and accurate sequence alignment profiling on GPGPU with PaSWAS.

    Science.gov (United States)

    Warris, Sven; Yalcin, Feyruz; Jackson, Katherine J L; Nap, Jan Peter

    2015-01-01

    To obtain large-scale sequence alignments in a fast and flexible way is an important step in the analyses of next generation sequencing data. Applications based on the Smith-Waterman (SW) algorithm are often either not fast enough, limited to dedicated tasks or not sufficiently accurate due to statistical issues. Current SW implementations that run on graphics hardware do not report the alignment details necessary for further analysis. With the Parallel SW Alignment Software (PaSWAS) it is possible (a) to have easy access to the computational power of NVIDIA-based general purpose graphics processing units (GPGPUs) to perform high-speed sequence alignments, and (b) retrieve relevant information such as score, number of gaps and mismatches. The software reports multiple hits per alignment. The added value of the new SW implementation is demonstrated with two test cases: (1) tag recovery in next generation sequence data and (2) isotype assignment within an immunoglobulin 454 sequence data set. Both cases show the usability and versatility of the new parallel Smith-Waterman implementation.

  13. Flexible, fast and accurate sequence alignment profiling on GPGPU with PaSWAS

    NARCIS (Netherlands)

    Warris, S.; Yalcin, F.; Jackson, K.J.; Nap, J.P.H.

    2015-01-01

    Motivation To obtain large-scale sequence alignments in a fast and flexible way is an important step in the analyses of next generation sequencing data. Applications based on the Smith-Waterman (SW) algorithm are often either not fast enough, limited to dedicated tasks or not sufficiently accurate

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

    Energy Technology Data Exchange (ETDEWEB)

    Bushnell, Brian

    2014-03-17

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

  15. A practical strategy for the accurate measurement of residual dipolar couplings in strongly aligned small molecules

    Science.gov (United States)

    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.

  16. Accessing the molecular frame through strong-field alignment of distributions of gas phase molecules

    Science.gov (United States)

    Reid, Katharine L.

    2018-03-01

    A rationale for creating highly aligned distributions of molecules is that it enables vector properties referenced to molecule-fixed axes (the molecular frame) to be determined. In the present work, the degree of alignment that is necessary for this to be achieved in practice is explored. Alignment is commonly parametrized in experiments by a single parameter, ?, which is insufficient to enable predictive calculations to be performed. Here, it is shown that, if the full distribution of molecular axes takes a Gaussian form, this single parameter can be used to determine the complete set of alignment moments needed to characterize the distribution. In order to demonstrate the degree of alignment that is required to approach the molecular frame, the alignment moments corresponding to a few chosen values of ? are used to project a model molecular frame photoelectron angular distribution into the laboratory frame. These calculations show that ? needs to approach 0.9 in order to avoid significant blurring to be caused by averaging. This article is part of the theme issue `Modern theoretical chemistry'.

  17. Identification of BKCa channel openers by molecular field alignment and patent data-driven analysis

    Directory of Open Access Journals (Sweden)

    Yaseen Gigani

    2016-01-01

    Full Text Available In this work, we present the first comprehensive molecular field analysis of patent structures on how the chemical structure of drugs impacts the biological binding. This task was formulated as searching for drug structures to reveal shared effects of substitutions across a common scaffold and the chemical features that may be responsible. We used the SureChEMBL patent database, which provides search of the patent literature using keyword-based functionality, as a query engine. The extraction of data of the BKCa channel openers and aligning them for molecular field similarity with newly designed structures did provide a probable validation method with accurate values. Therefore, in an attempt to increase the true positives, we report a procedure that functions on a multiple analyses modeled on molecular field similarity and common sub-structural search with consensus scoring and high confidence values to obtain greater accuracy during conventional virtual screening.

  18. Molecular alignment dependent electron interference in attosecond ultraviolet photoionization

    Directory of Open Access Journals (Sweden)

    Kai-Jun Yuan

    2015-01-01

    Full Text Available We present molecular photoionization processes by intense attosecond ultraviolet laser pulses from numerical solutions of time-dependent Schrödinger equations. Simulations preformed on a single electron diatomic H2+ show minima in molecular photoelectron energy spectra resulting from two center interference effects which depend strongly on molecular alignment. We attribute such sensitivity to the spatial orientation asymmetry of the photoionization process from the two nuclei. A similar influence on photoelectron kinetic energies is also presented.

  19. Molecular alignment dependent electron interference in attosecond ultraviolet photoionization

    Science.gov (United States)

    Yuan, Kai-Jun; Bandrauk, André D.

    2015-01-01

    We present molecular photoionization processes by intense attosecond ultraviolet laser pulses from numerical solutions of time-dependent Schrödinger equations. Simulations preformed on a single electron diatomic H2+ show minima in molecular photoelectron energy spectra resulting from two center interference effects which depend strongly on molecular alignment. We attribute such sensitivity to the spatial orientation asymmetry of the photoionization process from the two nuclei. A similar influence on photoelectron kinetic energies is also presented. PMID:26798785

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-08-14

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

  1. Fermi level alignment in molecular nanojunctions and its relation to charge transfer

    DEFF Research Database (Denmark)

    Stadler, Robert; Jacobsen, Karsten Wedel

    2006-01-01

    The alignment of the Fermi level of a metal electrode within the gap of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of a molecule is a key quantity in molecular electronics, which can vary the electron transparency of a single-molecule junction...... by orders of magnitude. We present a quantitative analysis of the relation between this level alignment (which can be estimated from charging free molecules) and charge transfer for bipyridine and biphenyl dithiolate (BPDT) molecules attached to gold leads based on density functional theory calculations...... end of the gap in the transmission function for bipyridine and at its lower end for BPDT....

  2. Rapid detection, classification and accurate alignment of up to a million or more related protein sequences.

    Science.gov (United States)

    Neuwald, Andrew F

    2009-08-01

    The patterns of sequence similarity and divergence present within functionally diverse, evolutionarily related proteins contain implicit information about corresponding biochemical similarities and differences. A first step toward accessing such information is to statistically analyze these patterns, which, in turn, requires that one first identify and accurately align a very large set of protein sequences. Ideally, the set should include many distantly related, functionally divergent subgroups. Because it is extremely difficult, if not impossible for fully automated methods to align such sequences correctly, researchers often resort to manual curation based on detailed structural and biochemical information. However, multiply-aligning vast numbers of sequences in this way is clearly impractical. This problem is addressed using Multiply-Aligned Profiles for Global Alignment of Protein Sequences (MAPGAPS). The MAPGAPS program uses a set of multiply-aligned profiles both as a query to detect and classify related sequences and as a template to multiply-align the sequences. It relies on Karlin-Altschul statistics for sensitivity and on PSI-BLAST (and other) heuristics for speed. Using as input a carefully curated multiple-profile alignment for P-loop GTPases, MAPGAPS correctly aligned weakly conserved sequence motifs within 33 distantly related GTPases of known structure. By comparison, the sequence- and structurally based alignment methods hmmalign and PROMALS3D misaligned at least 11 and 23 of these regions, respectively. When applied to a dataset of 65 million protein sequences, MAPGAPS identified, classified and aligned (with comparable accuracy) nearly half a million putative P-loop GTPase sequences. A C++ implementation of MAPGAPS is available at http://mapgaps.igs.umaryland.edu. Supplementary data are available at Bioinformatics online.

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

    Science.gov (United States)

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

    2016-02-01

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

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

    Science.gov (United States)

    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.

  5. Accurate marker-free alignment with simultaneous geometry determination and reconstruction of tilt series in electron tomography

    International Nuclear Information System (INIS)

    Winkler, Hanspeter; Taylor, Kenneth A.

    2006-01-01

    An image alignment method for electron tomography is presented which is based on cross-correlation techniques and which includes a simultaneous refinement of the tilt geometry. A coarsely aligned tilt series is iteratively refined with a procedure consisting of two steps for each cycle: area matching and subsequent geometry correction. The first step, area matching, brings into register equivalent specimen regions in all images of the tilt series. It determines four parameters of a linear two-dimensional transformation, not just translation and rotation as is done during the preceding coarse alignment with conventional methods. The refinement procedure also differs from earlier methods in that the alignment references are now computed from already aligned images by reprojection of a backprojected volume. The second step, geometry correction, refines the initially inaccurate estimates of the geometrical parameters, including the direction of the tilt axis, a tilt angle offset, and the inclination of the specimen with respect to the support film or specimen holder. The correction values serve as an indicator for the progress of the refinement. For each new iteration, the correction values are used to compute an updated set of geometry parameters by a least squares fit. Model calculations show that it is essential to refine the geometrical parameters as well as the accurate alignment of the images to obtain a faithful map of the original structure

  6. Conductance of Conjugated Molecular Wires: Length Dependence, Anchoring Groups, and Band Alignment

    DEFF Research Database (Denmark)

    Peng, Guowen; Strange, Mikkel; Thygesen, Kristian Sommer

    2009-01-01

    , is not solely determined by the intrinsic band gap of the molecular wire but also depends on the anchoring group. This is because the alignment of the metal Fermi level with respect to the molecular levels is controlled by charge transfer and interface dipoles which in turn are determined by the local chemistry...

  7. Effect of Internal Heteroatoms on Level Alignment at Metal/Molecular Monolayer/Si Interfaces

    NARCIS (Netherlands)

    Alon, Hadas; Garrick, Rachel; Pujari, Sidharam P.; Toledano, Tal; Sinai, Ofer; Kedem, Nir; Bendikov, Tatyana; Baio, Joe E.; Weidner, Tobias; Zuilhof, Han; Cahen, David; Kronik, Leeor; Sukenik, Chaim N.; Vilan, Ayelet

    2018-01-01

    Molecular monolayers at metal/semiconductor heterointerfaces affect electronic energy level alignment at the interface by modifying the interface's electrical dipole. On a free surface, the molecular dipole is usually manipulated by means of substitution at its external end. However, at an interface

  8. Importance of molecular diagnosis in the accurate diagnosis of ...

    Indian Academy of Sciences (India)

    1Department of Health and Environmental Sciences, Kyoto University Graduate School of Medicine, Yoshida Konoecho, ... of molecular diagnosis in the accurate diagnosis of systemic carnitine deficiency. .... 'affecting protein function' by SIFT.

  9. Molecular structure determination from x-ray scattering patterns of laser-aligned symmetric-top molecules

    International Nuclear Information System (INIS)

    Ho, P. J.; Starodub, D.; Saldin, D. K.; Shneerson, V. L.; Ourmazd, A.; Santra, R.

    2009-01-01

    We investigate the molecular structure information contained in the x-ray diffraction patterns of an ensemble of rigid CF 3 Br molecules aligned by an intense laser pulse at finite rotational temperature. The diffraction patterns are calculated at an x-ray photon energy of 20 keV to probe molecular structure at angstrom-scale resolution. We find that a structural reconstruction algorithm based on iterative phase retrieval fails to extract a reliable structure. However, the high atomic number of Br compared with C or F allows each diffraction pattern to be treated as a hologram. Using this approach, the azimuthal projection of the molecular electron density about the alignment axis may be retrieved.

  10. Field-free molecular alignment probed by the free electron laser in Hamburg (FLASH)

    Energy Technology Data Exchange (ETDEWEB)

    Johnsson, P; Rouzee, A; Siu, W; Huismans, Y; Vrakking, M J J [FOM Institute for Atomic and Molecular Physics (AMOLF), Science Park 113, 1098 XG Amsterdam (Netherlands); Lepine, F [Universite Lyon 1, CNRS, LASIM, UMR 5579, 43 bvd. du 11 novembre 1918, F-69622 Villeurbanne (France); Marchenko, T [Laboratoire d' Optique Applique, ENSTA/Ecole Polytechnique, Chemin de la Huniere, 91761 Palaiseau (France); Duesterer, S; Tavella, F; Stojanovic, N; Azima, A; Treusch, R [Hamburger Synchrotronstrahlungslabor (HASYLAB) at Deutsches Elektronen-Synchrotron (DESY) Notkestrasse 85, D-22607 Hamburg (Germany); Kling, M F [Max-Planck Institut fuer Quantenoptik, Hans-Kopfermann Strasse 1, D-85748 Garching (Germany)], E-mail: per.johnsson@fysik.lth.se

    2009-07-14

    High flux extreme ultraviolet (XUV) sources like the free electron laser (FEL) in Hamburg (FLASH) offer the possibility of diffractive imaging of small objects. Irrespective of whether the diffraction is based on the detection of photons or photoelectrons, it is required that the measurement is done in the reference frame of the molecule meaning that, for a sample of several molecules, it is necessary to pre-align the molecules in the sample. As a step towards performing molecular frame diffraction experiments, we report experiments on field-free molecular alignment performed at FLASH. The impulsive alignment induced by a 100 fs near-infrared laser pulse in a rotationally cold CO{sub 2} sample is characterized by ionizing and dissociating the molecules with a time-delayed XUV-FEL pulse. The time-dependent angular distributions of ionic fragments measured by a velocity map imaging spectrometer exhibit rapid changes associated with the induced rotational dynamics. The experimental results show hints of a dissociation process that depends nonlinearly on the XUV intensity.

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

    Science.gov (United States)

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

    2015-01-01

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

  12. Quasiparticle Level Alignment for Photocatalytic Interfaces.

    Science.gov (United States)

    Migani, Annapaoala; Mowbray, Duncan J; Zhao, Jin; Petek, Hrvoje; Rubio, Angel

    2014-05-13

    Electronic level alignment at the interface between an adsorbed molecular layer and a semiconducting substrate determines the activity and efficiency of many photocatalytic materials. Standard density functional theory (DFT)-based methods have proven unable to provide a quantitative description of this level alignment. This requires a proper treatment of the anisotropic screening, necessitating the use of quasiparticle (QP) techniques. However, the computational complexity of QP algorithms has meant a quantitative description of interfacial levels has remained elusive. We provide a systematic study of a prototypical interface, bare and methanol-covered rutile TiO2(110) surfaces, to determine the type of many-body theory required to obtain an accurate description of the level alignment. This is accomplished via a direct comparison with metastable impact electron spectroscopy (MIES), ultraviolet photoelectron spectroscopy (UPS), and two-photon photoemission (2PP) spectroscopy. We consider GGA DFT, hybrid DFT, and G0W0, scQPGW1, scQPGW0, and scQPGW QP calculations. Our results demonstrate that G0W0, or our recently introduced scQPGW1 approach, are required to obtain the correct alignment of both the highest occupied and lowest unoccupied interfacial molecular levels (HOMO/LUMO). These calculations set a new standard in the interpretation of electronic structure probe experiments of complex organic molecule/semiconductor interfaces.

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

    Science.gov (United States)

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

    2013-07-01

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

  14. Alignment of Gold Nanoparticle-Decorated DNA Origami Nanotubes: Substrate Prepatterning versus Molecular Combing.

    Science.gov (United States)

    Teschome, Bezu; Facsko, Stefan; Gothelf, Kurt V; Keller, Adrian

    2015-11-24

    DNA origami has become an established technique for designing well-defined nanostructures with any desired shape and for the controlled arrangement of functional nanostructures with few nanometer resolution. These unique features make DNA origami nanostructures promising candidates for use as scaffolds in nanoelectronics and nanophotonics device fabrication. Consequently, a number of studies have shown the precise organization of metallic nanoparticles on various DNA origami shapes. In this work, we fabricated large arrays of aligned DNA origami decorated with a high density of gold nanoparticles (AuNPs). To this end, we first demonstrate the high-yield assembly of high-density AuNP arrangements on DNA origami adsorbed to Si surfaces with few unbound background nanoparticles by carefully controlling the concentrations of MgCl2 and AuNPs in the hybridization buffer and the hybridization time. Then, we evaluate two methods, i.e., hybridization to prealigned DNA origami and molecular combing in a receding meniscus, with respect to their potential to yield large arrays of aligned AuNP-decorated DNA origami nanotubes. Because of the comparatively low MgCl2 concentration required for the efficient immobilization of the AuNPs, the prealigned DNA origami become mobile and displaced from their original positions, thereby decreasing the alignment yield. This increased mobility, on the other hand, makes the adsorbed origami susceptible to molecular combing, and a total alignment yield of 86% is obtained in this way.

  15. GraphAlignment: Bayesian pairwise alignment of biological networks

    Directory of Open Access Journals (Sweden)

    Kolář Michal

    2012-11-01

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

  16. Effect of the R dependence of laser-induced polarizability on molecular dynamic alignment in an intense femtosecond laser field

    International Nuclear Information System (INIS)

    Chen Jianxin; Cui Xiaomei; Huang Bomin; Wu Hongchun; Zhuo Shuangmu

    2006-01-01

    In the rotation equation of the angle θ between the molecular axis and the laser polarization direction, the dependence of laser-induced polarizability on the molecular internuclear distance R is considered. The effect of the R dependence of laser-induced polarizability on molecular dynamic alignment in an intense femtosecond laser field is investigated with 20 and 100 fs laser pulses for N 2 molecules and with 60 and 100 fs laser pulses for Br 2 molecules at intensities of 5x10 14 W cm -2 and 5x10 15 W cm -2 . This effect exists and only occurs during the dissociative process after the molecule is ionized. It enhances the degrees of molecular dynamic alignment and is more significant in reorienting the angular distributions of molecules towards the laser polarization direction in the conditions of high laser intensity and short pulse length. Compared with the N 2 molecule, the effect of the R dependence of laser-induced polarizability on molecular dynamic alignment for Br 2 is stronger. The reasons are presented and discussed

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

    Science.gov (United States)

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

    2012-07-15

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

  18. Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules

    Science.gov (United States)

    Wang, Xu; Le, Anh-Thu; Yu, Chao; Lucchese, R. R.; Lin, C. D.

    2016-01-01

    We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. A simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method. PMID:27025410

  19. Desktop aligner for fabrication of multilayer microfluidic devices.

    Science.gov (United States)

    Li, Xiang; Yu, Zeta Tak For; Geraldo, Dalton; Weng, Shinuo; Alve, Nitesh; Dun, Wu; Kini, Akshay; Patel, Karan; Shu, Roberto; Zhang, Feng; Li, Gang; Jin, Qinghui; Fu, Jianping

    2015-07-01

    Multilayer assembly is a commonly used technique to construct multilayer polydimethylsiloxane (PDMS)-based microfluidic devices with complex 3D architecture and connectivity for large-scale microfluidic integration. Accurate alignment of structure features on different PDMS layers before their permanent bonding is critical in determining the yield and quality of assembled multilayer microfluidic devices. Herein, we report a custom-built desktop aligner capable of both local and global alignments of PDMS layers covering a broad size range. Two digital microscopes were incorporated into the aligner design to allow accurate global alignment of PDMS structures up to 4 in. in diameter. Both local and global alignment accuracies of the desktop aligner were determined to be about 20 μm cm(-1). To demonstrate its utility for fabrication of integrated multilayer PDMS microfluidic devices, we applied the desktop aligner to achieve accurate alignment of different functional PDMS layers in multilayer microfluidics including an organs-on-chips device as well as a microfluidic device integrated with vertical passages connecting channels located in different PDMS layers. Owing to its convenient operation, high accuracy, low cost, light weight, and portability, the desktop aligner is useful for microfluidic researchers to achieve rapid and accurate alignment for generating multilayer PDMS microfluidic devices.

  20. Energy level alignment and molecular conformation at rubrene/Ag interfaces: Impact of contact contaminations on the interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Sinha, Sumona, E-mail: sumona.net.09@gmail.com [Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700064 (India); Wang, C.-H. [National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan (China); Mukherjee, M. [Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700064 (India)

    2017-07-01

    Highlights: • Impact of contact contaminations on the energy level alignment and molecular conformation at rubrene/Ag interfaces. • Adventitious contamination layer was acted as a spacer layer between Ag substrate surface and rubrene molecular layer. • Hole injection barrier height and interface dipole at rubrene/Ag interfaces depend on the cleanliness of Ag substrate. • Molecular conformation as well as orientation controlled by the cleanliness of Ag surface. • Resulted different surface morphology of rubrene thin films on unclean and clean Ag substrate. - Abstract: This paper addresses the impact of electrode contaminations on the interfacial energy level alignment, the molecular conformation, orientation and surface morphology deposited organic film at organic semiconductor/noble metal interfaces by varying of film thickness from sub-monolayer to multilayer, which currently draws significant attention with regard to its application in organic electronics. The UHV clean Ag and unclean Ag were employed as substrate whereas rubrene was used as an organic semiconducting material. The photoelectron spectroscopy (XPS and UPS) was engaged to investigate the evolution of interfacial energetics; polarization dependent near edge x-ray absorption fine structure spectroscopy (NEXAFS) was employed to understand the molecular conformation as well as orientation whereas atomic force microscopy (AFM) was used to investigate the surface morphologies of the films. The adventitious contamination layer was acted as a spacer layer between clean Ag substrate surface and rubrene molecular layer. As a consequence, hole injection barrier height, interface dipole as well as molecular-conformation, molecular-orientation and surface morphology of rubrene thin films were found to depend on the cleanliness of Ag substrate. The results have important inferences about the understanding of the impact of substrate contamination on the energy level alignment, the molecular conformation

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

    Science.gov (United States)

    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

  2. Quantum-Accurate Molecular Dynamics Potential for Tungsten

    Energy Technology Data Exchange (ETDEWEB)

    Wood, Mitchell; Thompson, Aidan P.

    2017-03-01

    The purpose of this short contribution is to report on the development of a Spectral Neighbor Analysis Potential (SNAP) for tungsten. We have focused on the characterization of elastic and defect properties of the pure material in order to support molecular dynamics simulations of plasma-facing materials in fusion reactors. A parallel genetic algorithm approach was used to efficiently search for fitting parameters optimized against a large number of objective functions. In addition, we have shown that this many-body tungsten potential can be used in conjunction with a simple helium pair potential1 to produce accurate defect formation energies for the W-He binary system.

  3. A statistically harmonized alignment-classification in image space enables accurate and robust alignment of noisy images in single particle analysis.

    Science.gov (United States)

    Kawata, Masaaki; Sato, Chikara

    2007-06-01

    In determining the three-dimensional (3D) structure of macromolecular assemblies in single particle analysis, a large representative dataset of two-dimensional (2D) average images from huge number of raw images is a key for high resolution. Because alignments prior to averaging are computationally intensive, currently available multireference alignment (MRA) software does not survey every possible alignment. This leads to misaligned images, creating blurred averages and reducing the quality of the final 3D reconstruction. We present a new method, in which multireference alignment is harmonized with classification (multireference multiple alignment: MRMA). This method enables a statistical comparison of multiple alignment peaks, reflecting the similarities between each raw image and a set of reference images. Among the selected alignment candidates for each raw image, misaligned images are statistically excluded, based on the principle that aligned raw images of similar projections have a dense distribution around the correctly aligned coordinates in image space. This newly developed method was examined for accuracy and speed using model image sets with various signal-to-noise ratios, and with electron microscope images of the Transient Receptor Potential C3 and the sodium channel. In every data set, the newly developed method outperformed conventional methods in robustness against noise and in speed, creating 2D average images of higher quality. This statistically harmonized alignment-classification combination should greatly improve the quality of single particle analysis.

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

    International Nuclear Information System (INIS)

    Sasuga, Tsuneo

    1978-01-01

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

  5. Molecular alignment effect on the photoassociation process via a pump-dump scheme

    Science.gov (United States)

    Wang, Bin-Bin; Han, Yong-Chang; Cong, Shu-Lin

    2015-09-01

    The photoassociation processes via the pump-dump scheme for the heternuclear (Na + H → NaH) and the homonuclear (Na + Na → Na2) molecular systems are studied, respectively, using the time-dependent quantum wavepacket method. For both systems, the initial atom pair in the continuum of the ground electronic state (X1Σ+) is associated into the molecule in the bound states of the excited state (A1Σ+) by the pump pulse. Then driven by a time-delayed dumping pulse, the prepared excited-state molecule can be transferred to the bound states of the ground electronic state. It is found that the pump process can induce a superposition of the rovibrational levels |v, j> on the excited state, which can lead to the field-free alignment of the excited-state molecule. The molecular alignment can affect the dumping process by varying the effective coupling intensity between the two electronic states or by varying the population transfer pathways. As a result, the final population transferred to the bound states of the ground electronic state varies periodically with the delay time of the dumping pulse.

  6. Towards Robust and Accurate Multi-View and Partially-Occluded Face Alignment.

    Science.gov (United States)

    Xing, Junliang; Niu, Zhiheng; Huang, Junshi; Hu, Weiming; Zhou, Xi; Yan, Shuicheng

    2018-04-01

    Face alignment acts as an important task in computer vision. Regression-based methods currently dominate the approach to solving this problem, which generally employ a series of mapping functions from the face appearance to iteratively update the face shape hypothesis. One keypoint here is thus how to perform the regression procedure. In this work, we formulate this regression procedure as a sparse coding problem. We learn two relational dictionaries, one for the face appearance and the other one for the face shape, with coupled reconstruction coefficient to capture their underlying relationships. To deploy this model for face alignment, we derive the relational dictionaries in a stage-wised manner to perform close-loop refinement of themselves, i.e., the face appearance dictionary is first learned from the face shape dictionary and then used to update the face shape hypothesis, and the updated face shape dictionary from the shape hypothesis is in return used to refine the face appearance dictionary. To improve the model accuracy, we extend this model hierarchically from the whole face shape to face part shapes, thus both the global and local view variations of a face are captured. To locate facial landmarks under occlusions, we further introduce an occlusion dictionary into the face appearance dictionary to recover face shape from partially occluded face appearance. The occlusion dictionary is learned in a data driven manner from background images to represent a set of elemental occlusion patterns, a sparse combination of which models various practical partial face occlusions. By integrating all these technical innovations, we obtain a robust and accurate approach to locate facial landmarks under different face views and possibly severe occlusions for face images in the wild. Extensive experimental analyses and evaluations on different benchmark datasets, as well as two new datasets built by ourselves, have demonstrated the robustness and accuracy of our proposed

  7. Machine learning of accurate energy-conserving molecular force fields

    Science.gov (United States)

    Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel E.; Poltavsky, Igor; Schütt, Kristof T.; Müller, Klaus-Robert

    2017-01-01

    Using conservation of energy—a fundamental property of closed classical and quantum mechanical systems—we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to reproduce global potential energy surfaces of intermediate-sized molecules with an accuracy of 0.3 kcal mol−1 for energies and 1 kcal mol−1 Å̊−1 for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods. PMID:28508076

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

    Science.gov (United States)

    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.

  9. Accurate overlaying for mobile augmented reality

    NARCIS (Netherlands)

    Pasman, W; van der Schaaf, A; Lagendijk, RL; Jansen, F.W.

    1999-01-01

    Mobile augmented reality requires accurate alignment of virtual information with objects visible in the real world. We describe a system for mobile communications to be developed to meet these strict alignment criteria using a combination of computer vision. inertial tracking and low-latency

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

    Directory of Open Access Journals (Sweden)

    Andrew Kuziemko

    2011-10-01

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

  11. NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes.

    Directory of Open Access Journals (Sweden)

    Gabriel A Al-Ghalith

    2016-01-01

    Full Text Available The explosion of bioinformatics technologies in the form of next generation sequencing (NGS has facilitated a massive influx of genomics data in the form of short reads. Short read mapping is therefore a fundamental component of next generation sequencing pipelines which routinely match these short reads against reference genomes for contig assembly. However, such techniques have seldom been applied to microbial marker gene sequencing studies, which have mostly relied on novel heuristic approaches. We propose NINJA Is Not Just Another OTU-Picking Solution (NINJA-OPS, or NINJA for short, a fast and highly accurate novel method enabling reference-based marker gene matching (picking Operational Taxonomic Units, or OTUs. NINJA takes advantage of the Burrows-Wheeler (BW alignment using an artificial reference chromosome composed of concatenated reference sequences, the "concatesome," as the BW input. Other features include automatic support for paired-end reads with arbitrary insert sizes. NINJA is also free and open source and implements several pre-filtering methods that elicit substantial speedup when coupled with existing tools. We applied NINJA to several published microbiome studies, obtaining accuracy similar to or better than previous reference-based OTU-picking methods while achieving an order of magnitude or more speedup and using a fraction of the memory footprint. NINJA is a complete pipeline that takes a FASTA-formatted input file and outputs a QIIME-formatted taxonomy-annotated BIOM file for an entire MiSeq run of human gut microbiome 16S genes in under 10 minutes on a dual-core laptop.

  12. XUV ionization of aligned molecules

    Energy Technology Data Exchange (ETDEWEB)

    Kelkensberg, F.; Siu, W.; Gademann, G. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Rouzee, A.; Vrakking, M. J. J. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Max-Born-Institut, Max-Born Strasse 2A, D-12489 Berlin (Germany); Johnsson, P. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Department of Physics, Lund University, Post Office Box 118, SE-221 00 Lund (Sweden); Lucchini, M. [Department of Physics, Politecnico di Milano, Istituto di Fotonica e Nanotecnologie CNR-IFN, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Lucchese, R. R. [Department of Chemistry, Texas A and M University, College Station, Texas 77843-3255 (United States)

    2011-11-15

    New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO{sub 2} molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

  13. XUV ionization of aligned molecules

    International Nuclear Information System (INIS)

    Kelkensberg, F.; Siu, W.; Gademann, G.; Rouzee, A.; Vrakking, M. J. J.; Johnsson, P.; Lucchini, M.; Lucchese, R. R.

    2011-01-01

    New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO 2 molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

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

    International Nuclear Information System (INIS)

    Gauntt, David M.; Barnes, Gary T.

    2010-01-01

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

  15. Constrained-DFT method for accurate energy-level alignment of metal/molecule interfaces

    KAUST Repository

    Souza, A. M.

    2013-10-07

    We present a computational scheme for extracting the energy-level alignment of a metal/molecule interface, based on constrained density functional theory and local exchange and correlation functionals. The method, applied here to benzene on Li(100), allows us to evaluate charge-transfer energies, as well as the spatial distribution of the image charge induced on the metal surface. We systematically study the energies for charge transfer from the molecule to the substrate as function of the molecule-substrate distance, and investigate the effects arising from image-charge confinement and local charge neutrality violation. For benzene on Li(100) we find that the image-charge plane is located at about 1.8 Å above the Li surface, and that our calculated charge-transfer energies compare perfectly with those obtained with a classical electrostatic model having the image plane located at the same position. The methodology outlined here can be applied to study any metal/organic interface in the weak coupling limit at the computational cost of a total energy calculation. Most importantly, as the scheme is based on total energies and not on correcting the Kohn-Sham quasiparticle spectrum, accurate results can be obtained with local/semilocal exchange and correlation functionals. This enables a systematic approach to convergence.

  16. Constrained-DFT method for accurate energy-level alignment of metal/molecule interfaces

    KAUST Repository

    Souza, A. M.; Rungger, I.; Pemmaraju, C. D.; Schwingenschlö gl, Udo; Sanvito, S.

    2013-01-01

    We present a computational scheme for extracting the energy-level alignment of a metal/molecule interface, based on constrained density functional theory and local exchange and correlation functionals. The method, applied here to benzene on Li(100), allows us to evaluate charge-transfer energies, as well as the spatial distribution of the image charge induced on the metal surface. We systematically study the energies for charge transfer from the molecule to the substrate as function of the molecule-substrate distance, and investigate the effects arising from image-charge confinement and local charge neutrality violation. For benzene on Li(100) we find that the image-charge plane is located at about 1.8 Å above the Li surface, and that our calculated charge-transfer energies compare perfectly with those obtained with a classical electrostatic model having the image plane located at the same position. The methodology outlined here can be applied to study any metal/organic interface in the weak coupling limit at the computational cost of a total energy calculation. Most importantly, as the scheme is based on total energies and not on correcting the Kohn-Sham quasiparticle spectrum, accurate results can be obtained with local/semilocal exchange and correlation functionals. This enables a systematic approach to convergence.

  17. GOSSIP: a method for fast and accurate global alignment of protein structures.

    Science.gov (United States)

    Kifer, I; Nussinov, R; Wolfson, H J

    2011-04-01

    The database of known protein structures (PDB) is increasing rapidly. This results in a growing need for methods that can cope with the vast amount of structural data. To analyze the accumulating data, it is important to have a fast tool for identifying similar structures and clustering them by structural resemblance. Several excellent tools have been developed for the comparison of protein structures. These usually address the task of local structure alignment, an important yet computationally intensive problem due to its complexity. It is difficult to use such tools for comparing a large number of structures to each other at a reasonable time. Here we present GOSSIP, a novel method for a global all-against-all alignment of any set of protein structures. The method detects similarities between structures down to a certain cutoff (a parameter of the program), hence allowing it to detect similar structures at a much higher speed than local structure alignment methods. GOSSIP compares many structures in times which are several orders of magnitude faster than well-known available structure alignment servers, and it is also faster than a database scanning method. We evaluate GOSSIP both on a dataset of short structural fragments and on two large sequence-diverse structural benchmarks. Our conclusions are that for a threshold of 0.6 and above, the speed of GOSSIP is obtained with no compromise of the accuracy of the alignments or of the number of detected global similarities. A server, as well as an executable for download, are available at http://bioinfo3d.cs.tau.ac.il/gossip/.

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

    Science.gov (United States)

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

    2013-01-01

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

  19. Molecular acidity: An accurate description with information-theoretic approach in density functional reactivity theory.

    Science.gov (United States)

    Cao, Xiaofang; Rong, Chunying; Zhong, Aiguo; Lu, Tian; Liu, Shubin

    2018-01-15

    Molecular acidity is one of the important physiochemical properties of a molecular system, yet its accurate calculation and prediction are still an unresolved problem in the literature. In this work, we propose to make use of the quantities from the information-theoretic (IT) approach in density functional reactivity theory and provide an accurate description of molecular acidity from a completely new perspective. To illustrate our point, five different categories of acidic series, singly and doubly substituted benzoic acids, singly substituted benzenesulfinic acids, benzeneseleninic acids, phenols, and alkyl carboxylic acids, have been thoroughly examined. We show that using IT quantities such as Shannon entropy, Fisher information, Ghosh-Berkowitz-Parr entropy, information gain, Onicescu information energy, and relative Rényi entropy, one is able to simultaneously predict experimental pKa values of these different categories of compounds. Because of the universality of the quantities employed in this work, which are all density dependent, our approach should be general and be applicable to other systems as well. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  20. Energy level alignment and electron transport through metal/organic contacts. From interfaces to molecular electronics

    Energy Technology Data Exchange (ETDEWEB)

    Abad, Enrique

    2013-07-01

    A new calculational approach to describing metal/organic interfaces. A valuable step towards a better understanding of molecular electronics. Nominated as an outstanding contribution by the Autonomous University of Madrid. In recent years, ever more electronic devices have started to exploit the advantages of organic semiconductors. The work reported in this thesis focuses on analyzing theoretically the energy level alignment of different metal/organic interfaces, necessary to tailor devices with good performance. Traditional methods based on density functional theory (DFT), are not appropriate for analyzing them because they underestimate the organic energy gap and fail to correctly describe the van der Waals forces. Since the size of these systems prohibits the use of more accurate methods, corrections to those DFT drawbacks are desirable. In this work a combination of a standard DFT calculation with the inclusion of the charging energy (U) of the molecule, calculated from first principles, is presented. Regarding the dispersion forces, incorrect long range interaction is substituted by a van der Waals potential. With these corrections, the C60, benzene, pentacene, TTF and TCNQ/Au(111) interfaces are analyzed, both for single molecules and for a monolayer. The results validate the induced density of interface states model.

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

    Directory of Open Access Journals (Sweden)

    Hartmann Stefanie

    2008-03-01

    Full Text Available Abstract Background While full genome sequences are still only available for a handful of taxa, large collections of partial gene sequences are available for many more. The alignment of partial gene sequences results in a multiple sequence alignment containing large gaps that are arranged in a staggered pattern. The consequences of this pattern of missing data on the accuracy of phylogenetic analysis are not well understood. We conducted a simulation study to determine the accuracy of phylogenetic trees obtained from gappy alignments using three commonly used phylogenetic reconstruction methods (Neighbor Joining, Maximum Parsimony, and Maximum Likelihood and studied ways to improve the accuracy of trees obtained from such datasets. Results We found that the pattern of gappiness in multiple sequence alignments derived from partial gene sequences substantially compromised phylogenetic accuracy even in the absence of alignment error. The decline in accuracy was beyond what would be expected based on the amount of missing data. The decline was particularly dramatic for Neighbor Joining and Maximum Parsimony, where the majority of gappy alignments contained 25% to 40% incorrect quartets. To improve the accuracy of the trees obtained from a gappy multiple sequence alignment, we examined two approaches. In the first approach, alignment masking, potentially problematic columns and input sequences are excluded from from the dataset. Even in the absence of alignment error, masking improved phylogenetic accuracy up to 100-fold. However, masking retained, on average, only 83% of the input sequences. In the second approach, alignment subdivision, the missing data is statistically modelled in order to retain as many sequences as possible in the phylogenetic analysis. Subdivision resulted in more modest improvements to alignment accuracy, but succeeded in including almost all of the input sequences. Conclusion These results demonstrate that partial gene

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

    Science.gov (United States)

    Hartmann, Stefanie; Vision, Todd J

    2008-03-26

    While full genome sequences are still only available for a handful of taxa, large collections of partial gene sequences are available for many more. The alignment of partial gene sequences results in a multiple sequence alignment containing large gaps that are arranged in a staggered pattern. The consequences of this pattern of missing data on the accuracy of phylogenetic analysis are not well understood. We conducted a simulation study to determine the accuracy of phylogenetic trees obtained from gappy alignments using three commonly used phylogenetic reconstruction methods (Neighbor Joining, Maximum Parsimony, and Maximum Likelihood) and studied ways to improve the accuracy of trees obtained from such datasets. We found that the pattern of gappiness in multiple sequence alignments derived from partial gene sequences substantially compromised phylogenetic accuracy even in the absence of alignment error. The decline in accuracy was beyond what would be expected based on the amount of missing data. The decline was particularly dramatic for Neighbor Joining and Maximum Parsimony, where the majority of gappy alignments contained 25% to 40% incorrect quartets. To improve the accuracy of the trees obtained from a gappy multiple sequence alignment, we examined two approaches. In the first approach, alignment masking, potentially problematic columns and input sequences are excluded from from the dataset. Even in the absence of alignment error, masking improved phylogenetic accuracy up to 100-fold. However, masking retained, on average, only 83% of the input sequences. In the second approach, alignment subdivision, the missing data is statistically modelled in order to retain as many sequences as possible in the phylogenetic analysis. Subdivision resulted in more modest improvements to alignment accuracy, but succeeded in including almost all of the input sequences. These results demonstrate that partial gene sequences and gappy multiple sequence alignments can pose a

  3. PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases.

    Science.gov (United States)

    Floden, Evan W; Tommaso, Paolo D; Chatzou, Maria; Magis, Cedrik; Notredame, Cedric; Chang, Jia-Ming

    2016-07-08

    The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main novelty of this server is to allow databases of reduced complexity to rapidly perform homology extension. This server also gives the possibility to use transmembrane proteins (TMPs) reference databases to allow even faster homology extension on this important category of proteins. Aside from an MSA, the server also outputs topological prediction of TMPs using the HMMTOP algorithm. Previous benchmarking of the method has shown this approach outperforms the most accurate alignment methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™. The web server is available at http://tcoffee.crg.cat/tmcoffee. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. THE ATLAS INNER DETECTOR TRACK BASED ALIGNMENT

    CERN Document Server

    Marti i Garcia, Salvador; The ATLAS collaboration

    2018-01-01

    The alignment of the ATLAS Inner Detector is performed with a track-based alignment algorithm. Its goal is to provide an accurate description of the detector geometry such that track parameters are accurately determined and free from biases. Its software implementation is modular and configurable, with a clear separation of the alignment algorithm from the detector system specifics and the database handling. The alignment must cope with the rapid movements of the detector as well as with the slow drift of the different mechanical units. Prompt alignment constants are derived for every run at the calibration stage. These sets of constants are then dynamically split from the beginning of the run in many chunks, allowing to describe the tracker geometry as it evolves with time. The alignment of the Inner Detector is validated and improved by studying resonance decays (Z and J/psi to mu+mu-), as well as using information from the calorimeter system with the E/p method with electrons. A detailed study of these res...

  5. Aligned Layers of Silver Nano-Fibers

    Directory of Open Access Journals (Sweden)

    Andrii B. Golovin

    2012-02-01

    Full Text Available We describe a new dichroic polarizers made by ordering silver nano-fibers to aligned layers. The aligned layers consist of nano-fibers and self-assembled molecular aggregates of lyotropic liquid crystals. Unidirectional alignment of the layers is achieved by means of mechanical shearing. Aligned layers of silver nano-fibers are partially transparent to a linearly polarized electromagnetic radiation. The unidirectional alignment and density of the silver nano-fibers determine degree of polarization of transmitted light. The aligned layers of silver nano-fibers might be used in optics, microwave applications, and organic electronics.

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

    DEFF Research Database (Denmark)

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

    2017-01-01

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

  7. Searching for an Accurate Marker-Based Prediction of an Individual Quantitative Trait in Molecular Plant Breeding.

    Science.gov (United States)

    Fu, Yong-Bi; Yang, Mo-Hua; Zeng, Fangqin; Biligetu, Bill

    2017-01-01

    Molecular plant breeding with the aid of molecular markers has played an important role in modern plant breeding over the last two decades. Many marker-based predictions for quantitative traits have been made to enhance parental selection, but the trait prediction accuracy remains generally low, even with the aid of dense, genome-wide SNP markers. To search for more accurate trait-specific prediction with informative SNP markers, we conducted a literature review on the prediction issues in molecular plant breeding and on the applicability of an RNA-Seq technique for developing function-associated specific trait (FAST) SNP markers. To understand whether and how FAST SNP markers could enhance trait prediction, we also performed a theoretical reasoning on the effectiveness of these markers in a trait-specific prediction, and verified the reasoning through computer simulation. To the end, the search yielded an alternative to regular genomic selection with FAST SNP markers that could be explored to achieve more accurate trait-specific prediction. Continuous search for better alternatives is encouraged to enhance marker-based predictions for an individual quantitative trait in molecular plant breeding.

  8. Evolutionary rates at codon sites may be used to align sequences and infer protein domain function

    Directory of Open Access Journals (Sweden)

    Hazelhurst Scott

    2010-03-01

    Full Text Available Abstract Background Sequence alignments form part of many investigations in molecular biology, including the determination of phylogenetic relationships, the prediction of protein structure and function, and the measurement of evolutionary rates. However, to obtain meaningful results, a significant degree of sequence similarity is required to ensure that the alignments are accurate and the inferences correct. Limitations arise when sequence similarity is low, which is particularly problematic when working with fast-evolving genes, evolutionary distant taxa, genomes with nucleotide biases, and cases of convergent evolution. Results A novel approach was conceptualized to address the "low sequence similarity" alignment problem. We developed an alignment algorithm termed FIRE (Functional Inference using the Rates of Evolution, which aligns sequences using the evolutionary rate at codon sites, as measured by the dN/dS ratio, rather than nucleotide or amino acid residues. FIRE was used to test the hypotheses that evolutionary rates can be used to align sequences and that the alignments may be used to infer protein domain function. Using a range of test data, we found that aligning domains based on evolutionary rates was possible even when sequence similarity was very low (for example, antibody variable regions. Furthermore, the alignment has the potential to infer protein domain function, indicating that domains with similar functions are subject to similar evolutionary constraints. These data suggest that an evolutionary rate-based approach to sequence analysis (particularly when combined with structural data may be used to study cases of convergent evolution or when sequences have very low similarity. However, when aligning homologous gene sets with sequence similarity, FIRE did not perform as well as the best traditional alignment algorithms indicating that the conventional approach of aligning residues as opposed to evolutionary rates remains the

  9. Molecular orientation in aligned electrospun polyimide nanofibers by polarized FT-IR spectroscopy.

    Science.gov (United States)

    Yang, Haoqi; Jiang, Shaohua; Fang, Hong; Hu, Xiaowu; Duan, Gaigai; Hou, Haoqing

    2018-07-05

    Quantitative explanation on the improved mechanical properties of aligned electrospun polyimide (PI) nanofibers as the increased imidization temperatures is highly required. In this work, polarized FT-IR spectroscopy is applied to solve this problem. Based on the polarized FT-IR spectroscopy and the molecular model in the fibers, the length of the repeat unit of PI molecule, the angle between the fiber axis and the symmetric stretching direction of carbonyl group on the imide ring, and the angle between the PI molecular axis and fiber axis are all investigated. The Mark-Howink equation is used to calculate the number-average molar mass of PI molecules. The orientation states of PI molecules in the electrospun nanofibers are studied from the number-average molar mass of PI molecules and the average fiber diameter. Quantitative analysis of the orientation factor of PI molecules in the electrospun nanofibers is performed by polarized FT-IR spectroscopy. Copyright © 2018 Elsevier B.V. All rights reserved.

  10. Laser alignment of rotating equipment at PNL

    International Nuclear Information System (INIS)

    Berndt, R.H.

    1994-05-01

    Lateral vibration in direct-drive equipment is usually caused by misalignment. Over the years, because of the need to improve on techniques and ways of working more efficiently, various types of alignment methods have evolved. In the beginning, craftsmen used a straight-edge scale across the coupling with a feeler gauge measuring the misalignment error. This is still preferred today for aligning small couplings. The industry has since decided that alignment of large direct-drive equipment needed a more accurate type of instrumentation. Rim and face is another of the first alignment methods and is used on all sizes of equipment. A disadvantage of the rim and face method is that in most cases the coupling has to be disassembled. This can cause alignment problems when the coupling is reassembled. Also, the rim and face method is not fast enough to work satisfactorily on alignment of thermally hot equipment. Another concern is that the coupling has to be manufactured accurately for correct rim and face readings. Reverse dial alignment is an improvement over the rim and face method, and depending on the operator's experience, this method can be very accurate. A good training program along with field experience will bring the operator to a proper level of proficiency for a successful program. A hand-held computer with reverse dial calculations in memory is a must for job efficiency. An advantage over the rim and face method is that the coupling is not disassembled and remains locked together. Reverse dial instrumentation measures from both shaft center lines, rather than the coupling surface so the machining of the coupling during manufacture is not a major concern

  11. Fabrication and characterization of a solid-state nanopore with self-aligned carbon nanoelectrodes for molecular detection

    International Nuclear Information System (INIS)

    Spinney, Patrick S; Collins, Scott D; Smith, Rosemary L; Howitt, David G

    2012-01-01

    Stochastic molecular sensors based on resistive pulse nanopore modalities are envisioned as facile DNA sequencers. However, recent advances in nanotechnology fabrication have highlighted promising alternative detection mechanisms with higher sensitivity and potential single-base resolution. In this paper we present the novel self-aligned fabrication of a solid-state nanopore device with integrated transverse graphene-like carbon nanoelectrodes for polyelectrolyte molecular detection. The electrochemical transduction mechanism is characterized and found to result primarily from thermionic emission between the two transverse electrodes. Response of the nanopore to Lambda dsDNA and short (16-mer) ssDNA is demonstrated and distinguished. (paper)

  12. Intramedullary versus extramedullary alignment of the tibial component in the Triathlon knee

    LENUS (Irish Health Repository)

    Cashman, James P

    2011-08-20

    Abstract Background Long term survivorship in total knee arthroplasty is significantly dependant on prosthesis alignment. Our aim was determine which alignment guide was more accurate in positioning of the tibial component in total knee arthroplasty. We also aimed to assess whether there was any difference in short term patient outcome. Method A comparison of intramedullary versus extramedullary alignment jig was performed. Radiological alignment of tibial components and patient outcomes of 103 Triathlon total knee arthroplasties were analysed. Results Use of the intramedullary was found to be significantly more accurate in determining coronal alignment (p = 0.02) while use of the extramedullary jig was found to give more accurate results in sagittal alignment (p = 0.04). There was no significant difference in WOMAC or SF-36 at six months. Conclusion Use of an intramedullary jig is preferable for positioning of the tibial component using this knee system.

  13. An improved Hough transform-based fingerprint alignment approach

    CSIR Research Space (South Africa)

    Mlambo, CS

    2014-11-01

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

  14. Searching for an Accurate Marker-Based Prediction of an Individual Quantitative Trait in Molecular Plant Breeding

    Directory of Open Access Journals (Sweden)

    Yong-Bi Fu

    2017-07-01

    Full Text Available Molecular plant breeding with the aid of molecular markers has played an important role in modern plant breeding over the last two decades. Many marker-based predictions for quantitative traits have been made to enhance parental selection, but the trait prediction accuracy remains generally low, even with the aid of dense, genome-wide SNP markers. To search for more accurate trait-specific prediction with informative SNP markers, we conducted a literature review on the prediction issues in molecular plant breeding and on the applicability of an RNA-Seq technique for developing function-associated specific trait (FAST SNP markers. To understand whether and how FAST SNP markers could enhance trait prediction, we also performed a theoretical reasoning on the effectiveness of these markers in a trait-specific prediction, and verified the reasoning through computer simulation. To the end, the search yielded an alternative to regular genomic selection with FAST SNP markers that could be explored to achieve more accurate trait-specific prediction. Continuous search for better alternatives is encouraged to enhance marker-based predictions for an individual quantitative trait in molecular plant breeding.

  15. Searching for an Accurate Marker-Based Prediction of an Individual Quantitative Trait in Molecular Plant Breeding

    Science.gov (United States)

    Fu, Yong-Bi; Yang, Mo-Hua; Zeng, Fangqin; Biligetu, Bill

    2017-01-01

    Molecular plant breeding with the aid of molecular markers has played an important role in modern plant breeding over the last two decades. Many marker-based predictions for quantitative traits have been made to enhance parental selection, but the trait prediction accuracy remains generally low, even with the aid of dense, genome-wide SNP markers. To search for more accurate trait-specific prediction with informative SNP markers, we conducted a literature review on the prediction issues in molecular plant breeding and on the applicability of an RNA-Seq technique for developing function-associated specific trait (FAST) SNP markers. To understand whether and how FAST SNP markers could enhance trait prediction, we also performed a theoretical reasoning on the effectiveness of these markers in a trait-specific prediction, and verified the reasoning through computer simulation. To the end, the search yielded an alternative to regular genomic selection with FAST SNP markers that could be explored to achieve more accurate trait-specific prediction. Continuous search for better alternatives is encouraged to enhance marker-based predictions for an individual quantitative trait in molecular plant breeding. PMID:28729875

  16. Stochastic sampling of the RNA structural alignment space.

    Science.gov (United States)

    Harmanci, Arif Ozgun; Sharma, Gaurav; Mathews, David H

    2009-07-01

    A novel method is presented for predicting the common secondary structures and alignment of two homologous RNA sequences by sampling the 'structural alignment' space, i.e. the joint space of their alignments and common secondary structures. The structural alignment space is sampled according to a pseudo-Boltzmann distribution based on a pseudo-free energy change that combines base pairing probabilities from a thermodynamic model and alignment probabilities from a hidden Markov model. By virtue of the implicit comparative analysis between the two sequences, the method offers an improvement over single sequence sampling of the Boltzmann ensemble. A cluster analysis shows that the samples obtained from joint sampling of the structural alignment space cluster more closely than samples generated by the single sequence method. On average, the representative (centroid) structure and alignment of the most populated cluster in the sample of structures and alignments generated by joint sampling are more accurate than single sequence sampling and alignment based on sequence alone, respectively. The 'best' centroid structure that is closest to the known structure among all the centroids is, on average, more accurate than structure predictions of other methods. Additionally, cluster analysis identifies, on average, a few clusters, whose centroids can be presented as alternative candidates. The source code for the proposed method can be downloaded at http://rna.urmc.rochester.edu.

  17. R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.

    Science.gov (United States)

    Rahrig, Ryan R; Petrov, Anton I; Leontis, Neocles B; Zirbel, Craig L

    2013-07-01

    The R3D Align web server provides online access to 'RNA 3D Align' (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/.

  18. Evaluation of alignment marks using ASML ATHENA alignment system in 90nm BEOL process

    CERN Document Server

    Tan Chin Boon; Koh Hui Peng; Koo Chee, Kiong; Siew Yong Kong; Yeo Swee Hock

    2003-01-01

    As the critical dimension (CD) in integrated circuit (IC) device reduces, the total overlay budget needs to be more stringent. Typically, the allowable overlay error is 1/3 of the CD in the IC device. In this case, robustness of alignment mark is critical, as accurate signal is required by the scanner's alignment system to precisely align a layer of pattern to the previous layer. Alignment issue is more severe in back-end process partly due to the influenced of Chemical Mechanical Polishing (CMP), which contribute to the asymmetric or total destruction of the alignment marks. Alignment marks on the wafer can be placed along the scribe-line of the IC pattern. ASML scanner allows such type of wafer alignment using phase grating mark, known as Scribe-line Primary Mark (SPM) which can be fit into a standard 80um scribe-line. In this paper, we have studied the feasibility of introducing Narrow SPM (NSPM) to enable a smaller scribe-line. The width of NSPM has been shrunk down to 70% of the SPM and the length remain...

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

    Science.gov (United States)

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

    2014-06-01

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

  20. Node fingerprinting: an efficient heuristic for aligning biological networks.

    Science.gov (United States)

    Radu, Alex; Charleston, Michael

    2014-10-01

    With the continuing increase in availability of biological data and improvements to biological models, biological network analysis has become a promising area of research. An emerging technique for the analysis of biological networks is through network alignment. Network alignment has been used to calculate genetic distance, similarities between regulatory structures, and the effect of external forces on gene expression, and to depict conditional activity of expression modules in cancer. Network alignment is algorithmically complex, and therefore we must rely on heuristics, ideally as efficient and accurate as possible. The majority of current techniques for network alignment rely on precomputed information, such as with protein sequence alignment, or on tunable network alignment parameters, which may introduce an increased computational overhead. Our presented algorithm, which we call Node Fingerprinting (NF), is appropriate for performing global pairwise network alignment without precomputation or tuning, can be fully parallelized, and is able to quickly compute an accurate alignment between two biological networks. It has performed as well as or better than existing algorithms on biological and simulated data, and with fewer computational resources. The algorithmic validation performed demonstrates the low computational resource requirements of NF.

  1. Machine learning predictions of molecular properties: Accurate many-body potentials and nonlocality in chemical space

    International Nuclear Information System (INIS)

    Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; Pronobis, Wiktor; Lilienfeld, O. Anatole von; Müller, Klaus-Robert; Tkatchenko, Alexandre

    2015-01-01

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the 'holy grail' of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies

  2. Field-free molecular orientation of nonadiabatically aligned OCS

    Science.gov (United States)

    Sonoda, Kotaro; Iwasaki, Atsushi; Yamanouchi, Kaoru; Hasegawa, Hirokazu

    2018-02-01

    We investigate an enhancement of the orientation of OCS molecules by irradiating them with a near IR (ω) ultrashort laser pulse for alignment followed by another ultrashort laser pulse for orientation, which is synthesized by a phase-locked coherent superposition of the near IR laser pulse and its second harmonic (2ω). On the basis of the asymmetry in the ejection direction of S3+ fragment ions generated by the Coulomb explosion of multiply charged OCS, we show that the extent of the orientation of OCS is significantly enhanced when the delay between the alignment pulse and the orientation pulse is a quarter or three quarters of the rotational period. The recorded enhanced orientation was interpreted well by a numerical simulation of the temporal evolution of a rotational wave packet prepared by the alignment and orientation pulses.

  3. Efficient alignment-free DNA barcode analytics.

    Science.gov (United States)

    Kuksa, Pavel; Pavlovic, Vladimir

    2009-11-10

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

  4. Aligning molecules with intense nonresonant laser fields

    DEFF Research Database (Denmark)

    Larsen, J.J.; Safvan, C.P.; Sakai, H.

    1999-01-01

    Molecules in a seeded supersonic beam are aligned by the interaction between an intense nonresonant linearly polarized laser field and the molecular polarizability. We demonstrate the general applicability of the scheme by aligning I2, ICl, CS2, CH3I, and C6H5I molecules. The alignment is probed...... by mass selective two dimensional imaging of the photofragment ions produced by femtosecond laser pulses. Calculations on the degree of alignment of I2 are in good agreement with the experiments. We discuss some future applications of laser aligned molecules....

  5. Tidal alignment of galaxies

    Energy Technology Data Exchange (ETDEWEB)

    Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš

    2015-08-01

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

  6. GraphAlignment: Bayesian pairwise alignment of biological networks

    Czech Academy of Sciences Publication Activity Database

    Kolář, Michal; Meier, J.; Mustonen, V.; Lässig, M.; Berg, J.

    2012-01-01

    Roč. 6, November 21 (2012) ISSN 1752-0509 Grant - others:Deutsche Forschungsgemeinschaft(DE) SFB 680; Deutsche Forschungsgemeinschaft(DE) SFB-TR12; Deutsche Forschungsgemeinschaft(DE) BE 2478/2-1 Institutional research plan: CEZ:AV0Z50520514 Keywords : Graph alignment * Biological networks * Parameter estimation * Bioconductor Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.982, year: 2012

  7. Transient molecular orientation and rheology in flow aligning thermotropic liquid crystalline polymers

    International Nuclear Information System (INIS)

    Ugaz, Victor M.; Burghardt, Wesley R.; Zhou, Weijun; Kornfield, Julia A.

    2001-01-01

    Quantitative measurements of molecular orientation and rheology are reported for various transient shear flows of a nematic semiflexible copolyether. Unlike the case of lyotropic liquid crystalline polymers (LCPs), whose structure and rheology in shear are dominated by director tumbling, this material exhibits flow aligning behavior. The observed behavior is quite similar to that seen in a copolyester that we have recently studied [Ugaz and Burghardt (1998)], suggesting that flow aligning dynamics may predominate in main-chain thermotropes that incorporate significant chain flexibility. Since the flow aligning regime has received little attention in previous attempts to model the rheology of textured, polydomain LCPs, we attempt to determine whether available models are capable of predicting the orientation and stress response of this class of LCP. We first examine the predictions of the polydomain Ericksen model, an adaptation of Ericksen's transversely isotropic fluid model which accounts for the polydomain distribution of director orientation while neglecting distortional elasticity. This simple model captures a number of qualitative and quantitative features associated with the evolution of orientation and stress during shear flow inception, but cannot cope with reversing flows. To consider the possible role of distortional elasticity in the re-orientation dynamics upon reversal, we evaluate the mesoscopically averaged domain theory of Larson and Doi [Larson and Doi (1991)], which incorporates a phenomenological description of distortional elastic effects. To date, their approach to account for polydomain structure has only been applied to describe tumbling LCPs. We find that it captures the qualitative transient orientation response to flow reversals, but is less successful in describing the evolution of stresses. This is linked to the decoupling approximation adopted during the model's development. Finally, a modified polydomain Ericksen model is introduced

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Science.gov (United States)

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

    2015-11-01

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

  10. Research on localization and alignment technology for transfer cask

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jingchuan, E-mail: jchwang@sjtu.edu.cn [Department of Automation, Shanghai Jiao Tong University, Shanghai (China); Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai (China); Yang, Ming; Chen, Weidong [Department of Automation, Shanghai Jiao Tong University, Shanghai (China); Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai (China)

    2015-10-15

    Highlights: • A method for the alignment between TB and HCB based on localizability is proposed. • A localization method based on the localizability estimation is proposed to realize the cask's localization accurately and ensures the transfer cask's accurate docking in the front of the window of Tokmak Building. • The experimental results show that the proposed algorithm works well in the indoor simulation environment. This system will be test in EAST of China. - Abstract: According to the long length characteristics of transfer cask compared to the environment space between Tokmak Building (TB) and HCB (Hot Cell Building), this paper proposes an autonomous localization and alignment method for the internal components transportation and replacement. A localization method based on the localizability estimation is used to realize the cask's localization and navigation accurately. Once the cask arrives at the front of the TB window, the position and attitude measurement system is used to detect the relative alignment error between the seal door of pallet and the window of TB real-time. The alignment between seal door and TB window could be realized based on this offset. The simulation experiment based on the real model is designed according to the real TB situation. The experiment results show that the proposed localization and alignment method can be used for transfer cask.

  11. Preoperative core needle biopsy is accurate in determining molecular subtypes in invasive breast cancer

    International Nuclear Information System (INIS)

    Chen, Xiaosong; Yuan, Ying; Fei, Xiaochun; Jin, Xiaolong; Shen, Kunwei; Sun, Long; Mao, Yan; Zhu, Siji; Wu, Jiayi; Huang, Ou; Li, Yafen; Chen, Weiguo; Wang, Jianhua

    2013-01-01

    Estrogen receptor (ER), progesterone receptor (PgR), HER2, and Ki67 have been increasingly evaluated by core needle biopsy (CNB) and are recommended for classifying breast cancer into molecular subtypes. However, the concordance rate between CNB and open excision biopsy (OEB) has not been well documented. Patients with paired CNB and OEB samples from Oct. 2009 to Feb. 2012 in Ruijin Hospital were included. ER, PgR, HER2, and Ki67 were determined by immunohistochemistry (IHC). Patients with HER2 IHC 2+ were further examined by FISH. Cutoff value for Ki67 high expression was 14%. Molecular subtypes were constructed as follows: Luminal A, Luminal B, Triple Negative, and HER2 positive. There were 298 invasive breast cancer patients analyzed. Concordance rates for ER, PgR, and HER2 were 93.6%, 85.9%, and 96.3%, respectively. Ki67 expression was slightly higher in OEB than in CNB samples (29.3% vs. 26.8%, P = 0.046). Good agreement (κ = 0.658) was demonstrated in evaluating molecular subtypes between CNB and OEB, with a concordance rate of 77.2%. We also used a different Ki67 cutoff value (20%) for determining Luminal A and B subtypes in HR (hormone receptor) +/HER2- diseases and the overall concordance rate was 79.2%. However, using a cut-point of Ki67 either 14% or 20% for both specimens, there will be about 14% of HR+/HER2- specimens that are called Luminal A on CNB and Luminal B on OEB. CNB was accurate in determining ER, PgR, and HER2 status as well as non-Luminal molecular subtypes in invasive breast cancer. Ki67 should be retested on OEB samples in HR+/HER2- patients to accurately distinguish Luminal A from B tumors

  12. Study on orientation mechanisms of poly(vinylidenefluoride-trifluoroethylene) molecules aligned by atomic force microscopy

    International Nuclear Information System (INIS)

    Kimura, Kuniko; Kobayashi, Kei; Yamada, Hirofumi; Horiuchi, Toshihisa; Ishida, Kenji; Matsushige, Kazumi

    2006-01-01

    We have developed a molecular orientation control technique for polymers utilizing contact-mode atomic force microscopy (AFM). In this paper, we studied the molecular alignment mechanism of this technique by applying it to poly(vinylidenefluoride-trifluoroethylene) (P(VDF-TrFE)). The resultant alignment and formed crystal size were strongly dependent on the temperature during the modification. They also depended on the scan line spacing of the modification. These results made the alignment mechanism clear. The obtained molecular alignment was stable against the heat treatment even at the temperatures just below T m

  13. Fast and accurate phylogeny reconstruction using filtered spaced-word matches

    Science.gov (United States)

    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

  14. Solving the shrinkage-induced PDMS alignment registration issue in multilayer soft lithography

    International Nuclear Information System (INIS)

    Moraes, Christopher; Sun, Yu; Simmons, Craig A

    2009-01-01

    Shrinkage of polydimethylsiloxane (PDMS) complicates alignment registration between layers during multilayer soft lithography fabrication. This often hinders the development of large-scale microfabricated arrayed devices. Here we report a rapid method to construct large-area, multilayered devices with stringent alignment requirements. This technique, which exploits a previously unrecognized aspect of sandwich mold fabrication, improves device yield, enables highly accurate alignment over large areas of multilayered devices and does not require strict regulation of fabrication conditions or extensive calibration processes. To demonstrate this technique, a microfabricated Braille display was developed and characterized. High device yield and accurate alignment within 15 µm were achieved over three layers for an array of 108 Braille units spread over a 6.5 cm 2 area, demonstrating the fabrication of well-aligned devices with greater ease and efficiency than previously possible

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

    Directory of Open Access Journals (Sweden)

    Liviu P Dinu

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

  16. Simulation of beamline alignment operations

    International Nuclear Information System (INIS)

    Annese, C; Miller, M G.

    1999-01-01

    distributions rather than static values. The only way to accurately understand resource utilization and time requirements for a complex industrial application such as alignment, is to utilize simulation tools such as Simprocess to model the system

  17. SFESA: a web server for pairwise alignment refinement by secondary structure shifts.

    Science.gov (United States)

    Tong, Jing; Pei, Jimin; Grishin, Nick V

    2015-09-03

    Protein sequence alignment is essential for a variety of tasks such as homology modeling and active site prediction. Alignment errors remain the main cause of low-quality structure models. A bioinformatics tool to refine alignments is needed to make protein alignments more accurate. We developed the SFESA web server to refine pairwise protein sequence alignments. Compared to the previous version of SFESA, which required a set of 3D coordinates for a protein, the new server will search a sequence database for the closest homolog with an available 3D structure to be used as a template. For each alignment block defined by secondary structure elements in the template, SFESA evaluates alignment variants generated by local shifts and selects the best-scoring alignment variant. A scoring function that combines the sequence score of profile-profile comparison and the structure score of template-derived contact energy is used for evaluation of alignments. PROMALS pairwise alignments refined by SFESA are more accurate than those produced by current advanced alignment methods such as HHpred and CNFpred. In addition, SFESA also improves alignments generated by other software. SFESA is a web-based tool for alignment refinement, designed for researchers to compute, refine, and evaluate pairwise alignments with a combined sequence and structure scoring of alignment blocks. To our knowledge, the SFESA web server is the only tool that refines alignments by evaluating local shifts of secondary structure elements. The SFESA web server is available at http://prodata.swmed.edu/sfesa.

  18. GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters.

    Science.gov (United States)

    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.

  19. Concurrent and Accurate Short Read Mapping on Multicore Processors.

    Science.gov (United States)

    Martínez, Héctor; Tárraga, Joaquín; Medina, Ignacio; Barrachina, Sergio; Castillo, Maribel; Dopazo, Joaquín; Quintana-Ortí, Enrique S

    2015-01-01

    We introduce a parallel aligner with a work-flow organization for fast and accurate mapping of RNA sequences on servers equipped with multicore processors. Our software, HPG Aligner SA (HPG Aligner SA is an open-source application. The software is available at http://www.opencb.org, exploits a suffix array to rapidly map a large fraction of the RNA fragments (reads), as well as leverages the accuracy of the Smith-Waterman algorithm to deal with conflictive reads. The aligner is enhanced with a careful strategy to detect splice junctions based on an adaptive division of RNA reads into small segments (or seeds), which are then mapped onto a number of candidate alignment locations, providing crucial information for the successful alignment of the complete reads. The experimental results on a platform with Intel multicore technology report the parallel performance of HPG Aligner SA, on RNA reads of 100-400 nucleotides, which excels in execution time/sensitivity to state-of-the-art aligners such as TopHat 2+Bowtie 2, MapSplice, and STAR.

  20. Active manipulation of the selective alignment by two laser pulses

    International Nuclear Information System (INIS)

    Zeng-Qiang, Yang; Zhi-Rong, Guo; Gui-Xian, Ge

    2010-01-01

    This paper solves numerically the full time-dependent Schrödinger equation based on the rigid rotor model, and proposes a novel strategy to determine the optimal time delay of the two laser pulses to manipulate the molecular selective alignment. The results illustrate that the molecular alignment generated by the first pulse can be suppressed or enhanced selectively, the relative populations of even and odd rotational states in the final rotational wave packet can be manipulated selectively by precisely inserting the peak of the second laser pulse at the time when the slope for the alignment parameter by the first laser locates a local maximum for the even rotational states and a local minimum for the odds, and vice versa. The selective alignment can be further optimised by selecting the intensity ratio of the two laser pulses on the condition that the total laser intensity and pulse duration are kept constant. (atomic and molecular physics)

  1. Hohlraum Target Alignment from X-ray Detector Images using Starburst Design Patterns

    International Nuclear Information System (INIS)

    Leach, R.R.; Conder, A.; Edwards, O.; Kroll, J.; Kozioziemski, B.; Mapoles, E.; McGuigan, D.; Wilhelmsen, K.

    2010-01-01

    National Ignition Facility (NIF) is a high-energy laser facility comprised of 192 laser beams focused with enough power and precision on a hydrogen-filled spherical, cryogenic target to initiate a fusion reaction. The target container, or hohlraum, must be accurately aligned to an x-ray imaging system to allow careful monitoring of the frozen fuel layer in the target. To achieve alignment, x-ray images are acquired through starburst-shaped windows cut into opposite sides of the hohlraum. When the hohlraum is in alignment, the starburst pattern pairs match nearly exactly and allow a clear view of the ice layer formation on the edge of the target capsule. During the alignment process, x-ray image analysis is applied to determine the direction and magnitude of adjustment required. X-ray detector and source are moved in concert during the alignment process. The automated pointing alignment system described here is both accurate and efficient. In this paper, we describe the control and associated image processing that enables automation of the starburst pointing alignment.

  2. Initial Alignment for SINS Based on Pseudo-Earth Frame in Polar Regions.

    Science.gov (United States)

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

    2017-06-16

    An accurate initial alignment must be required for inertial navigation system (INS). The performance of initial alignment directly affects the following navigation accuracy. However, the rapid convergence of meridians and the small horizontalcomponent of rotation of Earth make the traditional alignment methods ineffective in polar regions. In this paper, from the perspective of global inertial navigation, a novel alignment algorithm based on pseudo-Earth frame and backward process is proposed to implement the initial alignment in polar regions. Considering that an accurate coarse alignment of azimuth is difficult to obtain in polar regions, the dynamic error modeling with large azimuth misalignment angle is designed. At the end of alignment phase, the strapdown attitude matrix relative to local geographic frame is obtained without influence of position errors and cumbersome computation. As a result, it would be more convenient to access the following polar navigation system. Then, it is also expected to unify the polar alignment algorithm as much as possible, thereby further unifying the form of external reference information. Finally, semi-physical static simulation and in-motion tests with large azimuth misalignment angle assisted by unscented Kalman filter (UKF) validate the effectiveness of the proposed method.

  3. SPA: a probabilistic algorithm for spliced alignment.

    Directory of Open Access Journals (Sweden)

    2006-04-01

    Full Text Available Recent large-scale cDNA sequencing efforts show that elaborate patterns of splice variation are responsible for much of the proteome diversity in higher eukaryotes. To obtain an accurate account of the repertoire of splice variants, and to gain insight into the mechanisms of alternative splicing, it is essential that cDNAs are very accurately mapped to their respective genomes. Currently available algorithms for cDNA-to-genome alignment do not reach the necessary level of accuracy because they use ad hoc scoring models that cannot correctly trade off the likelihoods of various sequencing errors against the probabilities of different gene structures. Here we develop a Bayesian probabilistic approach to cDNA-to-genome alignment. Gene structures are assigned prior probabilities based on the lengths of their introns and exons, and based on the sequences at their splice boundaries. A likelihood model for sequencing errors takes into account the rates at which misincorporation, as well as insertions and deletions of different lengths, occurs during sequencing. The parameters of both the prior and likelihood model can be automatically estimated from a set of cDNAs, thus enabling our method to adapt itself to different organisms and experimental procedures. We implemented our method in a fast cDNA-to-genome alignment program, SPA, and applied it to the FANTOM3 dataset of over 100,000 full-length mouse cDNAs and a dataset of over 20,000 full-length human cDNAs. Comparison with the results of four other mapping programs shows that SPA produces alignments of significantly higher quality. In particular, the quality of the SPA alignments near splice boundaries and SPA's mapping of the 5' and 3' ends of the cDNAs are highly improved, allowing for more accurate identification of transcript starts and ends, and accurate identification of subtle splice variations. Finally, our splice boundary analysis on the human dataset suggests the existence of a novel non

  4. Molecular bond formation in Na* + N2 energy transfer: Crossed beam study of atomic alignment and orientation

    International Nuclear Information System (INIS)

    Reiland, W.; Jamieson, G.; Tittes, U.; Hertel, I.V.

    1982-01-01

    We report the first full analysis of collisionally induced atomic alignment and orientation for a molecular collision process. In an experiment with crossed supersonic beams of N 2 and laser excited Na(3 2 Psub(3/2)) we have studied the dependence of angular and energy resolved differential quenching cross sections as a function of the linear and circular polarization of the exciting laser light. The ansisotropies observed in the linear polarization data range up to 2:1 when corrected for electron and nuclear spin relaxation. The maximum effect is found at small scattering angles and intermediate energy transfer where the cross section is also largest. The atomic alignment angle most favourable for quenching relates to the scattering angle and can be understood in a model picture in such a way that the (NaN 2 )* molecular system is formed at internuclear distances as low as R = 10a 0 . The circular asymmetry is small but with significant structure and is attributed to interaction on different potential surfaces at R > 10a 0 . Full analysis of the four measurable parameter is given in terms of the density matrix in a frame with z-axis perpendicular to collision plane which allows a clear understanding of the properties of atomic reflection symmetry and coherence of the scattering process. (orig.)

  5. Isotope-selective ionization using four-pulse alignment

    International Nuclear Information System (INIS)

    Akagi, Hiroshi; Kasajima, Tatsuya; Kumada, Takayuki; Itakura, Ryuji; Yokoyama, Atsushi; Hasegawa, Hirokazu; Ohshima, Yasuhiro

    2013-01-01

    We have proposed a laser isotope separation method utilizing molecular alignment and non-resonant multiphoton ionization, and demonstrated isotope-selective ionization of 14 N 2 and 15 N 2 isotopomers, using one-pulse alignment. In the present work, we used a train of four identical pulses, instead of one pulse, to obtain the higher selectivity. (author)

  6. Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering

    Science.gov (United States)

    Martinek, Tomas; Duboué-Dijon, Elise; Timr, Štěpán; Mason, Philip E.; Baxová, Katarina; Fischer, Henry E.; Schmidt, Burkhard; Pluhařová, Eva; Jungwirth, Pavel

    2018-06-01

    We present a combination of force field and ab initio molecular dynamics simulations together with neutron scattering experiments with isotopic substitution that aim at characterizing ion hydration and pairing in aqueous calcium chloride and formate/acetate solutions. Benchmarking against neutron scattering data on concentrated solutions together with ion pairing free energy profiles from ab initio molecular dynamics allows us to develop an accurate calcium force field which accounts in a mean-field way for electronic polarization effects via charge rescaling. This refined calcium parameterization is directly usable for standard molecular dynamics simulations of processes involving this key biological signaling ion.

  7. Fiber optics welder having movable aligning mirror

    Science.gov (United States)

    Higgins, Robert W.; Robichaud, Roger E.

    1981-01-01

    A system for welding fiber optic waveguides together. The ends of the two fibers to be joined together are accurately, collinearly aligned in a vertical orientation and subjected to a controlled, diffuse arc to effect welding and thermal conditioning. A front-surfaced mirror mounted at a 45.degree. angle to the optical axis of a stereomicroscope mounted for viewing the junction of the ends provides two orthogonal views of the interface during the alignment operation.

  8. A third order accurate Lagrangian finite element scheme for the computation of generalized molecular stress function fluids

    DEFF Research Database (Denmark)

    Fasano, Andrea; Rasmussen, Henrik K.

    2017-01-01

    A third order accurate, in time and space, finite element scheme for the numerical simulation of three- dimensional time-dependent flow of the molecular stress function type of fluids in a generalized formu- lation is presented. The scheme is an extension of the K-BKZ Lagrangian finite element me...

  9. Communication: Strong laser alignment of solvent-solute aggregates in the gas-phase

    Science.gov (United States)

    Trippel, Sebastian; Wiese, Joss; Mullins, Terry; Küpper, Jochen

    2018-03-01

    Strong quasi-adiabatic laser alignment of the indole-water-dimer clusters, an amino-acid chromophore bound to a single water molecule through a hydrogen bond, was experimentally realized. The alignment was visualized through ion and electron imaging following strong-field ionization. Molecular-frame photoelectron angular distributions showed a clear suppression of the electron yield in the plane of the ionizing laser's polarization, which was analyzed as strong alignment of the molecular cluster with ⟨cos2 θ2D⟩ ≥ 0.9.

  10. Alignment of the HERA-B RICH optical system with data

    International Nuclear Information System (INIS)

    Gorisek, A.; Krizan, P.; Korpar, S.; Staric, M.

    1999-01-01

    We present a method for alignment of the mirror segments in the Ring Image Cherenkov Counter of the HERA-B spectrometer. The method will use recorded data, and was tested by using simulated events. The study shows that the mirrors can be aligned accurately enough to make the corresponding error in Cherenkov angle measurement negligible compared to other contributions. The mirrors are aligned relative to one mirror segment which can be chosen arbitrarily

  11. Ancestral sequence alignment under optimal conditions

    Directory of Open Access Journals (Sweden)

    Brown Daniel G

    2005-11-01

    success of aligning ancestral sequences containing ambiguity is very sensitive to the choice of gap open cost. Surprisingly, we find that using maximum likelihood to infer ancestral sequences results in less accurate alignments than when using parsimony to infer ancestral sequences. Finally, we find that the sum-of-pairs methods produce better alignments than all of the ancestral alignment methods.

  12. A large catalog of accurate distances to molecular clouds from PS1 photometry

    Energy Technology Data Exchange (ETDEWEB)

    Schlafly, E. F.; Rix, H.-W.; Martin, N. F. [Max Planck Institute for Astronomy, Königstuhl 17, D-69117 Heidelberg (Germany); Green, G.; Finkbeiner, D. P. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Bell, E. F. [Department of Astronomy, University of Michigan, 500 Church Street, Ann Arbor, MI 48109 (United States); Burgett, W. S.; Chambers, K. C.; Hodapp, K. W.; Kaiser, N.; Magnier, E. A.; Tonry, J. L. [Institute for Astronomy, University of Hawaii, 2680 Woodlawn Drive, Honolulu, HI 96822 (United States); Draper, P. W.; Metcalfe, N. [Department of Physics, Durham University, South Road, Durham DH1 3LE (United Kingdom); Price, P. A. [Department of Astrophysical Sciences, Princeton University, Princeton, NJ 08544 (United States)

    2014-05-01

    Distance measurements to molecular clouds are important but are often made separately for each cloud of interest, employing very different data and techniques. We present a large, homogeneous catalog of distances to molecular clouds, most of which are of unprecedented accuracy. We determine distances using optical photometry of stars along lines of sight toward these clouds, obtained from PanSTARRS-1. We simultaneously infer the reddenings and distances to these stars, tracking the full probability distribution function using a technique presented in Green et al. We fit these star-by-star measurements using a simple dust screen model to find the distance to each cloud. We thus estimate the distances to almost all of the clouds in the Magnani et al. catalog, as well as many other well-studied clouds, including Orion, Perseus, Taurus, Cepheus, Polaris, California, and Monoceros R2, avoiding only the inner Galaxy. Typical statistical uncertainties in the distances are 5%, though the systematic uncertainty stemming from the quality of our stellar models is about 10%. The resulting catalog is the largest catalog of accurate, directly measured distances to molecular clouds. Our distance estimates are generally consistent with available distance estimates from the literature, though in some cases the literature estimates are off by a factor of more than two.

  13. Exploring the relationship between sequence similarity and accurate phylogenetic trees.

    Science.gov (United States)

    Cantarel, Brandi L; Morrison, Hilary G; Pearson, William

    2006-11-01

    We have characterized the relationship between accurate phylogenetic reconstruction and sequence similarity, testing whether high levels of sequence similarity can consistently produce accurate evolutionary trees. We generated protein families with known phylogenies using a modified version of the PAML/EVOLVER program that produces insertions and deletions as well as substitutions. Protein families were evolved over a range of 100-400 point accepted mutations; at these distances 63% of the families shared significant sequence similarity. Protein families were evolved using balanced and unbalanced trees, with ancient or recent radiations. In families sharing statistically significant similarity, about 60% of multiple sequence alignments were 95% identical to true alignments. To compare recovered topologies with true topologies, we used a score that reflects the fraction of clades that were correctly clustered. As expected, the accuracy of the phylogenies was greatest in the least divergent families. About 88% of phylogenies clustered over 80% of clades in families that shared significant sequence similarity, using Bayesian, parsimony, distance, and maximum likelihood methods. However, for protein families with short ancient branches (ancient radiation), only 30% of the most divergent (but statistically significant) families produced accurate phylogenies, and only about 70% of the second most highly conserved families, with median expectation values better than 10(-60), produced accurate trees. These values represent upper bounds on expected tree accuracy for sequences with a simple divergence history; proteins from 700 Giardia families, with a similar range of sequence similarities but considerably more gaps, produced much less accurate trees. For our simulated insertions and deletions, correct multiple sequence alignments did not perform much better than those produced by T-COFFEE, and including sequences with expressed sequence tag-like sequencing errors did not

  14. Alignment of the ATLAS Inner Detector Tracking System

    CERN Document Server

    Lacuesta, V; The ATLAS collaboration

    2010-01-01

    ATLAS is a multipurpose experiment that records the LHC collisions. To reconstruct trajectories of charged particles produced in these collisions, ATLAS tracking system is equipped with silicon planar sensors and drift‐tube based detectors. They constitute the ATLAS Inner Detector. In order to achieve its scientific goals, the alignment of the ATLAS tracking system requires the determine accurately its almost 36000 degrees of freedom. Thus the demanded precision for the alignment of the silicon sensors is below 10 micrometers. This implies to use a large sample of high momentum and isolated charge particle tracks. The high level trigger selects those tracks online. Then the raw data with the hits information of the triggered tracks is stored in a calibration stream. Tracks from cosmic trigger during empty LHC bunches are also used as input for the alignment. The implementation of the track based alignment within the ATLAS software framework unifies different alignment approaches and allows the alignment of ...

  15. Controlling single-molecule junction conductance by molecular interactions

    Science.gov (United States)

    Kitaguchi, Y.; Habuka, S.; Okuyama, H.; Hatta, S.; Aruga, T.; Frederiksen, T.; Paulsson, M.; Ueba, H.

    2015-01-01

    For the rational design of single-molecular electronic devices, it is essential to understand environmental effects on the electronic properties of a working molecule. Here we investigate the impact of molecular interactions on the single-molecule conductance by accurately positioning individual molecules on the electrode. To achieve reproducible and precise conductivity measurements, we utilize relatively weak π-bonding between a phenoxy molecule and a STM-tip to form and cleave one contact to the molecule. The anchoring to the other electrode is kept stable using a chalcogen atom with strong bonding to a Cu(110) substrate. These non-destructive measurements permit us to investigate the variation in single-molecule conductance under different but controlled environmental conditions. Combined with density functional theory calculations, we clarify the role of the electrostatic field in the environmental effect that influences the molecular level alignment. PMID:26135251

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

    Science.gov (United States)

    Eastwood, Brian S; Childs, Elisabeth C

    2012-01-09

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

  17. Evaluation of microRNA alignment techniques

    Science.gov (United States)

    Kaspi, Antony; El-Osta, Assam

    2016-01-01

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

  18. Implementation of a Parallel Protein Structure Alignment Service on Cloud

    Directory of Open Access Journals (Sweden)

    Che-Lun Hung

    2013-01-01

    Full Text Available Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform.

  19. Design of practical alignment device in KSTAR Thomson diagnostic

    Energy Technology Data Exchange (ETDEWEB)

    Lee, J. H., E-mail: jhlee@nfri.re.kr [National Fusion Research Institute, Daejeon (Korea, Republic of); University of Science and Technology (UST), Daejeon (Korea, Republic of); Lee, S. H. [National Fusion Research Institute, Daejeon (Korea, Republic of); Yamada, I. [National Institute for Fusion Science, Toki (Japan)

    2016-11-15

    The precise alignment of the laser path and collection optics in Thomson scattering measurements is essential for accurately determining electron temperature and density in tokamak experiments. For the last five years, during the development stage, the KSTAR tokamak’s Thomson diagnostic system has had alignment fibers installed in its optical collection modules, but these lacked a proper alignment detection system. In order to address these difficulties, an alignment verifying detection device between lasers and an object field of collection optics is developed. The alignment detection device utilizes two types of filters: a narrow laser band wavelength for laser, and a broad wavelength filter for Thomson scattering signal. Four such alignment detection devices have been successfully developed for the KSTAR Thomson scattering system in this year, and these will be tested in KSTAR experiments in 2016. In this paper, we present the newly developed alignment detection device for KSTAR’s Thomson scattering diagnostics.

  20. Anatomically Plausible Surface Alignment and Reconstruction

    DEFF Research Database (Denmark)

    Paulsen, Rasmus R.; Larsen, Rasmus

    2010-01-01

    With the increasing clinical use of 3D surface scanners, there is a need for accurate and reliable algorithms that can produce anatomically plausible surfaces. In this paper, a combined method for surface alignment and reconstruction is proposed. It is based on an implicit surface representation...

  1. Multiple sequence alignment accuracy and phylogenetic inference.

    Science.gov (United States)

    Ogden, T Heath; Rosenberg, Michael S

    2006-04-01

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

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

    International Nuclear Information System (INIS)

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

    2004-01-01

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

  3. Molecular orientation and electronic structure at organic heterojunction interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Zhong, Shu [Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore (Singapore); Zhong, Jian Qiang; Wee, Andrew T.S. [Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore (Singapore); Chen, Wei, E-mail: phycw@nus.edu.sg [Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore (Singapore); Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore (Singapore); National University of Singapore (Suzhou) Research Institute, Suzhou (China)

    2015-10-01

    Highlights: • Molecular orientation at the organic heterojunction interfaces. • Energy level alignments at the organic heterojunction interfaces. • Gap-states mediated interfacial energy level alignment. - Abstract: Due to the highly anisotropic nature of π-conjugated molecules, the molecular orientation in organic thin films can significantly affect light absorption, charge transport, energy level alignment (ELA) and hence device performance. Synchrotron-based near-edge X-ray absorption fine structure (NEXAFS) spectroscopy represents a powerful technique for probing molecular orientation. The aim of this review paper is to provide a balanced assessment on the investigation of molecular orientation at the organic–organic heterojunction (OOH) interface by NEXAFS, as well as the gap-states mediated orientation dependent energy level alignment at OOH interfaces. We highlight recent progress in elucidating molecular orientation at OOH interfaces dominated by various interfacial interactions, gap-states controlled orientation dependent energy level alignments at OOH interfaces, and the manipulations of molecular orientation and ELA in OOH.

  4. Seeking the perfect alignment

    CERN Multimedia

    2002-01-01

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

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

    Science.gov (United States)

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

    2006-12-15

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

  6. Validation of the CLIC alignment strategy on short range

    CERN Document Server

    Mainaud Durand, H; Griffet, S; Kemppinen, J; Rude, V; Sosin, M

    2012-01-01

    The pre-alignment of CLIC consists of aligning the components of linacs and beam delivery systems (BDS) in the most accurate possible way, so that a first pilot beam can circulate and allow the implementation of the beam based alignment. Taking into account the precision and accuracy needed: 10 µm rms over sliding windows of 200m, this pre-alignment must be active and it can be divided into two parts: the determination of a straight reference over 20 km, thanks to a metrological network and the determination of the component positions with respect to this reference, and their adjustment. The second part is the object of the paper, describing the steps of the proposed strategy: firstly the fiducialisation of the different components of CLIC; secondly, the alignment of these components on common supports and thirdly the active alignment of these supports using sensors and actuators. These steps have been validated on a test setup over a length of 4m, and the obtained results are analysed.

  7. TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction.

    Science.gov (United States)

    Chang, Jia-Ming; Di Tommaso, Paolo; Lefort, Vincent; Gascuel, Olivier; Notredame, Cedric

    2015-07-01

    This article introduces the Transitive Consistency Score (TCS) web server; a service making it possible to estimate the local reliability of protein multiple sequence alignments (MSAs) using the TCS index. The evaluation can be used to identify the aligned positions most likely to contain structurally analogous residues and also most likely to support an accurate phylogenetic reconstruction. The TCS scoring scheme has been shown to be accurate predictor of structural alignment correctness among commonly used methods. It has also been shown to outperform common filtering schemes like Gblocks or trimAl when doing MSA post-processing prior to phylogenetic tree reconstruction. The web server is available from http://tcoffee.crg.cat/tcs. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. Energy level alignment at hybridized organic-metal interfaces from a GW projection approach

    Science.gov (United States)

    Chen, Yifeng; Tamblyn, Isaac; Quek, Su Ying

    Energy level alignments at organic-metal interfaces are of profound importance in numerous (opto)electronic applications. Standard density functional theory (DFT) calculations generally give incorrect energy level alignments and missing long-range polarization effects. Previous efforts to address this problem using the many-electron GW method have focused on physisorbed systems where hybridization effects are insignificant. Here, we use state-of-the-art GW methods to predict the level alignment at the amine-Au interface, where molecular levels do hybridize with metallic states. This non-trivial hybridization implies that DFT result is a poor approximation to the quasiparticle states. However, we find that the self-energy operator is approximately diagonal in the molecular basis, allowing us to use a projection approach to predict the level alignments. Our results indicate that the metallic substrate reduces the HOMO-LUMO gap by 3.5 4.0 eV, depending on the molecular coverage/presence of Au adatoms. Our GW results are further compared with those of a simple image charge model that describes the level alignment in physisorbed systems. Syq and YC acknowledge Grant NRF-NRFF2013-07 and the medium-sized centre program from the National Research Foundation, Singapore.

  9. Role of intrinsic molecular dipole in energy level alignment at organic interfaces

    NARCIS (Netherlands)

    Lindell, L.; Cakir, Deniz; Brocks, G.; Fahlman, M.; Braun, S.

    2013-01-01

    The energy level alignment in metal-organic and organic-organic junctions of the widely used materials tris-(8-hydroxyquinoline)aluminum (Alq3) and 1,4,5,8-naphthalenetetracarboxylic dianhydride (NTCDA) is investigated. The measured alignment schemes for single and bilayer films of Alq3 and NTCDA

  10. Energy-level alignment at interfaces between manganese phthalocyanine and C60

    Directory of Open Access Journals (Sweden)

    Daniel Waas

    2017-04-01

    Full Text Available We have used photoelectron spectroscopy to determine the energy-level alignment at organic heterojunctions made of manganese phthalocyanine (MnPc and the fullerene C60. We show that this energy-level alignment depends upon the preparation sequence, which is explained by different molecular orientations. Moreover, our results demonstrate that MnPc/C60 interfaces are hardly suited for application in organic photovoltaic devices, since the energy difference of the two lowest unoccupied molecular orbitals (LUMOs is rather small.

  11. Absorber Alignment Measurement Tool for Solar Parabolic Trough Collectors: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Stynes, J. K.; Ihas, B.

    2012-04-01

    As we pursue efforts to lower the capital and installation costs of parabolic trough solar collectors, it is essential to maintain high optical performance. While there are many optical tools available to measure the reflector slope errors of parabolic trough solar collectors, there are few tools to measure the absorber alignment. A new method is presented here to measure the absorber alignment in two dimensions to within 0.5 cm. The absorber alignment is measured using a digital camera and four photogrammetric targets. Physical contact with the receiver absorber or glass is not necessary. The alignment of the absorber is measured along its full length so that sagging of the absorber can be quantified with this technique. The resulting absorber alignment measurement provides critical information required to accurately determine the intercept factor of a collector.

  12. CAST: a new program package for the accurate characterization of large and flexible molecular systems.

    Science.gov (United States)

    Grebner, Christoph; Becker, Johannes; Weber, Daniel; Bellinger, Daniel; Tafipolski, Maxim; Brückner, Charlotte; Engels, Bernd

    2014-09-15

    The presented program package, Conformational Analysis and Search Tool (CAST) allows the accurate treatment of large and flexible (macro) molecular systems. For the determination of thermally accessible minima CAST offers the newly developed TabuSearch algorithm, but algorithms such as Monte Carlo (MC), MC with minimization, and molecular dynamics are implemented as well. For the determination of reaction paths, CAST provides the PathOpt, the Nudge Elastic band, and the umbrella sampling approach. Access to free energies is possible through the free energy perturbation approach. Along with a number of standard force fields, a newly developed symmetry-adapted perturbation theory-based force field is included. Semiempirical computations are possible through DFTB+ and MOPAC interfaces. For calculations based on density functional theory, a Message Passing Interface (MPI) interface to the Graphics Processing Unit (GPU)-accelerated TeraChem program is available. The program is available on request. Copyright © 2014 Wiley Periodicals, Inc.

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

    Directory of Open Access Journals (Sweden)

    Qi Zheng

    2016-10-01

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

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

    Science.gov (United States)

    Zheng, Qi; Grice, Elizabeth A

    2016-10-01

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

  15. Face Alignment via Regressing Local Binary Features.

    Science.gov (United States)

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

    2016-03-01

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

  16. Tracing magnetic fields with aligned grains

    International Nuclear Information System (INIS)

    Lazarian, A.

    2007-01-01

    Magnetic fields play a crucial role in various astrophysical processes, including star formation, accretion of matter, transport processes (e.g., transport of heat), and cosmic rays. One of the easiest ways to determine the magnetic field direction is via polarization of radiation resulting from extinction or/and emission by aligned dust grains. Reliability of interpretation of the polarization maps in terms of magnetic fields depends on how well we understand the grain-alignment theory. Explaining what makes grains aligned has been one of the big issues of the modern astronomy. Numerous exciting physical effects have been discovered in the course of research undertaken in this field. As both the theory and observations matured, it became clear that the grain-alignment phenomenon is inherent not only in diffuse interstellar medium or molecular clouds but also is a generic property of the dust in circumstellar regions, interplanetary space and cometary comae. Currently the grain-alignment theory is a predictive one, and its results nicely match observations. Among its predictions is a subtle phenomenon of radiative torques. This phenomenon, after having stayed in oblivion for many years after its discovery, is currently viewed as the most powerful means of alignment. In this article, I shall review the basic physical processes involved in grain alignment, and the currently known mechanisms of alignment. I shall also discuss possible niches for different alignment mechanisms. I shall dwell on the importance of the concept of grain helicity for understanding of many properties of grain alignment, and shall demonstrate that rather arbitrarily shaped grains exhibit helicity when they interact with gaseous and radiative flows

  17. Alignment modification for pencil eye shields

    International Nuclear Information System (INIS)

    Evans, M.D.; Pla, M.; Podgorsak, E.B.

    1989-01-01

    Accurate alignment of pencil beam eye shields to protect the lens of the eye may be made easier by means of a simple modification of existing apparatus. This involves drilling a small hole through the center of the shield to isolate the rayline directed to the lens and fabricating a suitable plug for this hole

  18. Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver

    Science.gov (United States)

    Blanquart, François; Golubchik, Tanya; Gall, Astrid; Bakker, Margreet; Bezemer, Daniela; Croucher, Nicholas J; Hall, Matthew; Hillebregt, Mariska; Ratmann, Oliver; Albert, Jan; Bannert, Norbert; Fellay, Jacques; Fransen, Katrien; Gourlay, Annabelle; Grabowski, M Kate; Gunsenheimer-Bartmeyer, Barbara; Günthard, Huldrych F; Kivelä, Pia; Kouyos, Roger; Laeyendecker, Oliver; Liitsola, Kirsi; Meyer, Laurence; Porter, Kholoud; Ristola, Matti; van Sighem, Ard; Cornelissen, Marion; Kellam, Paul; Reiss, Peter

    2018-01-01

    Abstract Studying the evolution of viruses and their molecular epidemiology relies on accurate viral sequence data, so that small differences between similar viruses can be meaningfully interpreted. Despite its higher throughput and more detailed minority variant data, next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of large between- and within-host diversity, including frequent indels, may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions. De novo assembly avoids this bias by aligning the reads to themselves, producing a set of sequences called contigs. However contigs provide only a partial summary of the reads, misassembly may result in their having an incorrect structure, and no information is available at parts of the genome where contigs could not be assembled. To address these problems we developed the tool shiver to pre-process reads for quality and contamination, then map them to a reference tailored to the sample using corrected contigs supplemented with the user’s choice of existing reference sequences. Run with two commands per sample, it can easily be used for large heterogeneous data sets. We used shiver to reconstruct the consensus sequence and minority variant information from paired-end short-read whole-genome data produced with the Illumina platform, for sixty-five existing publicly available samples and fifty new samples. We show the systematic superiority of mapping to shiver’s constructed reference compared with mapping the same reads to the closest of 3,249 real references: median values of 13 bases called differently and more accurately, 0 bases called differently and less accurately, and 205 bases of missing sequence recovered. We also

  19. Aligning Metabolic Pathways Exploiting Binary Relation of Reactions.

    Directory of Open Access Journals (Sweden)

    Yiran Huang

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

  20. MANGO: a new approach to multiple sequence alignment.

    Science.gov (United States)

    Zhang, Zefeng; Lin, Hao; Li, Ming

    2007-01-01

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

  1. Automated and Adaptable Quantification of Cellular Alignment from Microscopic Images for Tissue Engineering Applications

    Science.gov (United States)

    Xu, Feng; Beyazoglu, Turker; Hefner, Evan; Gurkan, Umut Atakan

    2011-01-01

    Cellular alignment plays a critical role in functional, physical, and biological characteristics of many tissue types, such as muscle, tendon, nerve, and cornea. Current efforts toward regeneration of these tissues include replicating the cellular microenvironment by developing biomaterials that facilitate cellular alignment. To assess the functional effectiveness of the engineered microenvironments, one essential criterion is quantification of cellular alignment. Therefore, there is a need for rapid, accurate, and adaptable methodologies to quantify cellular alignment for tissue engineering applications. To address this need, we developed an automated method, binarization-based extraction of alignment score (BEAS), to determine cell orientation distribution in a wide variety of microscopic images. This method combines a sequenced application of median and band-pass filters, locally adaptive thresholding approaches and image processing techniques. Cellular alignment score is obtained by applying a robust scoring algorithm to the orientation distribution. We validated the BEAS method by comparing the results with the existing approaches reported in literature (i.e., manual, radial fast Fourier transform-radial sum, and gradient based approaches). Validation results indicated that the BEAS method resulted in statistically comparable alignment scores with the manual method (coefficient of determination R2=0.92). Therefore, the BEAS method introduced in this study could enable accurate, convenient, and adaptable evaluation of engineered tissue constructs and biomaterials in terms of cellular alignment and organization. PMID:21370940

  2. Vacuum mechatronic laser alignment system on the Nova laser

    International Nuclear Information System (INIS)

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

    1991-11-01

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

  3. Reproducible Molecularly Imprinted Piezoelectric Sensor for Accurate and Sensitive Detection of Ractopamine in Swine and Feed Products

    Directory of Open Access Journals (Sweden)

    Mingfei Pan

    2018-06-01

    Full Text Available This paper describes the development of a reproducible molecularly imprinted piezoelectric sensor for the accurate and sensitive detection of ractopamine (RAC in swine and feed products. The synthesized molecularly imprinted polymer (MIP was directly immobilized on the surface of a quartz crystal microbalance (QCM Au chip as the recognition element. The experimental parameters in the fabrication, measurement and regeneration process were evaluated in detail to produce an MIP-based piezoelectric sensor with high sensing capability. The developed piezoelectric sensor was verified to perform favorably in the RAC analysis of swine and feed products, with acceptable accuracy (recovery: 75.9–93.3%, precision [relative standard deviation (n = 3: 2.3–6.4%], and sensitivity [limit of detection: 0.46 ng g−1 (swine and 0.38 ng g−1 (feed]. This portable MIP-based chip for the piezoelectric sensing of RAC could be reused for at least 30 cycles and easily stored for a long time. These results demonstrated that the developed MIP-based piezoelectric sensor presents an accurate, sensitive and cost-effective method for the quantitative detection of RAC in complex samples. This research offers a promising strategy for the development of novel effective devices used for use in food safety analysis.

  4. HeurAA: accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.

    Directory of Open Access Journals (Sweden)

    Lőrinc S Pongor

    Full Text Available Next generation sequencing (NGS of PCR amplicons is a standard approach to detect genetic variations in personalized medicine such as cancer diagnostics. Computer programs used in the NGS community often miss insertions and deletions (indels that constitute a large part of known human mutations. We have developed HeurAA, an open source, heuristic amplicon aligner program. We tested the program on simulated datasets as well as experimental data from multiplex sequencing of 40 amplicons in 12 oncogenes collected on a 454 Genome Sequencer from lung cancer cell lines. We found that HeurAA can accurately detect all indels, and is more than an order of magnitude faster than previous programs. HeurAA can compare reads and reference sequences up to several thousand base pairs in length, and it can evaluate data from complex mixtures containing reads of different gene-segments from different samples. HeurAA is written in C and Perl for Linux operating systems, the code and the documentation are available for research applications at http://sourceforge.net/projects/heuraa/

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

    Science.gov (United States)

    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.

  6. Grain alignment in starless cores

    International Nuclear Information System (INIS)

    Jones, T. J.; Bagley, M.; Krejny, M.; Andersson, B.-G.; Bastien, P.

    2015-01-01

    We present near-IR polarimetry data of background stars shining through a selection of starless cores taken in the K band, probing visual extinctions up to A V ∼48. We find that P K /τ K continues to decline with increasing A V with a power law slope of roughly −0.5. Examination of published submillimeter (submm) polarimetry of starless cores suggests that by A V ≳20 the slope for P versus τ becomes ∼−1, indicating no grain alignment at greater optical depths. Combining these two data sets, we find good evidence that, in the absence of a central illuminating source, the dust grains in dense molecular cloud cores with no internal radiation source cease to become aligned with the local magnetic field at optical depths greater than A V ∼20. A simple model relating the alignment efficiency to the optical depth into the cloud reproduces the observations well.

  7. Grain alignment in starless cores

    Energy Technology Data Exchange (ETDEWEB)

    Jones, T. J.; Bagley, M. [Minnesota Institute for Astrophysics, University of Minnesota, Minneapolis, MN 55455 (United States); Krejny, M. [Cree Inc., 4600 Silicon Dr., Durham, NC (United States); Andersson, B.-G. [SOFIA Science Center, USRA, Moffett Field, CA (United States); Bastien, P., E-mail: tjj@astro.umn.edu [Centre de recherche en astrophysique du Québec and Départment de Physique, Université de Montréal, Montréal (Canada)

    2015-01-01

    We present near-IR polarimetry data of background stars shining through a selection of starless cores taken in the K band, probing visual extinctions up to A{sub V}∼48. We find that P{sub K}/τ{sub K} continues to decline with increasing A{sub V} with a power law slope of roughly −0.5. Examination of published submillimeter (submm) polarimetry of starless cores suggests that by A{sub V}≳20 the slope for P versus τ becomes ∼−1, indicating no grain alignment at greater optical depths. Combining these two data sets, we find good evidence that, in the absence of a central illuminating source, the dust grains in dense molecular cloud cores with no internal radiation source cease to become aligned with the local magnetic field at optical depths greater than A{sub V}∼20. A simple model relating the alignment efficiency to the optical depth into the cloud reproduces the observations well.

  8. Can a semi-automated surface matching and principal axis-based algorithm accurately quantify femoral shaft fracture alignment in six degrees of freedom?

    Science.gov (United States)

    Crookshank, Meghan C; Beek, Maarten; Singh, Devin; Schemitsch, Emil H; Whyne, Cari M

    2013-07-01

    Accurate alignment of femoral shaft fractures treated with intramedullary nailing remains a challenge for orthopaedic surgeons. The aim of this study is to develop and validate a cone-beam CT-based, semi-automated algorithm to quantify the malalignment in six degrees of freedom (6DOF) using a surface matching and principal axes-based approach. Complex comminuted diaphyseal fractures were created in nine cadaveric femora and cone-beam CT images were acquired (27 cases total). Scans were cropped and segmented using intensity-based thresholding, producing superior, inferior and comminution volumes. Cylinders were fit to estimate the long axes of the superior and inferior fragments. The angle and distance between the two cylindrical axes were calculated to determine flexion/extension and varus/valgus angulation and medial/lateral and anterior/posterior translations, respectively. Both surfaces were unwrapped about the cylindrical axes. Three methods of matching the unwrapped surface for determination of periaxial rotation were compared based on minimizing the distance between features. The calculated corrections were compared to the input malalignment conditions. All 6DOF were calculated to within current clinical tolerances for all but two cases. This algorithm yielded accurate quantification of malalignment of femoral shaft fractures for fracture gaps up to 60 mm, based on a single CBCT image of the fractured limb. Copyright © 2012 IPEM. Published by Elsevier Ltd. All rights reserved.

  9. Mango: multiple alignment with N gapped oligos.

    Science.gov (United States)

    Zhang, Zefeng; Lin, Hao; Li, Ming

    2008-06-01

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

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

    Science.gov (United States)

    Lee, Hui Sun; Im, Wonpil

    2013-01-01

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

  11. Beam based alignment at the KEK accelerator test facility

    International Nuclear Information System (INIS)

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

    2002-01-01

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

  12. Effect of Terminal Modification on the Molecular Assembly and Mechanical Properties of Protein-Based Block Copolymers.

    Science.gov (United States)

    Jacobsen, Matthew M; Tokareva, Olena S; Ebrahimi, Davoud; Huang, Wenwen; Ling, Shengjie; Dinjaski, Nina; Li, David; Simon, Marc; Staii, Cristian; Buehler, Markus J; Kaplan, David L; Wong, Joyce Y

    2017-09-01

    Accurate prediction and validation of the assembly of bioinspired peptide sequences into fibers with defined mechanical characteristics would aid significantly in designing and creating materials with desired properties. This process may also be utilized to provide insight into how the molecular architecture of many natural protein fibers is assembled. In this work, computational modeling and experimentation are used in tandem to determine how peptide terminal modification affects a fiber-forming core domain. Modeling shows that increased terminal molecular weight and hydrophilicity improve peptide chain alignment under shearing conditions and promote consolidation of semicrystalline domains. Mechanical analysis shows acute improvements to strength and elasticity, but significantly reduced extensibility and overall toughness. These results highlight an important entropic function that terminal domains of fiber-forming peptides exhibit as chain alignment promoters, which ultimately has notable consequences on the mechanical behavior of the final fiber products. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Kinematically complete study on electron impact ionisation of aligned hydrogen molecules

    Energy Technology Data Exchange (ETDEWEB)

    Senftleben, Arne

    2009-10-28

    Within the work presented here, single ionisation of spatially aligned hydrogen molecules by 200 eV electrons was studied in a kinematically complete experiment. For the first time, a comprehensive set of fully differential cross sections (FDCS) was obtained for this process on a molecular target. The direction of the internuclear axis was derived from the fragment emission of post-collision dissociation of the residual H{sub 2}{sup +} ion. Therefore, a protonic fragment was detected in coincidence with the two final-state electrons using a dedicated reaction microscope and sophisticated data analysis. For direct ionisation into the ionic ground state, existing theoretical cross sections for aligned molecules were tested. Additionally, we observed molecular frame angular distributions of Auger electrons emitted through dissociative autoionisation of H{sub 2}. Earlier findings of kinematically incomplete experiments were reproduced, but the FDCS reveal structures so far unknown. Furthermore, for random alignment, differential cross sections at two distinct values of the mean internuclear distance were obtained, providing new arguments in the current discussion on the nature of discrepancies observed between atomic and molecular collisions. (orig.)

  14. LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs

    DEFF Research Database (Denmark)

    Will, Sebastian; Joshi, Tejal; Hofacker, Ivo L.

    2012-01-01

    Current genomic screens for noncoding RNAs (ncRNAs) predict a large number of genomic regions containing potential structural ncRNAs. The analysis of these data requires highly accurate prediction of ncRNA boundaries and discrimination of promising candidate ncRNAs from weak predictions. Existing...... methods struggle with these goals because they rely on sequence-based multiple sequence alignments, which regularly misalign RNA structure and therefore do not support identification of structural similarities. To overcome this limitation, we compute columnwise and global reliabilities of alignments based...... on sequence and structure similarity; we refer to these structure-based alignment reliabilities as STARs. The columnwise STARs of alignments, or STAR profiles, provide a versatile tool for the manual and automatic analysis of ncRNAs. In particular, we improve the boundary prediction of the widely used nc...

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

    International Nuclear Information System (INIS)

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

    2012-01-01

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

  16. Accurate protein structure modeling using sparse NMR data and homologous structure information.

    Science.gov (United States)

    Thompson, James M; Sgourakis, Nikolaos G; Liu, Gaohua; Rossi, Paolo; Tang, Yuefeng; Mills, Jeffrey L; Szyperski, Thomas; Montelione, Gaetano T; Baker, David

    2012-06-19

    While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that allows robust modeling of protein structures of up to 225 residues by combining (1)H(N), (13)C, and (15)N backbone and (13)Cβ chemical shift data, distance restraints derived from homologous structures, and a physically realistic all-atom energy function. Accurate models are distinguished from inaccurate models generated using incorrect sequence alignments by requiring that (i) the all-atom energies of models generated using the restraints are lower than models generated in unrestrained calculations and (ii) the low-energy structures converge to within 2.0 Å backbone rmsd over 75% of the protein. Benchmark calculations on known structures and blind targets show that the method can accurately model protein structures, even with very remote homology information, to a backbone rmsd of 1.2-1.9 Å relative to the conventional determined NMR ensembles and of 0.9-1.6 Å relative to X-ray structures for well-defined regions of the protein structures. This approach facilitates the accurate modeling of protein structures using backbone chemical shift data without need for side-chain resonance assignments and extensive analysis of NOESY cross-peak assignments.

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

    Science.gov (United States)

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

    2014-08-01

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

  18. Advanced Alignment of the ATLAS Inner Detector

    CERN Document Server

    Stahlman, JM; The ATLAS collaboration

    2012-01-01

    The primary goal of the ATLAS Inner Detector (ID) is to measure the trajectories of charged particles in the high particle density environment of the Large Hadron Collider (LHC) collisions. This is achieved using a combination of different technologies, including silicon pixels, silicon microstrips, and gaseous drift-tubes, all immersed in a 2 Tesla magnetic field. With over one million alignable degrees of freedom, it is crucial that an accurate model of the detector positions be produced using an automated and robust algorithm in order to achieve good tracking performance. This has been accomplished using a variety of alignment techniques resulting in near optimal hit and momentum resolutions.

  19. Alignment and orientation in ion/endash/atom collisions

    International Nuclear Information System (INIS)

    Kimura, M.; Lane, N.F.

    1987-01-01

    Recent progress in the theoretical study of alignment and orientation in atom-atom and ion-atom collisions at intermediate energies is reviewed. Recent systematic studies of the alignment and orientation of electronic charge cloud distributions of excited states resulting from such collisions clearly have provided more detailed information about the underlying collision dynamics. However, since accurate determination of these parameters is quite difficult, both theoretically and experimentally, a close collaboration between theory and experiment is necessary for a deeper understanding of the collision dynamics. A more complete approach, where the full density matrix is determined, is also discussed

  20. CMS Muon Alignment: System Description and first results

    CERN Document Server

    Sobron, M

    2008-01-01

    The CMS detector has been instrumented with a precise and complex opto-mechanical alignment subsystem that provides a common reference frame between Tracker and Muon detection systems by means of a net of laser beams. The system allows a continuous and accurate monitoring of the muon chambers positions with respect to the Tracker body. Preliminary results of operation during the test of the CMS 4T solenoid magnet, performed in 2006, are presented. These measurements complement the information provided by the use of survey techniques and the results of alignment algorithms based on muon tracks crossing the detector.

  1. pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment.

    Science.gov (United States)

    Warris, Sven; Timal, N Roshan N; Kempenaar, Marcel; Poortinga, Arne M; van de Geest, Henri; Varbanescu, Ana L; Nap, Jan-Peter

    2018-01-01

    Our previously published CUDA-only application PaSWAS for Smith-Waterman (SW) sequence alignment of any type of sequence on NVIDIA-based GPUs is platform-specific and therefore adopted less than could be. The OpenCL language is supported more widely and allows use on a variety of hardware platforms. Moreover, there is a need to promote the adoption of parallel computing in bioinformatics by making its use and extension more simple through more and better application of high-level languages commonly used in bioinformatics, such as Python. The novel application pyPaSWAS presents the parallel SW sequence alignment code fully packed in Python. It is a generic SW implementation running on several hardware platforms with multi-core systems and/or GPUs that provides accurate sequence alignments that also can be inspected for alignment details. Additionally, pyPaSWAS support the affine gap penalty. Python libraries are used for automated system configuration, I/O and logging. This way, the Python environment will stimulate further extension and use of pyPaSWAS. pyPaSWAS presents an easy Python-based environment for accurate and retrievable parallel SW sequence alignments on GPUs and multi-core systems. The strategy of integrating Python with high-performance parallel compute languages to create a developer- and user-friendly environment should be considered for other computationally intensive bioinformatics algorithms.

  2. A highly accurate positioning and orientation system based on the usage of four-cluster fibre optic gyros

    International Nuclear Information System (INIS)

    Zhang, Xiaoyue; Lin, Zhili; Zhang, Chunxi

    2013-01-01

    A highly accurate positioning and orientation technique based on four-cluster fibre optic gyros (FOGs) is presented. The four-cluster FOG inertial measurement unit (IMU) comprises three low-precision FOGs, one static high-precision FOG and three accelerometers. To realize high-precision positioning and orientation, the static alignment (north-seeking) before vehicle manoeuvre was divided into a low-precision self-alignment phase and a high-precision north-seeking (online calibration) phase. The high-precision FOG measurement information was introduced to obtain high-precision azimuth alignment (north-seeking) result and achieve online calibration of the low-precision three-cluster FOG. The results of semi-physical simulation were presented to validate the availability and utility of the highly accurate positioning and orientation technique based on the four-cluster FOGs. (paper)

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

    Science.gov (United States)

    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.

  4. Electron re-scattering from aligned linear molecules using the R-matrix method

    International Nuclear Information System (INIS)

    Harvey, A G; Tennyson, J

    2009-01-01

    Electron re-scattering in a strong laser field provides an important probe of molecular structure and processes. The laser field drives the ionization of the molecule, followed by acceleration and subsequent recollision of the electron with the parent molecular ion, the scattered electrons carry information about the nuclear geometry and electronic states of the molecular ion. It is advantageous in strong field experiments to work with aligned molecules, which introduces extra physics compared to the standard gas-phase, electron-molecule scattering problem. The formalism for scattering from oriented linear molecules is presented and applied to H 2 and CO 2 . Differential cross sections are presented for (re-)scattering by these systems concentrating on the most common, linear alignment. In H 2 these cross sections show significant angular structure which, particularly for a scattering angle of 90 deg., are predicted to vary significantly between re-collisions stimulated by an even or an odd number of photons. In CO 2 these cross sections are zero indicating the necessity of using non-parallel alignment with this molecule.

  5. Control rod housing alignment and repair method

    International Nuclear Information System (INIS)

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

    1992-01-01

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

  6. Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity

    Directory of Open Access Journals (Sweden)

    Lyngsø Rune

    2010-04-01

    Full Text Available Abstract Background The dynamic motions of many proteins are central to their function. It therefore follows that the dynamic requirements of a protein are evolutionary constrained. In order to assess and quantify this, one needs to compare the dynamic motions of different proteins. Comparing the dynamics of distinct proteins may also provide insight into how protein motions are modified by variations in sequence and, consequently, by structure. The optimal way of comparing complex molecular motions is, however, far from trivial. The majority of comparative molecular dynamics studies performed to date relied upon prior sequence or structural alignment to define which residues were equivalent in 3-dimensional space. Results Here we discuss an alternative methodology for comparative molecular dynamics that does not require any prior alignment information. We show it is possible to align proteins based solely on their dynamics and that we can use these dynamics-based alignments to quantify the dynamic similarity of proteins. Our method was tested on 10 representative members of the PDZ domain family. Conclusions As a result of creating pair-wise dynamics-based alignments of PDZ domains, we have found evolutionarily conserved patterns in their backbone dynamics. The dynamic similarity of PDZ domains is highly correlated with their structural similarity as calculated with Dali. However, significant differences in their dynamics can be detected indicating that sequence has a more refined role to play in protein dynamics than just dictating the overall fold. We suggest that the method should be generally applicable.

  7. Introduction of hind foot coronal alignment view

    International Nuclear Information System (INIS)

    Moon, Il Bong; Jeon, Ju Seob; Yoon, Kang Cheol; Choi, Nam Kil; Kim, Seung Kook

    2006-01-01

    Accurate clinical evaluation of the alignment of the calcaneus relative to the tibia in the coronal plane is essential in the evaluation and treatment of hind foot pathologic condition. Previously described standard anteroposterior, lateral, and oblique radiographic methods of the foot or ankle do not demonstrate alignment of the tibia relation to the calcaneus in the coronal plane. The purpose of this study was to introduce hind foot coronal alignment view. Both feet were imaged simultaneously on an elevated, radiolucent foot stand equipment. Both feet stood on a radiolucent platform with equal weight on both feet. Both feet are located foot axis longitudinal perpendicular to the platform. Silhouette tracing around both feet are made, and line is then drawn to bisect the silhouette of the second toe and the outline of the heel. The x-ray beam is angled down approximately 15 .deg. to 20 .deg. This image described tibial axis and medial, lateral tuberosity of calcaneus. Calcaneus do not rotated. The view is showed by talotibial joint space. Although computed tomographic and magnetic resonance imaging techniques are capable of demonstrating coronal hind foot alignment, they lack usefulness in most clinical situations because the foot is imaged in a non-weight bearing position. But hind foot coronal alignment view is obtained for evaluating position changing of inversion, eversion of the hind foot and varus, valgus deformity of calcaneus

  8. Beam alignment based on two-dimensional power spectral density of a near-field image.

    Science.gov (United States)

    Wang, Shenzhen; Yuan, Qiang; Zeng, Fa; Zhang, Xin; Zhao, Junpu; Li, Kehong; Zhang, Xiaolu; Xue, Qiao; Yang, Ying; Dai, Wanjun; Zhou, Wei; Wang, Yuanchen; Zheng, Kuixing; Su, Jingqin; Hu, Dongxia; Zhu, Qihua

    2017-10-30

    Beam alignment is crucial to high-power laser facilities and is used to adjust the laser beams quickly and accurately to meet stringent requirements of pointing and centering. In this paper, a novel alignment method is presented, which employs data processing of the two-dimensional power spectral density (2D-PSD) for a near-field image and resolves the beam pointing error relative to the spatial filter pinhole directly. Combining this with a near-field fiducial mark, the operation of beam alignment is achieved. It is experimentally demonstrated that this scheme realizes a far-field alignment precision of approximately 3% of the pinhole size. This scheme adopts only one near-field camera to construct the alignment system, which provides a simple, efficient, and low-cost way to align lasers.

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

    KAUST Repository

    Wan, Weiwei

    2014-03-01

    Nanoimprint lithography (NIL) is a cost-efficient nanopatterning technology because of its promising advantages of high throughput and high resolution. However, accurate multilevel overlay capability of NIL required for integrated circuit manufacturing remains a challenge due to the high cost of achieving mechanical alignment precision. Although self-aligned imprint lithography was developed to avoid the need of alignment for the vertical layered structures, it has limited usage in the manufacture of the coplanar structures, such as integrated plasmonic devices. In this paper, we develop a new process of planar self-alignment imprint lithography (P-SAIL) to fabricate the metallic and dielectric structures on the same plane. P-SAIL transfers the multilevel imprint processes to a single-imprint process which offers higher efficiency and less cost than existing manufacturing methods. Such concept is demonstrated in an example of fabricating planar plasmonic structures consisting of different materials. © 2014 Springer-Verlag Berlin Heidelberg.

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

    Science.gov (United States)

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

    2015-01-01

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

  11. Aligning the unalignable: bacteriophage whole genome alignments.

    Science.gov (United States)

    Bérard, Sèverine; Chateau, Annie; Pompidor, Nicolas; Guertin, Paul; Bergeron, Anne; Swenson, Krister M

    2016-01-13

    In recent years, many studies focused on the description and comparison of large sets of related bacteriophage genomes. Due to the peculiar mosaic structure of these genomes, few informative approaches for comparing whole genomes exist: dot plots diagrams give a mostly qualitative assessment of the similarity/dissimilarity between two or more genomes, and clustering techniques are used to classify genomes. Multiple alignments are conspicuously absent from this scene. Indeed, whole genome aligners interpret lack of similarity between sequences as an indication of rearrangements, insertions, or losses. This behavior makes them ill-prepared to align bacteriophage genomes, where even closely related strains can accomplish the same biological function with highly dissimilar sequences. In this paper, we propose a multiple alignment strategy that exploits functional collinearity shared by related strains of bacteriophages, and uses partial orders to capture mosaicism of sets of genomes. As classical alignments do, the computed alignments can be used to predict that genes have the same biological function, even in the absence of detectable similarity. The Alpha aligner implements these ideas in visual interactive displays, and is used to compute several examples of alignments of Staphylococcus aureus and Mycobacterium bacteriophages, involving up to 29 genomes. Using these datasets, we prove that Alpha alignments are at least as good as those computed by standard aligners. Comparison with the progressive Mauve aligner - which implements a partial order strategy, but whose alignments are linearized - shows a greatly improved interactive graphic display, while avoiding misalignments. Multiple alignments of whole bacteriophage genomes work, and will become an important conceptual and visual tool in comparative genomics of sets of related strains. A python implementation of Alpha, along with installation instructions for Ubuntu and OSX, is available on bitbucket (https://bitbucket.org/thekswenson/alpha).

  12. Adiabatic Field-Free Alignment of Asymmetric Top Molecules with an Optical Centrifuge.

    Science.gov (United States)

    Korobenko, A; Milner, V

    2016-05-06

    We use an optical centrifuge to align asymmetric top SO_{2} molecules by adiabatically spinning their most polarizable O-O axis. The effective centrifugal potential in the rotating frame confines the sulfur atoms to the plane of the laser-induced rotation, leading to the planar molecular alignment that persists after the molecules are released from the centrifuge. The periodic appearance of the full three-dimensional alignment, typically observed only with linear and symmetric top molecules, is also detected. Together with strong in-plane centrifugal forces, which bend the molecules by up to 10 deg, permanent field-free alignment offers new ways of controlling molecules with laser light.

  13. PR2ALIGN: a stand-alone software program and a web-server for protein sequence alignment using weighted biochemical properties of amino acids.

    Science.gov (United States)

    Kuznetsov, Igor B; McDuffie, Michael

    2015-05-07

    Alignment of amino acid sequences is the main sequence comparison method used in computational molecular biology. The selection of the amino acid substitution matrix best suitable for a given alignment problem is one of the most important decisions the user has to make. In a conventional amino acid substitution matrix all elements are fixed and their values cannot be easily adjusted. Moreover, most existing amino acid substitution matrices account for the average (dis)similarities between amino acid types and do not distinguish the contribution of a specific biochemical property to these (dis)similarities. PR2ALIGN is a stand-alone software program and a web-server that provide the functionality for implementing flexible user-specified alignment scoring functions and aligning pairs of amino acid sequences based on the comparison of the profiles of biochemical properties of these sequences. Unlike the conventional sequence alignment methods that use 20x20 fixed amino acid substitution matrices, PR2ALIGN uses a set of weighted biochemical properties of amino acids to measure the distance between pairs of aligned residues and to find an optimal minimal distance global alignment. The user can provide any number of amino acid properties and specify a weight for each property. The higher the weight for a given property, the more this property affects the final alignment. We show that in many cases the approach implemented in PR2ALIGN produces better quality pair-wise alignments than the conventional matrix-based approach. PR2ALIGN will be helpful for researchers who wish to align amino acid sequences by using flexible user-specified alignment scoring functions based on the biochemical properties of amino acids instead of the amino acid substitution matrix. To the best of the authors' knowledge, there are no existing stand-alone software programs or web-servers analogous to PR2ALIGN. The software is freely available from http://pr2align.rit.albany.edu.

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

    Science.gov (United States)

    Malod-Dognin, Noël; Pržulj, Nataša

    2015-07-01

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

  15. A Global Network Alignment Method Using Discrete Particle Swarm Optimization.

    Science.gov (United States)

    Huang, Jiaxiang; Gong, Maoguo; Ma, Lijia

    2016-10-19

    Molecular interactions data increase exponentially with the advance of biotechnology. This makes it possible and necessary to comparatively analyse the different data at a network level. Global network alignment is an important network comparison approach to identify conserved subnetworks and get insight into evolutionary relationship across species. Network alignment which is analogous to subgraph isomorphism is known to be an NP-hard problem. In this paper, we introduce a novel heuristic Particle-Swarm-Optimization based Network Aligner (PSONA), which optimizes a weighted global alignment model considering both protein sequence similarity and interaction conservations. The particle statuses and status updating rules are redefined in a discrete form by using permutation. A seed-and-extend strategy is employed to guide the searching for the superior alignment. The proposed initialization method "seeds" matches with high sequence similarity into the alignment, which guarantees the functional coherence of the mapping nodes. A greedy local search method is designed as the "extension" procedure to iteratively optimize the edge conservations. PSONA is compared with several state-of-art methods on ten network pairs combined by five species. The experimental results demonstrate that the proposed aligner can map the proteins with high functional coherence and can be used as a booster to effectively refine the well-studied aligners.

  16. Alignment of in-vessel components by metrology defined adaptive machining

    International Nuclear Information System (INIS)

    Wilson, David; Bernard, Nathanaël; Mariani, Antony

    2015-01-01

    Highlights: • Advanced metrology techniques developed for large volume high density in-vessel surveys. • Virtual alignment process employed to optimize the alignment of 440 blanket modules. • Auto-geometry construct, from survey data, using CAD proximity detection and orientation logic. • HMI developed to relocate blanket modules if customization limits on interfaces are exceeded. • Data export format derived for Catia parametric models, defining customization requirements. - Abstract: The assembly of ITER will involve the precise and accurate alignment of a large number of components and assemblies in areas where access will often be severely constrained and where process efficiency will be critical. One such area is the inside of the vacuum vessel where several thousand components shall be custom machined to provide the alignment references for in-vessel systems. The paper gives an overview of the process that will be employed; to survey the interfaces for approximately 3500 components then define and execute the customization process.

  17. Alignment of in-vessel components by metrology defined adaptive machining

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, David [ITER Organization, Route de Vinon sur Verdon, CS90 046, St Paul-lez-Durance (France); Bernard, Nathanaël [G2Métric, Launaguet 31140 (France); Mariani, Antony [Spatial Alignment Ltd., Witney (United Kingdom)

    2015-10-15

    Highlights: • Advanced metrology techniques developed for large volume high density in-vessel surveys. • Virtual alignment process employed to optimize the alignment of 440 blanket modules. • Auto-geometry construct, from survey data, using CAD proximity detection and orientation logic. • HMI developed to relocate blanket modules if customization limits on interfaces are exceeded. • Data export format derived for Catia parametric models, defining customization requirements. - Abstract: The assembly of ITER will involve the precise and accurate alignment of a large number of components and assemblies in areas where access will often be severely constrained and where process efficiency will be critical. One such area is the inside of the vacuum vessel where several thousand components shall be custom machined to provide the alignment references for in-vessel systems. The paper gives an overview of the process that will be employed; to survey the interfaces for approximately 3500 components then define and execute the customization process.

  18. MUMmer4: A fast and versatile genome alignment system.

    Directory of Open Access Journals (Sweden)

    Guillaume Marçais

    2018-01-01

    Full Text Available The MUMmer system and the genome sequence aligner nucmer included within it are among the most widely used alignment packages in genomics. Since the last major release of MUMmer version 3 in 2004, it has been applied to many types of problems including aligning whole genome sequences, aligning reads to a reference genome, and comparing different assemblies of the same genome. Despite its broad utility, MUMmer3 has limitations that can make it difficult to use for large genomes and for the very large sequence data sets that are common today. In this paper we describe MUMmer4, a substantially improved version of MUMmer that addresses genome size constraints by changing the 32-bit suffix tree data structure at the core of MUMmer to a 48-bit suffix array, and that offers improved speed through parallel processing of input query sequences. With a theoretical limit on the input size of 141Tbp, MUMmer4 can now work with input sequences of any biologically realistic length. We show that as a result of these enhancements, the nucmer program in MUMmer4 is easily able to handle alignments of large genomes; we illustrate this with an alignment of the human and chimpanzee genomes, which allows us to compute that the two species are 98% identical across 96% of their length. With the enhancements described here, MUMmer4 can also be used to efficiently align reads to reference genomes, although it is less sensitive and accurate than the dedicated read aligners. The nucmer aligner in MUMmer4 can now be called from scripting languages such as Perl, Python and Ruby. These improvements make MUMer4 one the most versatile genome alignment packages available.

  19. Efficient alignment of pyrosequencing reads for re-sequencing applications

    Directory of Open Access Journals (Sweden)

    Russo Luis MS

    2011-05-01

    Full Text Available Abstract Background Over the past few years, new massively parallel DNA sequencing technologies have emerged. These platforms generate massive amounts of data per run, greatly reducing the cost of DNA sequencing. However, these techniques also raise important computational difficulties mostly due to the huge volume of data produced, but also because of some of their specific characteristics such as read length and sequencing errors. Among the most critical problems is that of efficiently and accurately mapping reads to a reference genome in the context of re-sequencing projects. Results We present an efficient method for the local alignment of pyrosequencing reads produced by the GS FLX (454 system against a reference sequence. Our approach explores the characteristics of the data in these re-sequencing applications and uses state of the art indexing techniques combined with a flexible seed-based approach, leading to a fast and accurate algorithm which needs very little user parameterization. An evaluation performed using real and simulated data shows that our proposed method outperforms a number of mainstream tools on the quantity and quality of successful alignments, as well as on the execution time. Conclusions The proposed methodology was implemented in a software tool called TAPyR--Tool for the Alignment of Pyrosequencing Reads--which is publicly available from http://www.tapyr.net.

  20. Measurement of the attosecond emission from aligned molecules

    International Nuclear Information System (INIS)

    Boutu, W.; Merdji, H.; Fitour, R.; Monchicourt, P.; Breger, P.; Carre, B.; Salieres, P.

    2006-01-01

    Complete test of publication follows. Recently, a number of papers have demonstrated the interest of high-order harmonic generation (HHG) from molecules aligned with respect to the laser polarization. Itatani et al. (Nature 432, 867 (2004)) have shown that a precise characterization of the harmonic emission allows performing a tomographic reconstruction of the molecular orbitals that radiate. Kanai et al. (Nature 435, 470 (2005)) have evidenced quantum interferences in the recombination process of HHG that are directly related to the molecular structure. In all of these papers, only the HHG intensity was measured. The relative harmonic phase, though more difficult to measure, contains important information on the interference process, and is needed for an ab initio tomographic reconstruction. Finally, while the attosecond emission from atoms has been thoroughly studied, in particular by our group (Mairesse et al., Science (302, 1540 (2003)), it has not been investigated in molecules. In a first experiment (Wabnitz et al., EPJD (2006)), we measured the amplitude and relative phase of harmonics radiated by un-aligned nitrogen molecules. Small but reproducible deviations from the phase of harmonics generated in argon (same ionization potential as nitrogen) were measured for low orders. In a recent experiment, we have measured, up to high order, the harmonic amplitude and relative phase for aligned molecules (N 2 and CO 2 ). In order to align the molecules, we used the so-called nonadiabatic technique: a rotational wavepacket is created by a strong enough and short aligning pulse, so that a field-free alignment is obtained at the revival (a few ps after the aligning pulse). The measurement of phase locking between neighboring harmonics was performed through the photoionization of a target gas by the harmonic beam in presence of a sufficiently intense 'dressing' laser beam (RABITT technique). The harmonic phase measured when the CO 2 molecules are aligned parallel to

  1. Alignment of the Thomson scattering diagnostic on NSTX

    International Nuclear Information System (INIS)

    LeBlanc, B P; Diallo, A

    2013-01-01

    The Thomson scattering diagnostic can provide profile measurement of the electron temperature, T e , and density, n e , in plasmas. Proper laser beam path and optics arrangement permits profiles T e (R) and n e (R) measurement along the major radius R. Keeping proper alignment between the laser beam path and the collection optics is necessary for an accurate determination of the electron density. As time progresses the relative position of the collection optics field of view with respect to the laser beam path will invariably shift. This can be kept to a minimum by proper attention to the physical arrangement of the collection and laser-beam delivery optics. A system has been in place to monitor the relative position between laser beam and collection optics. Variation of the alignment can be detected before it begins to affect the quality of the profile data. This paper discusses details of the instrumentation and techniques used to maintain alignment during NSTX multi-month experimental campaigns

  2. Long Read Alignment with Parallel MapReduce Cloud Platform

    Science.gov (United States)

    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

  3. Magnetic Alignment of Block Copolymer Microdomains by Intrinsic Chain Anisotropy.

    Science.gov (United States)

    Rokhlenko, Yekaterina; Gopinadhan, Manesh; Osuji, Chinedum O; Zhang, Kai; O'Hern, Corey S; Larson, Steven R; Gopalan, Padma; Majewski, Paweł W; Yager, Kevin G

    2015-12-18

    We examine the role of intrinsic chain susceptibility anisotropy in magnetic field directed self-assembly of a block copolymer using in situ x-ray scattering. Alignment of a lamellar mesophase is observed on cooling across the disorder-order transition with the resulting orientational order inversely proportional to the cooling rate. We discuss the origin of the susceptibility anisotropy, Δχ, that drives alignment and calculate its magnitude using coarse-grained molecular dynamics to sample conformations of surface-tethered chains, finding Δχ≈2×10^{-8}. From field-dependent scattering data, we estimate that grains of ≈1.2  μm are present during alignment. These results demonstrate that intrinsic anisotropy is sufficient to support strong field-induced mesophase alignment and suggest a versatile strategy for field control of orientational order in block copolymers.

  4. A Python Script for Aligning the STIS Echelle Blaze Function

    Science.gov (United States)

    Baer, Malinda; Proffitt, Charles R.; Lockwood, Sean A.

    2018-01-01

    Accurate flux calibration for the STIS echelle modes is heavily dependent on the proper alignment of the blaze function for each spectral order. However, due to changes in the instrument alignment over time and between exposures, the blaze function can shift in wavelength. This may result in flux calibration inconsistencies of up to 10%. We present the stisblazefix Python module as a tool for STIS users to correct their echelle spectra. The stisblazefix module assumes that the error in the blaze alignment is a linear function of spectral order, and finds the set of shifts that minimizes the flux inconsistencies in the overlap between spectral orders. We discuss the uses and limitations of this tool, and show that its use can provide significant improvements to the default pipeline flux calibration for many observations.

  5. Differential evolution-simulated annealing for multiple sequence alignment

    Science.gov (United States)

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

    2017-10-01

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

  6. SAMMate: a GUI tool for processing short read alignments in SAM/BAM format

    Directory of Open Access Journals (Sweden)

    Flemington Erik

    2011-01-01

    Full Text Available Abstract Background Next Generation Sequencing (NGS technology generates tens of millions of short reads for each DNA/RNA sample. A key step in NGS data analysis is the short read alignment of the generated sequences to a reference genome. Although storing alignment information in the Sequence Alignment/Map (SAM or Binary SAM (BAM format is now standard, biomedical researchers still have difficulty accessing this information. Results We have developed a Graphical User Interface (GUI software tool named SAMMate. SAMMate allows biomedical researchers to quickly process SAM/BAM files and is compatible with both single-end and paired-end sequencing technologies. SAMMate also automates some standard procedures in DNA-seq and RNA-seq data analysis. Using either standard or customized annotation files, SAMMate allows users to accurately calculate the short read coverage of genomic intervals. In particular, for RNA-seq data SAMMate can accurately calculate the gene expression abundance scores for customized genomic intervals using short reads originating from both exons and exon-exon junctions. Furthermore, SAMMate can quickly calculate a whole-genome signal map at base-wise resolution allowing researchers to solve an array of bioinformatics problems. Finally, SAMMate can export both a wiggle file for alignment visualization in the UCSC genome browser and an alignment statistics report. The biological impact of these features is demonstrated via several case studies that predict miRNA targets using short read alignment information files. Conclusions With just a few mouse clicks, SAMMate will provide biomedical researchers easy access to important alignment information stored in SAM/BAM files. Our software is constantly updated and will greatly facilitate the downstream analysis of NGS data. Both the source code and the GUI executable are freely available under the GNU General Public License at http://sammate.sourceforge.net.

  7. CHANGE OF MAGNETIC FIELD-GAS ALIGNMENT AT THE GRAVITY-DRIVEN ALFVÉNIC TRANSITION IN MOLECULAR CLOUDS: IMPLICATIONS FOR DUST POLARIZATION OBSERVATIONS

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Che-Yu; King, Patrick K.; Li, Zhi-Yun [Department of Astronomy, University of Virginia, Charlottesville, VA 22901 (United States)

    2016-10-01

    Diffuse striations in molecular clouds are preferentially aligned with local magnetic fields, whereas dense filaments tend to be perpendicular to them. When and why this transition occurs remain uncertain. To explore the physics behind this transition, we compute the histogram of relative orientation (HRO) between the density gradient and the magnetic field in three-dimensional magnetohydrodynamic (MHD) simulations of prestellar core formation in shock-compressed regions within giant molecular clouds. We find that, in the magnetically dominated (sub-Alfvénic) post-shock region, the gas structure is preferentially aligned with the local magnetic field. For overdense sub-regions with super-Alfvénic gas, their elongation becomes preferentially perpendicular to the local magnetic field. The transition occurs when self-gravitating gas gains enough kinetic energy from the gravitational acceleration to overcome the magnetic support against the cross-field contraction, which results in a power-law increase of the field strength with density. Similar results can be drawn from HROs in projected two-dimensional maps with integrated column densities and synthetic polarized dust emission. We quantitatively analyze our simulated polarization properties, and interpret the reduced polarization fraction at high column densities as the result of increased distortion of magnetic field directions in trans- or super-Alfvénic gas. Furthermore, we introduce measures of the inclination and tangledness of the magnetic field along the line of sight as the controlling factors of the polarization fraction. Observations of the polarization fraction and angle dispersion can therefore be utilized in studying local magnetic field morphology in star-forming regions.

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

    International Nuclear Information System (INIS)

    Yang Zhengfan; Penczek, Pawel A.

    2008-01-01

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

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

    Science.gov (United States)

    Yang, Zhengfan; Penczek, Pawel A

    2008-08-01

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

  10. RNA structure alignment by a unit-vector approach.

    Science.gov (United States)

    Capriotti, Emidio; Marti-Renom, Marc A

    2008-08-15

    The recent discovery of tiny RNA molecules such as microRNAs and small interfering RNA are transforming the view of RNA as a simple information transfer molecule. Similar to proteins, the native three-dimensional structure of RNA determines its biological activity. Therefore, classifying the current structural space is paramount for functionally annotating RNA molecules. The increasing numbers of RNA structures deposited in the PDB requires more accurate, automatic and benchmarked methods for RNA structure comparison. In this article, we introduce a new algorithm for RNA structure alignment based on a unit-vector approach. The algorithm has been implemented in the SARA program, which results in RNA structure pairwise alignments and their statistical significance. The SARA program has been implemented to be of general applicability even when no secondary structure can be calculated from the RNA structures. A benchmark against the ARTS program using a set of 1275 non-redundant pairwise structure alignments results in inverted approximately 6% extra alignments with at least 50% structurally superposed nucleotides and base pairs. A first attempt to perform RNA automatic functional annotation based on structure alignments indicates that SARA can correctly assign the deepest SCOR classification to >60% of the query structures. The SARA program is freely available through a World Wide Web server http://sgu.bioinfo.cipf.es/services/SARA/. Supplementary data are available at Bioinformatics online.

  11. AlignMe—a membrane protein sequence alignment web server

    Science.gov (United States)

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

    2014-01-01

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

  12. Optimization of sequence alignment for simple sequence repeat regions

    Directory of Open Access Journals (Sweden)

    Ogbonnaya Francis C

    2011-07-01

    Full Text Available Abstract Background Microsatellites, or simple sequence repeats (SSRs, are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs. SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships. Findings To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type. When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm. Conclusions The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic

  13. Predicting RNA hyper-editing with a novel tool when unambiguous alignment is impossible.

    Science.gov (United States)

    McKerrow, Wilson H; Savva, Yiannis A; Rezaei, Ali; Reenan, Robert A; Lawrence, Charles E

    2017-07-10

    Repetitive elements are now known to have relevant cellular functions, including self-complementary sequences that form double stranded (ds) RNA. There are numerous pathways that determine the fate of endogenous dsRNA, and misregulation of endogenous dsRNA is a driver of autoimmune disease, particularly in the brain. Unfortunately, the alignment of high-throughput, short-read sequences to repeat elements poses a dilemma: Such sequences may align equally well to multiple genomic locations. In order to differentiate repeat elements, current alignment methods depend on sequence variation in the reference genome. Reads are discarded when no such variations are present. However, RNA hyper-editing, a possible fate for dsRNA, introduces enough variation to distinguish between repeats that are otherwise identical. To take advantage of this variation, we developed a new algorithm, RepProfile, that simultaneously aligns reads and predicts novel variations. RepProfile accurately aligns hyper-edited reads that other methods discard. In particular we predict hyper-editing of Drosophila melanogaster repeat elements in vivo at levels previously described only in vitro, and provide validation by Sanger sequencing sixty-two individual cloned sequences. We find that hyper-editing is concentrated in genes involved in cell-cell communication at the synapse, including some that are associated with neurodegeneration. We also find that hyper-editing tends to occur in short runs. Previous studies of RNA hyper-editing discarded ambiguously aligned reads, ignoring hyper-editing in long, perfect dsRNA - the perfect substrate for hyper-editing. We provide a method that simulation and Sanger validation show accurately predicts such RNA editing, yielding a superior picture of hyper-editing.

  14. Development of the laser alignment system with PSD used for shaft calibration

    Science.gov (United States)

    Jiao, Guohua; Li, Yulin; Hu, Baowen

    2006-02-01

    Shaft calibration is an important technique during installation and maintenance of a rotating machine. It requires unique and high-precision measurement instruments with calculation capability, and relies on experience on heavy, high-speed, or high-temperature machines. A high-precision laser alignment system has been designed using PSD (Position Sensing Detector) to change traditional manual way of shaft calibration and to make the measurement easier and more accurate. The system is comprised of two small measuring units (Laser transmitter and detector) and a hand operated control unit or a PC. Such a laser alignment system has been used in some actual shaft alignment with offset resolution 1.5μm and angular resolution 0.1°.

  15. Spreadsheet-based program for alignment of overlapping DNA sequences.

    Science.gov (United States)

    Anbazhagan, R; Gabrielson, E

    1999-06-01

    Molecular biology laboratories frequently face the challenge of aligning small overlapping DNA sequences derived from a long DNA segment. Here, we present a short program that can be used to adapt Excel spreadsheets as a tool for aligning DNA sequences, regardless of their orientation. The program runs on any Windows or Macintosh operating system computer with Excel 97 or Excel 98. The program is available for use as an Excel file, which can be downloaded from the BioTechniques Web site. Upon execution, the program opens a specially designed customized workbook and is capable of identifying overlapping regions between two sequence fragments and displaying the sequence alignment. It also performs a number of specialized functions such as recognition of restriction enzyme cutting sites and CpG island mapping without costly specialized software.

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

    International Nuclear Information System (INIS)

    Hill, S.L.

    1988-01-01

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

  17. In-Flight Self-Alignment Method Aided by Geomagnetism for Moving Basement of Guided Munitions

    Directory of Open Access Journals (Sweden)

    Shuang-biao Zhang

    2015-01-01

    Full Text Available Due to power-after-launch mode of guided munitions of high rolling speed, initial attitude of munitions cannot be determined accurately, and this makes it difficult for navigation and control system to work effectively and validly. An in-flight self-alignment method aided by geomagnetism that includes a fast in-flight coarse alignment method and an in-flight alignment model based on Kalman theory is proposed in this paper. Firstly a fast in-flight coarse alignment method is developed by using gyros, magnetic sensors, and trajectory angles. Then, an in-flight alignment model is derived by investigation of the measurement errors and attitude errors, which regards attitude errors as state variables and geomagnetic components in navigation frame as observed variables. Finally, fight data of a spinning projectile is used to verify the performance of the in-flight self-alignment method. The satisfying results show that (1 the precision of coarse alignment can attain below 5°; (2 the attitude errors by in-flight alignment model converge to 24′ at early of the latter half of the flight; (3 the in-flight alignment model based on Kalman theory has better adaptability, and show satisfying performance.

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

    Science.gov (United States)

    Nielsen, Morten; Lundegaard, Claus; Lund, Ole

    2007-07-04

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

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

    Directory of Open Access Journals (Sweden)

    Lund Ole

    2007-07-01

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

  20. Protein alignment using cellulose nanocrystals: practical considerations and range of application

    International Nuclear Information System (INIS)

    Denisov, Alexey Y.; Kloser, Elisabeth; Gray, Derek G.; Mittermaier, Anthony K.

    2010-01-01

    Cellulose nanocrystals (CNCs) form liquid crystals in aqueous solution that confer alignment to macromolecules and permit the measurement of residual dipolar couplings. CNCs possess many attractive features as an alignment medium. They are inexpensive, non-toxic, chemically inert, and robust to denaturants and temperature. Despite these advantages, CNCs are seldom employed as an alignment medium and the range of their applicability has not yet been explored. We have re-examined the use of CNCs in biomolecular NMR by analyzing the effects concentration, ionic strength, and temperature on molecular alignment. Stable alignment was obtained over wide ranges of temperature (10-70 o C) and pH (2.5-8.0), which makes CNCs potentially very useful in studies of thermophilic proteins and acid-stabilized molecules. Notably, we find that CNC suspensions are very sensitive to the concentrations of biological buffers, which must be taken into account when they are used in NMR analyses. These results have led us to develop a general procedure for preparing aligned samples with CNCs. Using the SH3 domain from the Fyn tyrosine kinase as a model system, we find that CNCs produce an alignment frame collinear with that of the commonly used Pf1 bacteriophage alignment medium, but of opposite magnitude.

  1. From protein interactions to functional annotation: graph alignment in Herpes

    Czech Academy of Sciences Publication Activity Database

    Kolář, Michal; Lassig, M.; Berg, J.

    2008-01-01

    Roč. 2, č. 90 (2008), e-e ISSN 1752-0509 Institutional research plan: CEZ:AV0Z50520514 Keywords : graph alignment * functional annotation * protein orthology Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.706, year: 2008

  2. Alignment independent 3D-QSAR, quantum calculations and molecular docking of Mer specific tyrosine kinase inhibitors as anticancer drugs

    Directory of Open Access Journals (Sweden)

    Fereshteh Shiri

    2016-03-01

    Full Text Available Mer receptor tyrosine kinase is a promising novel cancer therapeutic target in many human cancers, because abnormal activation of Mer has been implicated in survival signaling and chemoresistance. 3D-QSAR analyses based on alignment independent descriptors were performed on a series of 81 Mer specific tyrosine kinase inhibitors. The fractional factorial design (FFD and the enhanced replacement method (ERM were applied and tested as variable selection algorithms for the selection of optimal subsets of molecular descriptors from a much greater pool of such regression variables. The data set was split into 65 molecules as the training set and 16 compounds as the test set. All descriptors were generated by using the GRid INdependent descriptors (GRIND approach. After variable selection, GRIND were correlated with activity values (pIC50 by PLS regression. Of the two applied variable selection methods, ERM had a noticeable improvement on the statistical parameters of PLS model, and yielded a q2 value of 0.77, an rpred2 of 0.94, and a low RMSEP value of 0.25. The GRIND information contents influencing the affinity on Mer specific tyrosine kinase were also confirmed by docking studies. In a quantum calculation study, the energy difference between HOMO and LUMO (gap implied the high interaction of the most active molecule in the active site of the protein. In addition, the molecular electrostatic potential energy at DFT level confirmed results obtained from the molecular docking. The identified key features obtained from the molecular modeling, enabled us to design novel kinase inhibitors.

  3. Alignment independent 3D-QSAR, quantum calculations and molecular docking of Mer specific tyrosine kinase inhibitors as anticancer drugs.

    Science.gov (United States)

    Shiri, Fereshteh; Pirhadi, Somayeh; Ghasemi, Jahan B

    2016-03-01

    Mer receptor tyrosine kinase is a promising novel cancer therapeutic target in many human cancers, because abnormal activation of Mer has been implicated in survival signaling and chemoresistance. 3D-QSAR analyses based on alignment independent descriptors were performed on a series of 81 Mer specific tyrosine kinase inhibitors. The fractional factorial design (FFD) and the enhanced replacement method (ERM) were applied and tested as variable selection algorithms for the selection of optimal subsets of molecular descriptors from a much greater pool of such regression variables. The data set was split into 65 molecules as the training set and 16 compounds as the test set. All descriptors were generated by using the GRid INdependent descriptors (GRIND) approach. After variable selection, GRIND were correlated with activity values (pIC50) by PLS regression. Of the two applied variable selection methods, ERM had a noticeable improvement on the statistical parameters of PLS model, and yielded a q (2) value of 0.77, an [Formula: see text] of 0.94, and a low RMSEP value of 0.25. The GRIND information contents influencing the affinity on Mer specific tyrosine kinase were also confirmed by docking studies. In a quantum calculation study, the energy difference between HOMO and LUMO (gap) implied the high interaction of the most active molecule in the active site of the protein. In addition, the molecular electrostatic potential energy at DFT level confirmed results obtained from the molecular docking. The identified key features obtained from the molecular modeling, enabled us to design novel kinase inhibitors.

  4. Markov random field based automatic image alignment for electron tomography.

    Science.gov (United States)

    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.

  5. Automatic laser beam alignment using blob detection for an environment monitoring spectroscopy

    Science.gov (United States)

    Khidir, Jarjees; Chen, Youhua; Anderson, Gary

    2013-05-01

    This paper describes a fully automated system to align an infra-red laser beam with a small retro-reflector over a wide range of distances. The component development and test were especially used for an open-path spectrometer gas detection system. Using blob detection under OpenCV library, an automatic alignment algorithm was designed to achieve fast and accurate target detection in a complex background environment. Test results are presented to show that the proposed algorithm has been successfully applied to various target distances and environment conditions.

  6. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez.

    Since June of 2009, the muon alignment group has focused on providing new alignment constants and on finalizing the hardware alignment reconstruction. Alignment constants for DTs and CSCs were provided for CRAFT09 data reprocessing. For DT chambers, the track-based alignment was repeated using CRAFT09 cosmic ray muons and validated using segment extrapolation and split cosmic tools. One difference with respect to the previous alignment is that only five degrees of freedom were aligned, leaving the rotation around the local x-axis to be better determined by the hardware system. Similarly, DT chambers poorly aligned by tracks (due to limited statistics) were aligned by a combination of photogrammetry and hardware-based alignment. For the CSC chambers, the hardware system provided alignment in global z and rotations about local x. Entire muon endcap rings were further corrected in the transverse plane (global x and y) by the track-based alignment. Single chamber track-based alignment suffers from poor statistic...

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

    Directory of Open Access Journals (Sweden)

    Claros M Gonzalo

    2010-06-01

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

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

    Directory of Open Access Journals (Sweden)

    Dan Tufis

    2006-05-01

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

  9. CCD Camera Lens Interface for Real-Time Theodolite Alignment

    Science.gov (United States)

    Wake, Shane; Scott, V. Stanley, III

    2012-01-01

    Theodolites are a common instrument in the testing, alignment, and building of various systems ranging from a single optical component to an entire instrument. They provide a precise way to measure horizontal and vertical angles. They can be used to align multiple objects in a desired way at specific angles. They can also be used to reference a specific location or orientation of an object that has moved. Some systems may require a small margin of error in position of components. A theodolite can assist with accurately measuring and/or minimizing that error. The technology is an adapter for a CCD camera with lens to attach to a Leica Wild T3000 Theodolite eyepiece that enables viewing on a connected monitor, and thus can be utilized with multiple theodolites simultaneously. This technology removes a substantial part of human error by relying on the CCD camera and monitors. It also allows image recording of the alignment, and therefore provides a quantitative means to measure such error.

  10. Alignment dynamics of diffusive scalar gradient in a two-dimensional model flow

    Science.gov (United States)

    Gonzalez, M.

    2018-04-01

    The Lagrangian two-dimensional approach of scalar gradient kinematics is revisited accounting for molecular diffusion. Numerical simulations are performed in an analytic, parameterized model flow, which enables considering different regimes of scalar gradient dynamics. Attention is especially focused on the influence of molecular diffusion on Lagrangian statistical orientations and on the dynamics of scalar gradient alignment.

  11. Observation of enhanced field-free molecular alignment by two laser pulses

    DEFF Research Database (Denmark)

    Bisgaard, Christer; Poulsen, Mikael Dahlerup; Peronne, Emmanuel

    2004-01-01

    We show experimentally that field-free alignment of iodobenzene molecules, induced by a single, intense, linearly polarized 1.4-ps-long laser pulse, can be strongly enhanced by dividing the pulse into two optimally synchronized pulses of the same duration. For a given total energy of the two...

  12. BFAST: an alignment tool for large scale genome resequencing.

    Directory of Open Access Journals (Sweden)

    Nils Homer

    2009-11-01

    Full Text Available The new generation of massively parallel DNA sequencers, combined with the challenge of whole human genome resequencing, result in the need for rapid and accurate alignment of billions of short DNA sequence reads to a large reference genome. Speed is obviously of great importance, but equally important is maintaining alignment accuracy of short reads, in the 25-100 base range, in the presence of errors and true biological variation.We introduce a new algorithm specifically optimized for this task, as well as a freely available implementation, BFAST, which can align data produced by any of current sequencing platforms, allows for user-customizable levels of speed and accuracy, supports paired end data, and provides for efficient parallel and multi-threaded computation on a computer cluster. The new method is based on creating flexible, efficient whole genome indexes to rapidly map reads to candidate alignment locations, with arbitrary multiple independent indexes allowed to achieve robustness against read errors and sequence variants. The final local alignment uses a Smith-Waterman method, with gaps to support the detection of small indels.We compare BFAST to a selection of large-scale alignment tools -- BLAT, MAQ, SHRiMP, and SOAP -- in terms of both speed and accuracy, using simulated and real-world datasets. We show BFAST can achieve substantially greater sensitivity of alignment in the context of errors and true variants, especially insertions and deletions, and minimize false mappings, while maintaining adequate speed compared to other current methods. We show BFAST can align the amount of data needed to fully resequence a human genome, one billion reads, with high sensitivity and accuracy, on a modest computer cluster in less than 24 hours. BFAST is available at (http://bfast.sourceforge.net.

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

    Directory of Open Access Journals (Sweden)

    Shunichi Kosugi

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

  14. Comparison of Forced-Alignment Speech Recognition and Humans for Generating Reference VAD

    DEFF Research Database (Denmark)

    Kraljevski, Ivan; Tan, Zheng-Hua; Paola Bissiri, Maria

    2015-01-01

    This present paper aims to answer the question whether forced-alignment speech recognition can be used as an alternative to humans in generating reference Voice Activity Detection (VAD) transcriptions. An investigation of the level of agreement between automatic/manual VAD transcriptions and the ......This present paper aims to answer the question whether forced-alignment speech recognition can be used as an alternative to humans in generating reference Voice Activity Detection (VAD) transcriptions. An investigation of the level of agreement between automatic/manual VAD transcriptions...... and the reference ones produced by a human expert was carried out. Thereafter, statistical analysis was employed on the automatically produced and the collected manual transcriptions. Experimental results confirmed that forced-alignment speech recognition can provide accurate and consistent VAD labels....

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

    CERN Document Server

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

    2012-01-01

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

  16. Long Read Alignment with Parallel MapReduce Cloud Platform

    Directory of Open Access Journals (Sweden)

    Ahmed Abdulhakim Al-Absi

    2015-01-01

    Full Text Available 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.

  17. Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment

    Directory of Open Access Journals (Sweden)

    Daniels Noah M

    2012-10-01

    Full Text Available Abstract Background The quality of multiple protein structure alignments are usually computed and assessed based on geometric functions of the coordinates of the backbone atoms from the protein chains. These purely geometric methods do not utilize directly protein sequence similarity, and in fact, determining the proper way to incorporate sequence similarity measures into the construction and assessment of protein multiple structure alignments has proved surprisingly difficult. Results We present Formatt, a multiple structure alignment based on the Matt purely geometric multiple structure alignment program, that also takes into account sequence similarity when constructing alignments. We show that Formatt outperforms Matt and other popular structure alignment programs on the popular HOMSTRAD benchmark. For the SABMark twilight zone benchmark set that captures more remote homology, Formatt and Matt outperform other programs; depending on choice of embedded sequence aligner, Formatt produces either better sequence and structural alignments with a smaller core size than Matt, or similarly sized alignments with better sequence similarity, for a small cost in average RMSD. Conclusions Considering sequence information as well as purely geometric information seems to improve quality of multiple structure alignments, though defining what constitutes the best alignment when sequence and structural measures would suggest different alignments remains a difficult open question.

  18. Considerations in the identification of functional RNA structural elements in genomic alignments

    Directory of Open Access Journals (Sweden)

    Blencowe Benjamin J

    2007-01-01

    Full Text Available Abstract Background Accurate identification of novel, functional noncoding (nc RNA features in genome sequence has proven more difficult than for exons. Current algorithms identify and score potential RNA secondary structures on the basis of thermodynamic stability, conservation, and/or covariance in sequence alignments. Neither the algorithms nor the information gained from the individual inputs have been independently assessed. Furthermore, due to issues in modelling background signal, it has been difficult to gauge the precision of these algorithms on a genomic scale, in which even a seemingly small false-positive rate can result in a vast excess of false discoveries. Results We developed a shuffling algorithm, shuffle-pair.pl, that simultaneously preserves dinucleotide frequency, gaps, and local conservation in pairwise sequence alignments. We used shuffle-pair.pl to assess precision and recall of six ncRNA search tools (MSARI, QRNA, ddbRNA, RNAz, Evofold, and several variants of simple thermodynamic stability on a test set of 3046 alignments of known ncRNAs. Relative to mononucleotide shuffling, preservation of dinucleotide content in shuffling the alignments resulted in a drastic increase in estimated false-positive detection rates for ncRNA elements, precluding evaluation of higher order alignments, which cannot not be adequately shuffled maintaining both dinucleotides and alignment structure. On pairwise alignments, none of the covariance-based tools performed markedly better than thermodynamic scoring alone. Although the high false-positive rates call into question the veracity of any individual predicted secondary structural element in our analysis, we nevertheless identified intriguing global trends in human genome alignments. The distribution of ncRNA prediction scores in 75-base windows overlapping UTRs, introns, and intergenic regions analyzed using both thermodynamic stability and EvoFold (which has no thermodynamic component was

  19. The influence of atomic alignment on absorption and emission spectroscopy

    Science.gov (United States)

    Zhang, Heshou; Yan, Huirong; Richter, Philipp

    2018-06-01

    Spectroscopic observations play essential roles in astrophysics. They are crucial for determining physical parameters in the universe, providing information about the chemistry of various astronomical environments. The proper execution of the spectroscopic analysis requires accounting for all the physical effects that are compatible to the signal-to-noise ratio. We find in this paper the influence on spectroscopy from the atomic/ground state alignment owing to anisotropic radiation and modulated by interstellar magnetic field, has significant impact on the study of interstellar gas. In different observational scenarios, we comprehensively demonstrate how atomic alignment influences the spectral analysis and provide the expressions for correcting the effect. The variations are even more pronounced for multiplets and line ratios. We show the variation of the deduced physical parameters caused by the atomic alignment effect, including alpha-to-iron ratio ([X/Fe]) and ionisation fraction. Synthetic observations are performed to illustrate the visibility of such effect with current facilities. A study of PDRs in ρ Ophiuchi cloud is presented to demonstrate how to account for atomic alignment in practice. Our work has shown that due to its potential impact, atomic alignment has to be included in an accurate spectroscopic analysis of the interstellar gas with current observational capability.

  20. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez

    2010-01-01

    The main developments in muon alignment since March 2010 have been the production, approval and deployment of alignment constants for the ICHEP data reprocessing. In the barrel, a new geometry, combining information from both hardware and track-based alignment systems, has been developed for the first time. The hardware alignment provides an initial DT geometry, which is then anchored as a rigid solid, using the link alignment system, to a reference frame common to the tracker. The “GlobalPositionRecords” for both the Tracker and Muon systems are being used for the first time, and the initial tracker-muon relative positioning, based on the link alignment, yields good results within the photogrammetry uncertainties of the Tracker and alignment ring positions. For the first time, the optical and track-based alignments show good agreement between them; the optical alignment being refined by the track-based alignment. The resulting geometry is the most complete to date, aligning all 250 DTs, ...

  1. Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical

    International Nuclear Information System (INIS)

    Genova, Alessandro; Pavanello, Michele; Ceresoli, Davide

    2016-01-01

    In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange–correlation potentials that are linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH • radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH • radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.

  2. Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical.

    Science.gov (United States)

    Genova, Alessandro; Ceresoli, Davide; Pavanello, Michele

    2016-06-21

    In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange-correlation potentials that are linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH(•) radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH(•) radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.

  3. Uni- and tridimensional alignment of molecules by femto-second laser pulse

    International Nuclear Information System (INIS)

    Rouzee, Arnaud

    2007-01-01

    This thesis is devoted to the study of the alignment of linear and asymmetric top molecules generated by an intense laser pulse. In the case of short pulses with respect to molecular rotation, periodic alignment appears in field-free conditions after the extinction of the field. We study theoretically and experimentally the effects of intensity, temperature and polarization of the electric field on produced alignment. If the field is linearly polarized, the interaction leads to the alignment of the most polarizable axis of the molecule. If the field is elliptically polarized, the pulse can generate a simultaneous alignment of the three principal axes of inertia of an asymmetric top molecule (3-D alignment). This alignment can be characterized experimentally using pump-probe techniques which exploit the optical properties of the medium. They require the use of a second pulse of low intensity temporally delayed. Three techniques were exploited during this thesis. The first technique measures a depolarization due to the birefringence of the medium when the molecules are aligned. The second is based on the defocusing of the pulse on a gradient of index created following the space variation of alignment with respect to the spatial profile of the field. The last involves the creation of a grading of index to the intersection of two intense pulses, which causes the diffraction of the probe. Finally, we show experimentally that the birefringence technique can be used to quantify the 3-D alignment of an asymmetric top molecule like ethylene. (author) [fr

  4. Application of probabilistic modelling for the uncertainty evaluation of alignment measurements of large accelerator magnets assemblies

    Science.gov (United States)

    Doytchinov, I.; Tonnellier, X.; Shore, P.; Nicquevert, B.; Modena, M.; Mainaud Durand, H.

    2018-05-01

    Micrometric assembly and alignment requirements for future particle accelerators, and especially large assemblies, create the need for accurate uncertainty budgeting of alignment measurements. Measurements and uncertainties have to be accurately stated and traceable, to international standards, for metre-long sized assemblies, in the range of tens of µm. Indeed, these hundreds of assemblies will be produced and measured by several suppliers around the world, and will have to be integrated into a single machine. As part of the PACMAN project at CERN, we proposed and studied a practical application of probabilistic modelling of task-specific alignment uncertainty by applying a simulation by constraints calibration method. Using this method, we calibrated our measurement model using available data from ISO standardised tests (10360 series) for the metrology equipment. We combined this model with reference measurements and analysis of the measured data to quantify the actual specific uncertainty of each alignment measurement procedure. Our methodology was successfully validated against a calibrated and traceable 3D artefact as part of an international inter-laboratory study. The validated models were used to study the expected alignment uncertainty and important sensitivity factors in measuring the shortest and longest of the compact linear collider study assemblies, 0.54 m and 2.1 m respectively. In both cases, the laboratory alignment uncertainty was within the targeted uncertainty budget of 12 µm (68% confidence level). It was found that the remaining uncertainty budget for any additional alignment error compensations, such as the thermal drift error due to variation in machine operation heat load conditions, must be within 8.9 µm and 9.8 µm (68% confidence level) respectively.

  5. Impulsive Laser Induced Alignment of Molecules Dissolved in Helium Nanodroplets

    DEFF Research Database (Denmark)

    Pentlehner, Dominik; H. Nielsen, Jens; Slenczka, Alkwin

    2013-01-01

    We show that a 450 fs nonresonant, moderately intense, linearly polarized laser pulse can induce field-free molecular axis alignment of methyliodide (CH3I) molecules dissolved in a helium nanodroplet. Time-resolved measurements reveal rotational dynamics much slower than that of isolated molecules...

  6. Understanding Interfacial Alignment in Solution Coated Conjugated Polymer Thin Films

    International Nuclear Information System (INIS)

    Qu, Ge; Zhao, Xikang; Newbloom, Gregory M.; Zhang, Fengjiao; Mohammadi, Erfan

    2017-01-01

    Domain alignment in conjugated polymer thin films can significantly enhance charge carrier mobility. However, the alignment mechanism during meniscus-guided solution coating remains unclear. Furthermore, interfacial alignment has been rarely studied despite its direct relevance and critical importance to charge transport. In this study, we uncover a significantly higher degree of alignment at the top interface of solution coated thin films, using a donor–acceptor conjugated polymer, poly(diketopyrrolopyrrole-co-thiopheneco- thieno[3,2-b]thiophene-co-thiophene) (DPP2T-TT), as the model system. At the molecular level, we observe in-plane π–π stacking anisotropy of up to 4.8 near the top interface with the polymer backbone aligned parallel to the coating direction. The bulk of the film is only weakly aligned with the backbone oriented transverse to coating. At the mesoscale, we observe a well-defined fibril-like morphology at the top interface with the fibril long axis pointing toward the coating direction. Significantly smaller fibrils with poor orientational order are found on the bottom interface, weakly aligned orthogonal to the fibrils on the top interface. The high degree of alignment at the top interface leads to a charge transport anisotropy of up to 5.4 compared to an anisotropy close to 1 on the bottom interface. We attribute the formation of distinct interfacial morphology to the skin-layer formation associated with high Peclet number, which promotes crystallization on the top interface while suppressing it in the bulk. As a result, we further infer that the interfacial fibril alignment is driven by the extensional flow on the top interface arisen from increasing solvent evaporation rate closer to the meniscus front.

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

    Science.gov (United States)

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

    2010-06-01

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

  8. The SOAPS project – Spin-orbit alignment of planetary systems

    Directory of Open Access Journals (Sweden)

    Hebb L.

    2013-04-01

    Full Text Available The wealth of information rendered by Kepler planets and planet candidates is indispensable for statistically significant studies of distinct planet populations, in both single and multiple systems. Empirical evidences suggest that Kepler's planet population shows different physical properties as compared to the bulk of known exoplanets. The SOAPS project, aims to shed light on Kepler's planets formation, their migration and architecture. By measuring v sini accurately for Kepler hosts with rotation periods measured from their high-precision light curves, we will assess the alignment of the planetary orbit with respect to the stellar spin axis. This degree of alignment traces the formation history and evolution of the planetary systems, and thus, allows to distinguish between different proposed migration theories. SOAPS will increase by a factor of 2 the number of spin-orbit alignment measurements pushing the parameters space down to the SuperEarth domain. Here we present our preliminary results.

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

    International Nuclear Information System (INIS)

    Hong, Jung Moo; Zou Jun

    2008-01-01

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

  10. Improving model construction of profile HMMs for remote homology detection through structural alignment

    Directory of Open Access Journals (Sweden)

    Zaverucha Gerson

    2007-11-01

    Full Text Available Abstract Background Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs are one of the most successful approaches in addressing this important problem. pHMM packages present a relatively small computational cost, and perform particularly well at recognizing remote homologies. This raises the question of whether structural alignments could impact the performance of pHMMs trained from proteins in the Twilight Zone, as structural alignments are often more accurate than sequence alignments at identifying motifs and functional residues. Next, we assess the impact of using structural alignments in pHMM performance. Results We used the SCOP database to perform our experiments. Structural alignments were obtained using the 3DCOFFEE and MAMMOTH-mult tools; sequence alignments were obtained using CLUSTALW, TCOFFEE, MAFFT and PROBCONS. We performed leave-one-family-out cross-validation over super-families. Performance was evaluated through ROC curves and paired two tailed t-test. Conclusion We observed that pHMMs derived from structural alignments performed significantly better than pHMMs derived from sequence alignment in low-identity regions, mainly below 20%. We believe this is because structural alignment tools are better at focusing on the important patterns that are more often conserved through evolution, resulting in higher quality pHMMs. On the other hand, sensitivity of these tools is still quite low for these low-identity regions. Our results suggest a number of possible directions for improvements in this area.

  11. Improving model construction of profile HMMs for remote homology detection through structural alignment.

    Science.gov (United States)

    Bernardes, Juliana S; Dávila, Alberto M R; Costa, Vítor S; Zaverucha, Gerson

    2007-11-09

    Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs) are one of the most successful approaches in addressing this important problem. pHMM packages present a relatively small computational cost, and perform particularly well at recognizing remote homologies. This raises the question of whether structural alignments could impact the performance of pHMMs trained from proteins in the Twilight Zone, as structural alignments are often more accurate than sequence alignments at identifying motifs and functional residues. Next, we assess the impact of using structural alignments in pHMM performance. We used the SCOP database to perform our experiments. Structural alignments were obtained using the 3DCOFFEE and MAMMOTH-mult tools; sequence alignments were obtained using CLUSTALW, TCOFFEE, MAFFT and PROBCONS. We performed leave-one-family-out cross-validation over super-families. Performance was evaluated through ROC curves and paired two tailed t-test. We observed that pHMMs derived from structural alignments performed significantly better than pHMMs derived from sequence alignment in low-identity regions, mainly below 20%. We believe this is because structural alignment tools are better at focusing on the important patterns that are more often conserved through evolution, resulting in higher quality pHMMs. On the other hand, sensitivity of these tools is still quite low for these low-identity regions. Our results suggest a number of possible directions for improvements in this area.

  12. Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, Ronald C. [Case Western Reserve Univ., Cleveland, OH (United States)

    1991-11-01

    This thesis involved the construction of (1) a grammar that incorporates knowledge on base invariancy and secondary structure in a molecule and (2) a parser engine that uses the grammar to position bases into the structural subunits of the molecule. These concepts were combined with a novel pinning technique to form a tool that semi-automates insertion of a new species into the alignment for the 16S rRNA molecule (a component of the ribosome) maintained by Dr. Carl Woese`s group at the University of Illinois at Urbana. The tool was tested on species extracted from the alignment and on a group of entirely new species. The results were very encouraging, and the tool should be substantial aid to the curators of the 16S alignment. The construction of the grammar was itself automated, allowing application of the tool to alignments for other molecules. The logic programming language Prolog was used to construct all programs involved. The computational linguistics approach used here was found to be a useful way to attach the problem of insertion into an alignment.

  13. Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, R.C.

    1991-11-01

    This thesis involved the construction of (1) a grammar that incorporates knowledge on base invariancy and secondary structure in a molecule and (2) a parser engine that uses the grammar to position bases into the structural subunits of the molecule. These concepts were combined with a novel pinning technique to form a tool that semi-automates insertion of a new species into the alignment for the 16S rRNA molecule (a component of the ribosome) maintained by Dr. Carl Woese's group at the University of Illinois at Urbana. The tool was tested on species extracted from the alignment and on a group of entirely new species. The results were very encouraging, and the tool should be substantial aid to the curators of the 16S alignment. The construction of the grammar was itself automated, allowing application of the tool to alignments for other molecules. The logic programming language Prolog was used to construct all programs involved. The computational linguistics approach used here was found to be a useful way to attach the problem of insertion into an alignment.

  14. Incorporation of unique molecular identifiers in TruSeq adapters improves the accuracy of quantitative sequencing.

    Science.gov (United States)

    Hong, Jungeui; Gresham, David

    2017-11-01

    Quantitative analysis of next-generation sequencing (NGS) data requires discriminating duplicate reads generated by PCR from identical molecules that are of unique origin. Typically, PCR duplicates are identified as sequence reads that align to the same genomic coordinates using reference-based alignment. However, identical molecules can be independently generated during library preparation. Misidentification of these molecules as PCR duplicates can introduce unforeseen biases during analyses. Here, we developed a cost-effective sequencing adapter design by modifying Illumina TruSeq adapters to incorporate a unique molecular identifier (UMI) while maintaining the capacity to undertake multiplexed, single-index sequencing. Incorporation of UMIs into TruSeq adapters (TrUMIseq adapters) enables identification of bona fide PCR duplicates as identically mapped reads with identical UMIs. Using TrUMIseq adapters, we show that accurate removal of PCR duplicates results in improved accuracy of both allele frequency (AF) estimation in heterogeneous populations using DNA sequencing and gene expression quantification using RNA-Seq.

  15. Theoretical and practical feasibility demonstration of a micrometric remotely controlled pre-alignment system for the CLIC linear collider

    CERN Document Server

    Mainaud Durand, H; Chritin, N; Griffet, S; Kemppinen, J; Sosin, M; Touze, T

    2011-01-01

    The active pre-alignment of the Compact Linear Collider (CLIC) is one of the key points of the project: the components must be pre-aligned w.r.t. a straight line within a few microns over a sliding window of 200 m, along the two linacs of 20 km each. The proposed solution consists of stretched wires of more than 200 m, overlapping over half of their length, which will be the reference of alignment. Wire Positioning Sensors (WPS), coupled to the supports to be pre-aligned, will perform precise and accurate measurements within a few microns w.r.t. these wires. A micrometric fiducialisation of the components and a micrometric alignment of the components on common supports will make the strategy of pre-alignment complete. In this paper, the global strategy of active pre-alignment is detailed and illustrated by the latest results demonstrating the feasibility of the proposed solution.

  16. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez

    2010-01-01

    Most of the work in muon alignment since December 2009 has focused on the geometry reconstruction from the optical systems and improvements in the internal alignment of the DT chambers. The barrel optical alignment system has progressively evolved from reconstruction of single active planes to super-planes (December 09) to a new, full barrel reconstruction. Initial validation studies comparing this full barrel alignment at 0T with photogrammetry provide promising results. In addition, the method has been applied to CRAFT09 data, and the resulting alignment at 3.8T yields residuals from tracks (extrapolated from the tracker) which look smooth, suggesting a good internal barrel alignment with a small overall offset with respect to the tracker. This is a significant improvement, which should allow the optical system to provide a start-up alignment for 2010. The end-cap optical alignment has made considerable progress in the analysis of transfer line data. The next set of alignment constants for CSCs will there...

  17. Theory of strong-field ionization of aligned CO2

    DEFF Research Database (Denmark)

    Abu-Samha, Mahmoud; Madsen, Lars Bojer

    2009-01-01

    resonance states, and the alignment-dependent ionization yields do not follow the electron density of the initial states. The theory explains the breakdown of semianalytical theories, such as the molecular tunneling theory and strong-field approximation, where excited electronic structure is neglected....

  18. Rotational Mal-Alignment after Reamed Intramedullary Nailing for tibial shaft fracture.

    Science.gov (United States)

    Khan, Sher Baz; Mohib, Yasir; Rashid, Rizwan Haroon; Rashid, Haroonur

    2016-10-01

    Intra-medullary (IM) nailing is standard of care for unstable tibial shaft fractures. Malrotation is very common but it is under-recognised, inpart because of variation in normal anatomy and partly due to difficulty in accurately assessing rotation. This study was planned to evaluate the frequency of rotational mal-alignment after reamed tibia IMnailing. This cross-sectional study was conducted at Aga khan University Hospital, Karachi, and comprised patients with tibia shaft fractures managed with IMnailing from January to December 2014. All the patients were assessed intra-operatively for rotational alignment using the knee and ankle fluoroscopic images. There were 81 patients with a mean age of 38±16.9 years. There were 64(79%) male patients. Overall the incidence of malrotation was in 20(24.7%) cases. Rotational mal-alignment is one of the preventable complications after IMnailing which can be assesed intra-operatively under fluoroscope.

  19. Magnetic Field Alignment of PS-P4VP: a Non-Liquid Crystalline Coil-Coil Block Copolymer

    Science.gov (United States)

    Rokhlenko, Yekaterina; Zhang, Kai; Larson, Steven; Gopalan, Padma; O'Hern, Corey; Osuji, Chinedum

    2015-03-01

    Magnetic fields provide the ability to control alignment of self-assembled soft materials such as block copolymers. Most prior work in this area has relied on the presence of ordered assemblies of anisotropic liquid crystalline species to ensure sufficient magnetic anisotropy to drive alignment. Recent experiments with poly(styrene-b-4-vinylpyridine), a non-liquid crystalline BCP, however, show field-induced alignment of a lamellar microstructure during cooling across the order-disorder transition. Using in situ x-ray scattering, we examine the roles of field strength and cooling rate on the alignment response of this low MW coil-coil BCP. Alignment is first observed at field strengths as low as 1 Tesla and improves markedly with both increasing field strength and slower cooling. We present a geometric argument to illustrate the origin of a finite, non-trivial magnetic susceptibility anisotropy for highly stretched surface-tethered polymer chains and corroborate this using coarse-grained molecular dynamics simulations. We rationalize the magnetic field response of the system in terms of the mobility afforded by the absence of entanglements, the intrinsic anisotropy resulting from the stretched polymer chains and sterically constrained conjugated rings, and the large grain size in these low molecular weight materials.

  20. Alignment of the ATLAS Inner Detector

    CERN Document Server

    Marti-Garcia, Salvador; The ATLAS collaboration

    2016-01-01

    The Run-2 of the LHC has presented new challenges to track and vertex reconstruction with higher energies, denser jets and higher rates. In addition, the Insertable B-layer (IBL) is a fourth pixel layer, which has been deployed at the centre of ATLAS during the longshutdown-1 of the LHC. The physics performance of the experiment requires a high resolution and unbiased measurement of all charged particle kinematic parameters. In its turn, the performance of the tracking depends, among many other issues, on the accurate determination of the alignment parameters of the tracking sensors. The offline track based alignment of the ATLAS tracking system has to deal with more than 700,000 degrees of freedom (DoF). This represents a considerable numerical challenge in terms of both CPU time and precision. During Run-2, a mechanical distortion of the IBL staves up to 20um has been observed during data-taking, plus other short time scale movements. The talk will also describe the procedures implemented to detect and remo...

  1. Sensing Characteristics of A Precision Aligner Using Moire Gratings for Precision Alignment System

    Institute of Scientific and Technical Information of China (English)

    ZHOU Lizhong; Hideo Furuhashi; Yoshiyuki Uchida

    2001-01-01

    Sensing characteristics of a precision aligner using moire gratings for precision alignment sysem has been investigated. A differential moire alignment system and a modified alignment system were used. The influence of the setting accuracy of the gap length and inclination of gratings on the alignment accuracy has been studied experimentally and theoretically. Setting accuracy of the gap length less than 2.5μm is required in modified moire alignment. There is no influence of the gap length on the alignment accuracy in the differential alignment system. The inclination affects alignment accuracies in both differential and modified moire alignment systems.

  2. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    Z. Szillasi and G. Gomez.

    2013-01-01

    When CMS is opened up, major components of the Link and Barrel Alignment systems will be removed. This operation, besides allowing for maintenance of the detector underneath, is needed for making interventions that will reinforce the alignment measurements and make the operation of the alignment system more reliable. For that purpose and also for their general maintenance and recalibration, the alignment components will be transferred to the Alignment Lab situated in the ISR area. For the track-based alignment, attention is focused on the determination of systematic uncertainties, which have become dominant, since now there is a large statistics of muon tracks. This will allow for an improved Monte Carlo misalignment scenario and updated alignment position errors, crucial for high-momentum muon analysis such as Z′ searches.

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

    Energy Technology Data Exchange (ETDEWEB)

    Mohammadi, Shahin [Purdue Univ., West Lafayette, IN (United States); Gleich, David F. [Purdue Univ., West Lafayette, IN (United States); Kolda, Tamara G. [Sandia National Laboratories (SNL-CA), Livermore, CA (United States); Grama, Ananth [Purdue Univ., West Lafayette, IN (United States)

    2015-11-01

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

  4. Induced alignment and measurement of dipolar couplings of an SH2 domain through direct binding with filamentous phage

    International Nuclear Information System (INIS)

    Dahlke Ojennus, Deanna; Mitton-Fry, Rachel M.; Wuttke, Deborah S.

    1999-01-01

    Large residual 15 N- 1 H dipolar couplings have been measured in a Src homology II domain aligned at Pf1 bacteriophage concentrations an order of magnitude lower than used for induction of a similar degree of alignment of nucleic acids and highly acidic proteins. An increase in 1 H and 15 N protein linewidths and a decrease in T 2 and T 1 ρ relaxation time constants implicates a binding interaction between the protein and phage as the mechanism of alignment. However, the associated increased linewidth does not preclude the accurate measurement of large dipolar couplings in the aligned protein. A good correlation is observed between measured dipolar couplings and predicted values based on the high resolution NMR structure of the SH2 domain. The observation of binding-induced protein alignment promises to broaden the scope of alignment techniques by extending their applicability to proteins that are able to interact weakly with the alignment medium

  5. Estimates of statistical significance for comparison of individual positions in multiple sequence alignments

    Directory of Open Access Journals (Sweden)

    Sadreyev Ruslan I

    2004-08-01

    Full Text Available Abstract Background Profile-based analysis of multiple sequence alignments (MSA allows for accurate comparison of protein families. Here, we address the problems of detecting statistically confident dissimilarities between (1 MSA position and a set of predicted residue frequencies, and (2 between two MSA positions. These problems are important for (i evaluation and optimization of methods predicting residue occurrence at protein positions; (ii detection of potentially misaligned regions in automatically produced alignments and their further refinement; and (iii detection of sites that determine functional or structural specificity in two related families. Results For problems (1 and (2, we propose analytical estimates of P-value and apply them to the detection of significant positional dissimilarities in various experimental situations. (a We compare structure-based predictions of residue propensities at a protein position to the actual residue frequencies in the MSA of homologs. (b We evaluate our method by the ability to detect erroneous position matches produced by an automatic sequence aligner. (c We compare MSA positions that correspond to residues aligned by automatic structure aligners. (d We compare MSA positions that are aligned by high-quality manual superposition of structures. Detected dissimilarities reveal shortcomings of the automatic methods for residue frequency prediction and alignment construction. For the high-quality structural alignments, the dissimilarities suggest sites of potential functional or structural importance. Conclusion The proposed computational method is of significant potential value for the analysis of protein families.

  6. Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences.

    Science.gov (United States)

    Tan, Yen Hock; Huang, He; Kihara, Daisuke

    2006-08-15

    Aligning distantly related protein sequences is a long-standing problem in bioinformatics, and a key for successful protein structure prediction. Its importance is increasing recently in the context of structural genomics projects because more and more experimentally solved structures are available as templates for protein structure modeling. Toward this end, recent structure prediction methods employ profile-profile alignments, and various ways of aligning two profiles have been developed. More fundamentally, a better amino acid similarity matrix can improve a profile itself; thereby resulting in more accurate profile-profile alignments. Here we have developed novel amino acid similarity matrices from knowledge-based amino acid contact potentials. Contact potentials are used because the contact propensity to the other amino acids would be one of the most conserved features of each position of a protein structure. The derived amino acid similarity matrices are tested on benchmark alignments at three different levels, namely, the family, the superfamily, and the fold level. Compared to BLOSUM45 and the other existing matrices, the contact potential-based matrices perform comparably in the family level alignments, but clearly outperform in the fold level alignments. The contact potential-based matrices perform even better when suboptimal alignments are considered. Comparing the matrices themselves with each other revealed that the contact potential-based matrices are very different from BLOSUM45 and the other matrices, indicating that they are located in a different basin in the amino acid similarity matrix space.

  7. Accurate Kirkwood-Buff Integrals from Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Wedberg, Nils Hejle Rasmus Ingemar; O'Connell, John P.; Peters, Günther H.J.

    2010-01-01

    A method is proposed for obtaining thermodynamic properties via Kirkwood–Buff (KB) integrals from molecular simulations. In order to ensure that the KB integration converges, the pair distribution function is extrapolated to large distances using the extension method of Verlet, which enforces...... of state fitted to simulation results. Good agreement is achieved for both fluids at densities larger than 1.5 times the critical density....

  8. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez and J. Pivarski

    2011-01-01

    Alignment efforts in the first few months of 2011 have shifted away from providing alignment constants (now a well established procedure) and focussed on some critical remaining issues. The single most important task left was to understand the systematic differences observed between the track-based (TB) and hardware-based (HW) barrel alignments: a systematic difference in r-φ and in z, which grew as a function of z, and which amounted to ~4-5 mm differences going from one end of the barrel to the other. This difference is now understood to be caused by the tracker alignment. The systematic differences disappear when the track-based barrel alignment is performed using the new “twist-free” tracker alignment. This removes the largest remaining source of systematic uncertainty. Since the barrel alignment is based on hardware, it does not suffer from the tracker twist. However, untwisting the tracker causes endcap disks (which are aligned ...

  9. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    Gervasio Gomez

    The main progress of the muon alignment group since March has been in the refinement of both the track-based alignment for the DTs and the hardware-based alignment for the CSCs. For DT track-based alignment, there has been significant improvement in the internal alignment of the superlayers inside the DTs. In particular, the distance between superlayers is now corrected, eliminating the residual dependence on track impact angles, and good agreement is found between survey and track-based corrections. The new internal geometry has been approved to be included in the forthcoming reprocessing of CRAFT samples. The alignment of DTs with respect to the tracker using global tracks has also improved significantly, since the algorithms use the latest B-field mapping, better run selection criteria, optimized momentum cuts, and an alignment is now obtained for all six degrees of freedom (three spatial coordinates and three rotations) of the aligned DTs. This work is ongoing and at a stage where we are trying to unders...

  10. Alignment of dipole magnet in micro-beam line of HIRFL

    International Nuclear Information System (INIS)

    Wang Shaoming; Chen Wenjun; Yang Shengli; Cai Guozhu; Guo Yizhen; Zhou Guangming; Man Kaidi; Song Mingtao

    2010-01-01

    Microbeam irradiation facility is an experiment platform, which can reduce the beam-spot on the irradiated sample to micrometer level, and can accurately locate and count the radioactive particles. It is a powerful research tool for the irradiation material science, irradiation biology, irradiation biomedicine and micro mechanical machining. The microbeam irradiation facility requires the precise work for installation and alignment. These conditions make magnet's change for directions and positions because the location space of dipole magnets in micro-beam line of HIRFL (Heavy Ion Research Facility in Lanzhou) is very small. It is a challenge for the installation and alignment work of magnets. It was solved by transforming coordinates of benchmarks of magnets, which controlled the error of magnet setup within error tolerance range. (authors)

  11. Fabrication of uniaxially aligned 3D electrospun scaffolds for neural regeneration

    Energy Technology Data Exchange (ETDEWEB)

    Subramanian, Anuradha; Krishnan, Uma Maheswari; Sethuraman, Swaminathan, E-mail: swami@sastra.edu [Center for Nanotechnology and Advanced Biomaterials, SASTRA University, Thanjavur 613 401, Tamil Nadu (India)

    2011-04-15

    Nanofibrous scaffolds are very promising physical guidance substrates for regenerating nerves to traverse larger nerve gaps. In this study, we have attempted to develop 2D random and 3D longitudinally oriented nanofibers of poly(lactide-co-glycolide) (PLGA) by the modified electrospinning process and characterized the surface morphology, mechanical properties, porosity, degradation and wettability. The orientation of aligned fibers was optimized by varying the speed of the rotating mandrel in the electrospinning process. The mean diameter of random PLGA nanofibers was 197 {+-} 72 nm, whereas that of the aligned PLGA fiber was 187 {+-} 121 nm. The pore size of aligned PLGA nanofibers (3.5 {+-} 1.1 {mu}m) was significantly lower than their respective random nanofibers (8.0 {+-} 2.0 {mu}m) (p < 0.05). However, the percentage porosity of both scaffolds was comparable (p > 0.05). The mass loss percentage and molecular weight loss percentage due to degradation was higher in random PLGA fibers when compared to aligned PLGA after 5 weeks (p < 0.05). The tensile strength and Young's modulus of random PLGA fibers were significantly higher than those of the aligned PLGA nanofibers (p < 0.05). Both random and longitudinally aligned scaffolds were used for the in vitro culture of Schwann cells. Morphology and cell proliferation results demonstrated that the aligned fibers assist the direction of Schwann cells and a better proliferation rate than their random fibers. The results confirmed that aligned nanofibers have better deformability, slow degradation, comparable porosity and orientation cues than random nanofibers. Hence the longitudinally aligned nanofibers may be ideal scaffolds for nerve regeneration.

  12. Program for PET image alignment: Effects on calculated differences in cerebral metabolic rates for glucose

    International Nuclear Information System (INIS)

    Phillips, R.L.; London, E.D.; Links, J.M.; Cascella, N.G.

    1990-01-01

    A program was developed to align positron emission tomography images from multiple studies on the same subject. The program allowed alignment of two images with a fineness of one-tenth the width of a pixel. The indications and effects of misalignment were assessed in eight subjects from a placebo-controlled double-blind crossover study on the effects of cocaine on regional cerebral metabolic rates for glucose. Visual examination of a difference image provided a sensitive and accurate tool for assessing image alignment. Image alignment within 2.8 mm was essential to reduce variability of measured cerebral metabolic rates for glucose. Misalignment by this amount introduced errors on the order of 20% in the computed metabolic rate for glucose. These errors propagate to the difference between metabolic rates for a subject measured in basal versus perturbed states

  13. Scintillation counter: photomultiplier tube alignment

    International Nuclear Information System (INIS)

    Olson, R.E.

    1975-01-01

    A scintillation counter, particularly for counting gamma ray photons, includes a massive lead radiation shield surrounding a sample-receiving zone. The shield is disassembleable into a plurality of segments to allow facile installation and removal of a photomultiplier tube assembly, the segments being so constructed as to prevent straight-line access of external radiation through the shield into the sample receiving zone. Provisions are made for accurately aligning the photomultiplier tube with respect to one or more sample-transmitting bores extending through the shield to the sample receiving zone. A sample elevator, used in transporting samples into the zone, is designed to provide a maximum gamma-receiving aspect to maximize the gamma detecting efficiency. (auth)

  14. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez

    Since December, the muon alignment community has focused on analyzing the data recorded so far in order to produce new DT and CSC Alignment Records for the second reprocessing of CRAFT data. Two independent algorithms were developed which align the DT chambers using global tracks, thus providing, for the first time, a relative alignment of the barrel with respect to the tracker. These results are an important ingredient for the second CRAFT reprocessing and allow, for example, a more detailed study of any possible mis-modelling of the magnetic field in the muon spectrometer. Both algorithms are constructed in such a way that the resulting alignment constants are not affected, to first order, by any such mis-modelling. The CSC chambers have not yet been included in this global track-based alignment due to a lack of statistics, since only a few cosmics go through the tracker and the CSCs. A strategy exists to align the CSCs using the barrel as a reference until collision tracks become available. Aligning the ...

  15. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez

    2011-01-01

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

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

    Science.gov (United States)

    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.

  17. Alignment of non-covalent interactions at protein-protein interfaces.

    Directory of Open Access Journals (Sweden)

    Hongbo Zhu

    Full Text Available BACKGROUND: The study and comparison of protein-protein interfaces is essential for the understanding of the mechanisms of interaction between proteins. While there are many methods for comparing protein structures and protein binding sites, so far no methods have been reported for comparing the geometry of non-covalent interactions occurring at protein-protein interfaces. METHODOLOGY/PRINCIPAL FINDINGS: Here we present a method for aligning non-covalent interactions between different protein-protein interfaces. The method aligns the vector representations of van der Waals interactions and hydrogen bonds based on their geometry. The method has been applied to a dataset which comprises a variety of protein-protein interfaces. The alignments are consistent to a large extent with the results obtained using two other complementary approaches. In addition, we apply the method to three examples of protein mimicry. The method successfully aligns respective interfaces and allows for recognizing conserved interface regions. CONCLUSIONS/SIGNIFICANCE: The Galinter method has been validated in the comparison of interfaces in which homologous subunits are involved, including cases of mimicry. The method is also applicable to comparing interfaces involving non-peptidic compounds. Galinter assists users in identifying local interface regions with similar patterns of non-covalent interactions. This is particularly relevant to the investigation of the molecular basis of interaction mimicry.

  18. Alignment-Annotator web server: rendering and annotating sequence alignments.

    Science.gov (United States)

    Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

    2014-07-01

    Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. Simultaneous alignment and Lorentz angle calibration in the CMS silicon tracker using Millepede II

    CERN Document Server

    Bartosik, Nazar

    2013-01-01

    The CMS silicon tracker consists of 25 684 sensors that provide measurements of trajectories of charged particles that are used by almost every physics analysis at CMS. In order to achieve high measurement precision, the positions and orientations of all sensors have to be determined very accurately. This is achieved by track-based alignment using the global fit approach of the Millepede II program. This approach is capable of determining about 200 000 parameters simultaneously.The alignment precision reached such a high level that even small calibration inaccuracies are noticeable. Therefore the alignment framework has been extended to treat position sensitive calibration parameters. Of special interest is the Lorentz angle which affects the hit positions due to the drift of the signal electrons in the magnetic field. We present the results from measurements of the Lorentz angle and its time dependence during full 2012 data taking period as well as general description of the alignment and calibration procedu...

  20. Colour stabilities of three types of orthodontic clear aligners exposed to staining agents.

    Science.gov (United States)

    Liu, Chen-Lu; Sun, Wen-Tian; Liao, Wen; Lu, Wen-Xin; Li, Qi-Wen; Jeong, Yunho; Liu, Jun; Zhao, Zhi-He

    2016-12-16

    The aim of this study was to evaluate and compare the colour stabilities of three types of orthodontic clear aligners exposed to staining agents in vitro. Sixty clear orthodontic aligners produced by three manufacturers (Invisalign, Angelalign, and Smartee) were immersed in three staining solutions (coffee, black tea, and red wine) and one control solution (distilled water). After 12-h and 7-day immersions, the aligners were washed in an ultrasonic cleaner and measured with a colourimeter. The colour changes (ΔE*) were calculated on the basis of the Commission Internationale de I'Eclairage L*a*b* colour system (CIE L*a*b*), and the results were then converted into National Bureau of Standards (NBS) units. Fourier transformation infrared (FT-IR) spectroscopy and scanning electron microscopy (SEM) were conducted to observe the molecular and morphologic alterations to the aligner surfaces, respectively. The three types of aligners exhibited slight colour changes after 12 h of staining, with the exception of the Invisalign aligners stained with coffee. The Invisalign aligners exhibited significantly higher ΔE* values (ranging from 0.30 to 27.81) than those of the Angelalign and Smartee aligners (ΔE* values ranging from 0.33 to 1.89 and 0.32 to 1.61, respectively, Paligners did not exhibit significant chemical differences before and after the immersions. The SEM results revealed different surface alterations to the three types of aligner materials after the 7-day staining. The three types of aesthetic orthodontic appliances exhibited colour stability after the 12-h immersion, with the exception of the Invisalign aligners stained by coffee. The Invisalign aligners were more prone than the Angelalign and Smartee aligners to pigmentation. Aligner materials may be improved by considering aesthetic colour stability properties.

  1. FSO tracking and auto-alignment transceiver system

    Science.gov (United States)

    Cap, Gabriel A.; Refai, Hakki H.; Sluss, James J., Jr.

    2008-10-01

    Free-space optics (FSO) technology utilizes a modulated light beam to transmit information through the atmosphere. Due to reduced size and cost, and higher data rates, FSO can be more effective than wireless communication. Although atmospheric conditions can affect FSO communication, a line-of-sight connection between FSO transceivers is a necessary condition to maintain continuous exchange of data, voice, and video information. To date, the primary concentration of mobile FSO research and development has been toward accurate alignment between two transceivers. This study introduces a fully automatic, advanced alignment system that will maintain a line of sight connection for any FSO transceiver system. A complete transceiver system includes a position-sensing detector (PSD) to receive the signal, a laser to transmit the signal, a gimbal to move the transceiver to maintain alignment, and a computer to coordinate the necessary movements during motion. The FSO system was tested for mobility by employing one gimbal as a mobile unit and establishing another as a base station. Tests were performed to establish that alignment between two transceivers could be maintained during a given period of experiments and to determine the maximum speeds tolerated by the system. Implementation of the transceiver system can be realized in many ways, including vehicle-to-base station communication or vehicle-to-vehicle communication. This study is especially promising in that it suggests such a system is able to provide high-speed data in many applications where current wireless technology may not be effective. This phenomenon, coupled with the ability to maintain an autonomously realigned connection, opens the possibility of endless applications for both military and civilian use.

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

    Directory of Open Access Journals (Sweden)

    Kierzynka Michal

    2011-05-01

    Full Text Available Abstract Background 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. Results 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. Conclusions 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.

  3. Automatic alignment device for focal spot measurements in the center of the field for mammography

    International Nuclear Information System (INIS)

    Vieira, Marcelo A.C.; Watanabe, Alex O.; Oliveira Junior, Paulo D.; Schiabel, Homero

    2010-01-01

    Some quality control procedures used for mammography, such as focal spot evaluation, requires previous alignment of the measurement equipment with the X-ray central beam. However, alignment procedures are, in general, the most difficult task and the one that needs more time to be performed. Moreover, the operator sometimes is exposed to radiation during this procedure. This work presents an automatic alignment system for mammographic equipment that allows locating the central ray of the radiation beam and, immediately, aligns with it by dislocating itself automatically along the field. The system consists on a bidirectional moving device, connected to a CCD sensor for digital radiographic image acquisition. A computational analysis of a radiographic image, acquired at any position on the field, is performed in order to determine its positioning under the X-ray beam. Finally, a mechanical system for two moving directions, electronically controlled by a microcontroller under USB communication, makes the system to align automatically with the radiation beam central ray. The alignment process is fully automatic, fast and accurate, with no operator exposure to radiation, which allows a considerable time saving for quality control procedures achievement for mammography. (author)

  4. Alignment and qualification of the Gaia telescope using a Shack-Hartmann sensor

    Science.gov (United States)

    Dovillaire, G.; Pierot, D.

    2017-09-01

    Since almost 20 years, Imagine Optic develops, manufactures and offers to its worldwide customers reliable and accurate wavefront sensors and adaptive optics solutions. Long term collaboration between Imagine Optic and Airbus Defence and Space has been initiated on the Herschel program. More recently, a similar technology has been used to align and qualify the GAIA telescope.

  5. Alignment of the ATLAS Inner Detector Tracking System

    CERN Document Server

    Heller, C; The ATLAS collaboration

    2011-01-01

    ATLAS is one of the multipurpose experiments that records the products of the LHC proton-proton and heavy ion collisions. In order to reconstruct trajectories of charged particles produced in these collisions, ATLAS is equipped with a tracking system built using two different technologies, silicon planar sensors (pixel and microstrips) and drift-tube based detectors. Together they constitute the ATLAS Inner Detector, which is embedded in a 2 T axial field. Efficiently reconstructing tracks from charged particles traversing the detector, and precisely measure their momenta is of crucial importance for physics analyses. In order to achieve its scientific goals, an alignment of the ATLAS Inner Detector is required to accurately determine its more than 700,000 degrees of freedom. The goal of the alignment is set such that the limited knowledge of the sensor locations should not deteriorate the resolution of track parameters by more than 20% with respect to the intrinsic tracker resolution. The implementation of t...

  6. Apparatus for accurately measuring high temperatures

    Science.gov (United States)

    Smith, D.D.

    The present invention is a thermometer used for measuring furnace temperatures in the range of about 1800/sup 0/ to 2700/sup 0/C. The thermometer comprises a broadband multicolor thermal radiation sensor positioned to be in optical alignment with the end of a blackbody sight tube extending into the furnace. A valve-shutter arrangement is positioned between the radiation sensor and the sight tube and a chamber for containing a charge of high pressure gas is positioned between the valve-shutter arrangement and the radiation sensor. A momentary opening of the valve shutter arrangement allows a pulse of the high gas to purge the sight tube of air-borne thermal radiation contaminants which permits the radiation sensor to accurately measure the thermal radiation emanating from the end of the sight tube.

  7. Comparison of robust H∞ filter and Kalman filter for initial alignment of inertial navigation system

    Institute of Scientific and Technical Information of China (English)

    HAO Yan-ling; CHEN Ming-hui; LI Liang-jun; XU Bo

    2008-01-01

    There are many filtering methods that can be used for the initial alignment of an integrated inertial navigation system.This paper discussed the use of GPS,but focused on two kinds of filters for the initial alignment of an integrated strapdown inertial navigation system (SINS).One method is based on the Kalman filter (KF),and the other is based on the robust filter.Simulation results showed that the filter provides a quick transient response and a little more accurate estimate than KF,given substantial process noise or unknown noise statistics.So the robust filter is an effective and useful method for initial alignment of SINS.This research should make the use of SINS more popular,and is also a step for further research.

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

    International Nuclear Information System (INIS)

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

    2012-01-01

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

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

    Science.gov (United States)

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

    2017-08-01

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

  10. Voxel-based registration of simulated and real patient CBCT data for accurate dental implant pose estimation

    Science.gov (United States)

    Moreira, António H. J.; Queirós, Sandro; Morais, Pedro; Rodrigues, Nuno F.; Correia, André Ricardo; Fernandes, Valter; Pinho, A. C. M.; Fonseca, Jaime C.; Vilaça, João. L.

    2015-03-01

    The success of dental implant-supported prosthesis is directly linked to the accuracy obtained during implant's pose estimation (position and orientation). Although traditional impression techniques and recent digital acquisition methods are acceptably accurate, a simultaneously fast, accurate and operator-independent methodology is still lacking. Hereto, an image-based framework is proposed to estimate the patient-specific implant's pose using cone-beam computed tomography (CBCT) and prior knowledge of implanted model. The pose estimation is accomplished in a threestep approach: (1) a region-of-interest is extracted from the CBCT data using 2 operator-defined points at the implant's main axis; (2) a simulated CBCT volume of the known implanted model is generated through Feldkamp-Davis-Kress reconstruction and coarsely aligned to the defined axis; and (3) a voxel-based rigid registration is performed to optimally align both patient and simulated CBCT data, extracting the implant's pose from the optimal transformation. Three experiments were performed to evaluate the framework: (1) an in silico study using 48 implants distributed through 12 tridimensional synthetic mandibular models; (2) an in vitro study using an artificial mandible with 2 dental implants acquired with an i-CAT system; and (3) two clinical case studies. The results shown positional errors of 67+/-34μm and 108μm, and angular misfits of 0.15+/-0.08° and 1.4°, for experiment 1 and 2, respectively. Moreover, in experiment 3, visual assessment of clinical data results shown a coherent alignment of the reference implant. Overall, a novel image-based framework for implants' pose estimation from CBCT data was proposed, showing accurate results in agreement with dental prosthesis modelling requirements.

  11. DendroBLAST: approximate phylogenetic trees in the absence of multiple sequence alignments.

    Science.gov (United States)

    Kelly, Steven; Maini, Philip K

    2013-01-01

    The rapidly growing availability of genome information has created considerable demand for both fast and accurate phylogenetic inference algorithms. We present a novel method called DendroBLAST for reconstructing phylogenetic dendrograms/trees from protein sequences using BLAST. This method differs from other methods by incorporating a simple model of sequence evolution to test the effect of introducing sequence changes on the reliability of the bipartitions in the inferred tree. Using realistic simulated sequence data we demonstrate that this method produces phylogenetic trees that are more accurate than other commonly-used distance based methods though not as accurate as maximum likelihood methods from good quality multiple sequence alignments. In addition to tests on simulated data, we use DendroBLAST to generate input trees for a supertree reconstruction of the phylogeny of the Archaea. This independent analysis produces an approximate phylogeny of the Archaea that has both high precision and recall when compared to previously published analysis of the same dataset using conventional methods. Taken together these results demonstrate that approximate phylogenetic trees can be produced in the absence of multiple sequence alignments, and we propose that these trees will provide a platform for improving and informing downstream bioinformatic analysis. A web implementation of the DendroBLAST method is freely available for use at http://www.dendroblast.com/.

  12. DendroBLAST: approximate phylogenetic trees in the absence of multiple sequence alignments.

    Directory of Open Access Journals (Sweden)

    Steven Kelly

    Full Text Available The rapidly growing availability of genome information has created considerable demand for both fast and accurate phylogenetic inference algorithms. We present a novel method called DendroBLAST for reconstructing phylogenetic dendrograms/trees from protein sequences using BLAST. This method differs from other methods by incorporating a simple model of sequence evolution to test the effect of introducing sequence changes on the reliability of the bipartitions in the inferred tree. Using realistic simulated sequence data we demonstrate that this method produces phylogenetic trees that are more accurate than other commonly-used distance based methods though not as accurate as maximum likelihood methods from good quality multiple sequence alignments. In addition to tests on simulated data, we use DendroBLAST to generate input trees for a supertree reconstruction of the phylogeny of the Archaea. This independent analysis produces an approximate phylogeny of the Archaea that has both high precision and recall when compared to previously published analysis of the same dataset using conventional methods. Taken together these results demonstrate that approximate phylogenetic trees can be produced in the absence of multiple sequence alignments, and we propose that these trees will provide a platform for improving and informing downstream bioinformatic analysis. A web implementation of the DendroBLAST method is freely available for use at http://www.dendroblast.com/.

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

    Science.gov (United States)

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

    2016-07-01

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

  14. RevTrans: multiple alignment of coding DNA from aligned amino acid sequences

    DEFF Research Database (Denmark)

    Wernersson, Rasmus; Pedersen, Anders Gorm

    2003-01-01

    The simple fact that proteins are built from 20 amino acids while DNA only contains four different bases, means that the 'signal-to-noise ratio' in protein sequence alignments is much better than in alignments of DNA. Besides this information-theoretical advantage, protein alignments also benefit...... proteins. It is therefore preferable to align coding DNA at the amino acid level and it is for this purpose we have constructed the program RevTrans. RevTrans constructs a multiple DNA alignment by: (i) translating the DNA; (ii) aligning the resulting peptide sequences; and (iii) building a multiple DNA...

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

    Science.gov (United States)

    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.

  16. A handy time alignment probe for timing calibration of PET scanners

    International Nuclear Information System (INIS)

    Bergeron, Melanie; Pepin, Catherine M.; Arpin, Louis; Leroux, Jean-Daniel; Tetrault, Marc-Andre; Viscogliosi, Nicolas; Fontaine, Rejean; Lecomte, Roger

    2009-01-01

    Accurate time alignment of detectors in PET scanners is required for improving overall coincidence timing resolution. This is mandatory to reduce the coincidence time window of the scanner and limit as much as possible the rate of random events in images. Several techniques have been proposed so far, but most have shortcomings relating to difficult use, collection of huge amount of data or long acquisition times, not to mention transport regulation of radioactive source embedded in time alignment probes. A handy liquid scintillation beta probe was developed to overcome these problems. It consists of a PMT coupled to a small glass container that can be filled with a liquid scintillation cocktail loaded with radioactivity (such as 18 F). The PMT signal is processed by an analog CFD and a digital TDC supplying an accurate timestamp on positron detection. When tested in coincidence with a fast PMT/plastic detector, a timing resolution of 1.1 ns FWHM was obtained using a standard off-the-shelf liquid cocktail having a scintillation decay time of 6.2 ns. For time alignment, coincidences are recorded between positron detected by the probe and one of the two 511 keV annihilation photons reaching detectors in the scanner. Using this simple probe, it is possible to determine the time offsets for individual LYSO and LGSO crystals in LabPET TM scanners in about 15 min. Due to its ease of use and short acquisition time, the proposed timing calibration method was found ideal for tuning the APD bias of individual detectors to reach optimal timing resolution on every channel.

  17. Accurate estimation of short read mapping quality for next-generation genome sequencing

    Science.gov (United States)

    Ruffalo, Matthew; Koyutürk, Mehmet; Ray, Soumya; LaFramboise, Thomas

    2012-01-01

    Motivation: Several software tools specialize in the alignment of short next-generation sequencing reads to a reference sequence. Some of these tools report a mapping quality score for each alignment—in principle, this quality score tells researchers the likelihood that the alignment is correct. However, the reported mapping quality often correlates weakly with actual accuracy and the qualities of many mappings are underestimated, encouraging the researchers to discard correct mappings. Further, these low-quality mappings tend to correlate with variations in the genome (both single nucleotide and structural), and such mappings are important in accurately identifying genomic variants. Approach: We develop a machine learning tool, LoQuM (LOgistic regression tool for calibrating the Quality of short read mappings, to assign reliable mapping quality scores to mappings of Illumina reads returned by any alignment tool. LoQuM uses statistics on the read (base quality scores reported by the sequencer) and the alignment (number of matches, mismatches and deletions, mapping quality score returned by the alignment tool, if available, and number of mappings) as features for classification and uses simulated reads to learn a logistic regression model that relates these features to actual mapping quality. Results: We test the predictions of LoQuM on an independent dataset generated by the ART short read simulation software and observe that LoQuM can ‘resurrect’ many mappings that are assigned zero quality scores by the alignment tools and are therefore likely to be discarded by researchers. We also observe that the recalibration of mapping quality scores greatly enhances the precision of called single nucleotide polymorphisms. Availability: LoQuM is available as open source at http://compbio.case.edu/loqum/. Contact: matthew.ruffalo@case.edu. PMID:22962451

  18. The inhibition of methane hydrate formation by water alignment underneath surface adsorption of surfactants

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Ngoc N.; Nguyen, Anh V.; Dang, Liem X.

    2017-06-01

    Sodium dodecyl sulfate (SDS) has been widely shown to strongly promote the formation of methane hydrate. Here we show that SDS displays an extraordinary inhibition effect on methane hydrate formation when the surfactant is used in sub-millimolar concentration (around 0.3 mM). We have also employed Sum Frequency Generation vibrational spectroscopy (SFG) and molecular dynamics simulation (MDS) to elucidate the molecular mechanism of this inhibition. The SFG and MDS results revealed a strong alignment of water molecules underneath surface adsorption of SDS in its sub-millimolar solution. Interestingly, both the alignment of water and the inhibition effect (in 0.3 mM SDS solution) went vanishing when an oppositely-charged surfactant (tetra-n-butylammonium bromide, TBAB) was suitably added to produce a mixed solution of 0.3 mM SDS and 3.6 mM TBAB. Combining structural and kinetic results, we pointed out that the alignment of water underneath surface adsorption of dodecyl sulfate (DS-) anions gave rise to the unexpected inhibition of methane hydration formation in sub-millimolar solution of SDS. The adoption of TBAB mitigated the SDS-induced electrostatic field at the solution’s surface and, therefore, weakened the alignment of interfacial water which, in turn, erased the inhibition effect. We discussed this finding using the concept of activation energy of the interfacial formation of gas hydrate. The main finding of this work is to reveal the interplay of interfacial water in governing gas hydrate formation which sheds light on a universal molecular-scale understanding of the influence of surfactants on gas hydrate formation. This work was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. The calculations were carried out using computer resources provided by the Office of Basic Energy Sciences.

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

    DEFF Research Database (Denmark)

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

    2007-01-01

    and backtracked in a normal fashion. Finally, the FOLDALIGN algorithm has also been updated with a better memory implementation and an improved energy model. With these improvements in the algorithm, the FOLDALIGN software package provides the molecular biologist with an efficient and user-friendly tool...... the advantage of providing the constraints dynamically. This has been included in a new implementation of the FOLDALIGN algorithm for pairwise local or global structural alignment of RNA sequences. It is shown that time and memory requirements are dramatically lowered while overall performance is maintained....... Furthermore, a new divide and conquer method is introduced to limit the memory requirement during global alignment and backtrack of local alignment. All branch points in the computed RNA structure are found and used to divide the structure into smaller unbranched segments. Each segment is then realigned...

  20. Background Adjusted Alignment-Free Dissimilarity Measures Improve the Detection of Horizontal Gene Transfer

    Directory of Open Access Journals (Sweden)

    Kujin Tang

    2018-04-01

    Full Text Available Horizontal gene transfer (HGT plays an important role in the evolution of microbial organisms including bacteria. Alignment-free methods based on single genome compositional information have been used to detect HGT. Currently, Manhattan and Euclidean distances based on tetranucleotide frequencies are the most commonly used alignment-free dissimilarity measures to detect HGT. By testing on simulated bacterial sequences and real data sets with known horizontal transferred genomic regions, we found that more advanced alignment-free dissimilarity measures such as CVTree and d2* that take into account the background Markov sequences can solve HGT detection problems with significantly improved performance. We also studied the influence of different factors such as evolutionary distance between host and donor sequences, size of sliding window, and host genome composition on the performances of alignment-free methods to detect HGT. Our study showed that alignment-free methods can predict HGT accurately when host and donor genomes are in different order levels. Among all methods, CVTree with word length of 3, d2* with word length 3, Markov order 1 and d2* with word length 4, Markov order 1 outperform others in terms of their highest F1-score and their robustness under the influence of different factors.

  1. Accurate quantum chemical calculations

    Science.gov (United States)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    1989-01-01

    An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

  2. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    S. Szillasi

    2013-01-01

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

  3. Accurate density functional prediction of molecular electron affinity with the scaling corrected Kohn–Sham frontier orbital energies

    Science.gov (United States)

    Zhang, DaDi; Yang, Xiaolong; Zheng, Xiao; Yang, Weitao

    2018-04-01

    Electron affinity (EA) is the energy released when an additional electron is attached to an atom or a molecule. EA is a fundamental thermochemical property, and it is closely pertinent to other important properties such as electronegativity and hardness. However, accurate prediction of EA is difficult with density functional theory methods. The somewhat large error of the calculated EAs originates mainly from the intrinsic delocalisation error associated with the approximate exchange-correlation functional. In this work, we employ a previously developed non-empirical global scaling correction approach, which explicitly imposes the Perdew-Parr-Levy-Balduz condition to the approximate functional, and achieve a substantially improved accuracy for the calculated EAs. In our approach, the EA is given by the scaling corrected Kohn-Sham lowest unoccupied molecular orbital energy of the neutral molecule, without the need to carry out the self-consistent-field calculation for the anion.

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

    Science.gov (United States)

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

    2015-08-01

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

  5. MaxAlign: maximizing usable data in an alignment

    DEFF Research Database (Denmark)

    Oliveira, Rodrigo Gouveia; Sackett, Peter Wad; Pedersen, Anders Gorm

    2007-01-01

    Align. In this paper we also introduce a new simple measure of tree similarity, Normalized Symmetric Similarity (NSS) that we consider useful for comparing tree topologies. CONCLUSION: We demonstrate how MaxAlign is helpful in detecting misaligned or defective sequences without requiring manual inspection. We also...

  6. Aligning for Innovation - Alignment Strategy to Drive Innovation

    Science.gov (United States)

    Johnson, Hurel; Teltschik, David; Bussey, Horace, Jr.; Moy, James

    2010-01-01

    With the sudden need for innovation that will help the country achieve its long-term space exploration objectives, the question of whether NASA is aligned effectively to drive the innovation that it so desperately needs to take space exploration to the next level should be entertained. Authors such as Robert Kaplan and David North have noted that companies that use a formal system for implementing strategy consistently outperform their peers. They have outlined a six-stage management systems model for implementing strategy, which includes the aligning of the organization towards its objectives. This involves the alignment of the organization from the top down. This presentation will explore the impacts of existing U.S. industrial policy on technological innovation; assess the current NASA organizational alignment and its impacts on driving technological innovation; and finally suggest an alternative approach that may drive the innovation needed to take the world to the next level of space exploration, with NASA truly leading the way.

  7. Comprehensive Use of Curvature for Robust and Accurate Online Surface Reconstruction.

    Science.gov (United States)

    Lefloch, Damien; Kluge, Markus; Sarbolandi, Hamed; Weyrich, Tim; Kolb, Andreas

    2017-12-01

    Interactive real-time scene acquisition from hand-held depth cameras has recently developed much momentum, enabling applications in ad-hoc object acquisition, augmented reality and other fields. A key challenge to online reconstruction remains error accumulation in the reconstructed camera trajectory, due to drift-inducing instabilities in the range scan alignments of the underlying iterative-closest-point (ICP) algorithm. Various strategies have been proposed to mitigate that drift, including SIFT-based pre-alignment, color-based weighting of ICP pairs, stronger weighting of edge features, and so on. In our work, we focus on surface curvature as a feature that is detectable on range scans alone and hence does not depend on accurate multi-sensor alignment. In contrast to previous work that took curvature into consideration, however, we treat curvature as an independent quantity that we consistently incorporate into every stage of the real-time reconstruction pipeline, including densely curvature-weighted ICP, range image fusion, local surface reconstruction, and rendering. Using multiple benchmark sequences, and in direct comparison to other state-of-the-art online acquisition systems, we show that our approach significantly reduces drift, both when analyzing individual pipeline stages in isolation, as well as seen across the online reconstruction pipeline as a whole.

  8. EVIDENCE FOR H{sub 2} FORMATION DRIVEN DUST GRAIN ALIGNMENT IN IC 63

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, B-G; De Buizer, J.; Charcos-Llorens, M. [SOFIA Science Center, USRA, NASA Ames Research Center, M.S. N211-3 Moffett Field, CA 94035 (United States); Piirola, V. [Finnish Centre for Astronomy with ESO, University of Turku, Väisäläntie 20, FI-21500 Piikkiö (Finland); Clemens, D. P. [Institute for Astrophysical Research, Boston University, Boston, MA 02215 (United States); Uomoto, A. [Observatories of the Carnegie Institution, 813 Santa Barbara Street, Pasadena, CA 91101 (United States); Geballe, T. R. [Gemini Observatory, Northern Operations Center, 670 N. A' ohoku Place, Hilo, HI 96720 (United States); Lazarian, A.; Hoang, T. [Department of Astronomy, University of Wisconsin, 475 North Charter Street, Madison, WI 53706 (United States); Vornanen, T., E-mail: bg@sofia.usra.edu [Tuorla Observatory, University of Turku, Väisäläntie 20, FI-21500 Piikkiö (Finland)

    2013-10-01

    In the interstellar medium (ISM), molecular hydrogen is expected to form almost exclusively on the surfaces of dust grains. Due to that molecule's large formation energy (–4.5 eV), several dynamical effects are likely associated with the process, including the alignment of asymmetric dust grains with the ambient magnetic field. Such aligned dust grains are, in turn, believed to cause the broadband optical/infrared polarization observed in the ISM. Here, we present the first observational evidence for grain alignment driven by H{sub 2} formation, by showing that the polarization of the light from stars behind the reflection nebula IC 63 appears to correlate with the intensity of H{sub 2} fluorescence. While our results strongly suggest a role for 'Purcell rockets' in grain alignment, additional observations are needed to conclusively confirm their role. By showing a direct connection between H{sub 2} formation and a probe of the dust characteristics, these results also provide one of the first direct confirmations of the grain-surface formation of H{sub 2}. We compare our observations to ab initio modeling based on Radiative Torque Alignment (RAT) theory.

  9. Control rod housing alignment

    International Nuclear Information System (INIS)

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

    1990-01-01

    This patent describes a process for measuring the vertical alignment between a hole in a core plate and the top of a corresponding control rod drive housing within a boiling water reactor. It comprises: providing an alignment apparatus. The alignment apparatus including a lower end for fitting to the top of the control rod drive housing; an upper end for fitting to the aperture in the core plate, and a leveling means attached to the alignment apparatus to read out the difference in angularity with respect to gravity, and alignment pin registering means for registering to the alignment pin on the core plate; lowering the alignment device on a depending support through a lattice position in the top guide through the hole in the core plate down into registered contact with the top of the control rod drive housing; registering the upper end to the sides of the hole in the core plate; registering the alignment pin registering means to an alignment pin on the core plate to impart to the alignment device the required angularity; and reading out the angle of the control rod drive housing with respect to the hole in the core plate through the leveling devices whereby the angularity of the top of the control rod drive housing with respect to the hole in the core plate can be determined

  10. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez

    2012-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Genki Terashi

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

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

    Science.gov (United States)

    Terashi, Genki; Takeda-Shitaka, Mayuko

    2015-01-01

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

  13. Orientation dependent band alignment for p-NiO/n-ZnO heterojunctions

    International Nuclear Information System (INIS)

    Ma, M. J.; Lu, B.; Zhou, T. T.; Ye, Z. Z.; Lu, J. G.; Pan, X. H.

    2013-01-01

    Nonpolor a-plane and polar c-plane ZnO thin films were prepared on r-plane sapphire and quartz substrates, respectively. The electronic structure of the interface between subsequently fabricated NiO/ZnO heterojunctions has been investigated by x-ray photoelectron spectroscopy measurements and the band offsets are determined together with information yielded from UV-vis transition spectra. It is found that a type-II band alignment forms at the interface for both the samples. The revealed ZnO-orientation dependent band offsets are analyzed and are attributed mainly due to the variations in internal electric field arose from spontaneous polarization effect. The accurate determination of the band alignment is important for the design and application of NiO/ZnO based hybrid devices.

  14. Orientation dependent band alignment for p-NiO/n-ZnO heterojunctions

    Energy Technology Data Exchange (ETDEWEB)

    Ma, M. J.; Lu, B.; Zhou, T. T.; Ye, Z. Z.; Lu, J. G.; Pan, X. H. [State Key Laboratory of Silicon Materials, Cyrus Tang Center for Sensor Materials and Applications, Department of Materials Science and Engineering, Zhejiang University, Hangzhou 310027 (China)

    2013-04-28

    Nonpolor a-plane and polar c-plane ZnO thin films were prepared on r-plane sapphire and quartz substrates, respectively. The electronic structure of the interface between subsequently fabricated NiO/ZnO heterojunctions has been investigated by x-ray photoelectron spectroscopy measurements and the band offsets are determined together with information yielded from UV-vis transition spectra. It is found that a type-II band alignment forms at the interface for both the samples. The revealed ZnO-orientation dependent band offsets are analyzed and are attributed mainly due to the variations in internal electric field arose from spontaneous polarization effect. The accurate determination of the band alignment is important for the design and application of NiO/ZnO based hybrid devices.

  15. Quantitatively accurate calculations of conductance and thermopower of molecular junctions

    DEFF Research Database (Denmark)

    Markussen, Troels; Jin, Chengjun; Thygesen, Kristian Sommer

    2013-01-01

    Thermopower measurements of molecular junctions have recently gained interest as a characterization technique that supplements the more traditional conductance measurements. Here we investigate the electronic conductance and thermopower of benzenediamine (BDA) and benzenedicarbonitrile (BDCN...

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

    International Nuclear Information System (INIS)

    Downes, S.

    1996-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Shi Weisong

    2011-06-01

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

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

    Science.gov (United States)

    Nguyen, Tung; Shi, Weisong; Ruden, Douglas

    2011-06-06

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

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

    Science.gov (United States)

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

    2017-12-01

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

  20. Automatic frequency and phase alignment of in vivo J-difference-edited MR spectra by frequency domain correlation.

    Science.gov (United States)

    Wiegers, Evita C; Philips, Bart W J; Heerschap, Arend; van der Graaf, Marinette

    2017-12-01

    J-difference editing is often used to select resonances of compounds with coupled spins in 1 H-MR spectra. Accurate phase and frequency alignment prior to subtracting J-difference-edited MR spectra is important to avoid artefactual contributions to the edited resonance. In-vivo J-difference-edited MR spectra were aligned by maximizing the normalized scalar product between two spectra (i.e., the correlation over a spectral region). The performance of our correlation method was compared with alignment by spectral registration and by alignment of the highest point in two spectra. The correlation method was tested at different SNR levels and for a broad range of phase and frequency shifts. In-vivo application of the proposed correlation method showed reduced subtraction errors and increased fit reliability in difference spectra as compared with conventional peak alignment. The correlation method and the spectral registration method generally performed equally well. However, better alignment using the correlation method was obtained for spectra with a low SNR (down to ~2) and for relatively large frequency shifts. Our correlation method for simultaneously phase and frequency alignment is able to correct both small and large phase and frequency drifts and also performs well at low SNR levels.

  1. Alignment effects in two-photon double ionization of H2 in femtosecond xuv laser pulses

    International Nuclear Information System (INIS)

    Guan Xiaoxu; Bartschat, Klaus; Schneider, Barry I.

    2011-01-01

    Triple-differential cross sections for two-photon double ionization of the aligned hydrogen molecule at the equilibrium distance are presented for a central photon energy of 30 eV. The temporal response of the laser-driven molecule is investigated by solving the time-dependent Schroedinger equation in full dimensionality using two-center elliptical coordinates and a finite-element discrete-variable-representation approach. The molecular orientation is found to have a strong effect on the emission modes of the two correlated photoelectrons. This molecular effect is most noticeable when the molecular axis and the laser polarization vector are oriented parallel to each other. For intermediate cases between the parallel and perpendicular geometries, the dominant emission modes for two-electron ejection oscillate between those for the two extreme cases. The contributions from different ionization channels are also analyzed in detail. Depending on the emission direction of the reference electron, the interference contributions from the various channels can be constructive or destructive at small alignment angles, while they always contribute constructively to the triple-differential cross sections near the perpendicular geometry.

  2. Effects of variable attachment shapes and aligner material on aligner retention.

    Science.gov (United States)

    Dasy, Hiltrud; Dasy, Andreas; Asatrian, Greg; Rózsa, Noémi; Lee, Hao-Fu; Kwak, Jin Hee

    2015-11-01

    To evaluate the retention of four types of aligners on a dental arch with various attachments. For this study, three casts were manufactured, two of which contained attachments (ellipsoid and beveled), and one without any attachments to serve as a control. Four types of aligners were thermoformed: Clear-Aligner (CA)-soft, CA-medium, and CA-hard, with various thicknesses, and Essix ACE. Measurements of vertical displacement force during aligner removal were performed with the Gabo Qualimeter Eplexor. Means and standard deviations were next compared between different aligner thicknesses and attachment shapes. CA-soft, CA-medium, and CA-hard did not present a significant increase in retention, except when used in the presence of attachments. Additionally, CA-medium and CA-hard required significantly more force for removal. Essix ACE demonstrated a significant decrease in retention when used with ellipsoid attachments. The force value for Essix ACE removal from the cast with beveled attachments was comparable to that of CA-medium. Forces for aligner removal from the model without attachments showed a linear trend. Essix ACE did not show a continuous increase in retention for each model. Overall, ellipsoid attachments did not present a significant change in retention. In contrast, beveled attachments improved retention. Ellipsoid attachments had no significant influence on the force required for aligner removal and hence on aligner retention. Essix ACE showed significantly less retention than CA-hard on the models with attachments. Furthermore, beveled attachments were observed to increase retention significantly, compared with ellipsoid attachments and when using no attachments.

  3. Determination of the three-dimensional structure for weakly aligned biomolecules by NMR spectroscopy

    International Nuclear Information System (INIS)

    Shahkhatuni, Astghik A; Shahkhatuni, Aleksan G

    2002-01-01

    The key achievements and the potential of NMR spectroscopy for weakly aligned biomolecules are considered. Due to weak alignment, it becomes possible to determine a number of NMR parameters dependent on the orientation of biomolecules, which are averaged to zero in usual isotropic media. The addition of new orientational constraints to standard procedures of 3D structure determination markedly increases the achievable accuracy. The possibility of structure determination for biomolecules using only orientation-dependent parameters without invoking other NMR data is discussed. The methods of orientation, experimental techniques, and calculation methods are systematised. The main results obtained and the prospects of using NMR spectroscopy of weakly aligned systems to study different classes of biomolecules and to solve various problems of molecular biology are analysed. Examples of biomolecules whose structures have been determined using orientation-dependent parameters are given. The bibliography includes 508 references.

  4. Molecular heterojunctions of oligo(phenylene ethynylene)s with linear to cruciform framework

    DEFF Research Database (Denmark)

    Wei, Zhongming; Hansen, Tim; Santella, Marco

    2015-01-01

    Electrical transport properties of molecular junctions are fundamentally affected by the energy alignment between molecular frontier orbitals (highest occupied molecular orbital (HOMO) or lowest unoccupied molecular orbital (LUMO)) and Fermi level (or work function) of electrode metals. Dithiaful......Electrical transport properties of molecular junctions are fundamentally affected by the energy alignment between molecular frontier orbitals (highest occupied molecular orbital (HOMO) or lowest unoccupied molecular orbital (LUMO)) and Fermi level (or work function) of electrode metals......-tetrathiafulvalene (TTF) can form good self-assembled monolayers (SAMs) on Au substrates. Molecular heterojunctions based on these SAMs are investigated using conducting probe-atomic force microscopy with different tips (Ag, Au, and Pt) and Fermi levels. The calibrated conductance values follow the sequence OPE3-TTF...... > OPE3-DTF > OPE3 irrespective of the tip metal. Rectification properties (or diode behavior) are observed in case of the Ag tip for which the work function is furthest from the HOMO levels of the OPE3s. Quantum chemical calculations of the transmission qualitatively agree with the experimental data...

  5. Survey of local and global biological network alignment: the need to reconcile the two sides of the same coin.

    Science.gov (United States)

    Guzzi, Pietro Hiram; Milenković, Tijana

    2017-01-05

    Analogous to genomic sequence alignment that allows for across-species transfer of biological knowledge between conserved sequence regions, biological network alignment can be used to guide the knowledge transfer between conserved regions of molecular networks of different species. Hence, biological network alignment can be used to redefine the traditional notion of a sequence-based homology to a new notion of network-based homology. Analogous to genomic sequence alignment, there exist local and global biological network alignments. Here, we survey prominent and recent computational approaches of each network alignment type and discuss their (dis)advantages. Then, as it was recently shown that the two approach types are complementary, in the sense that they capture different slices of cellular functioning, we discuss the need to reconcile the two network alignment types and present a recent first step in this direction. We conclude with some open research problems on this topic and comment on the usefulness of network alignment in other domains besides computational biology. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  6. MetAlign: Interface-Driven, Versatile Metabolomics Tool for Hyphenated Full-Scan Mass Spectrometry Data Preprocessing

    NARCIS (Netherlands)

    Lommen, A.

    2009-01-01

    Hyphenated full-scan MS technology creates large amounts of data. A versatile easy to handle automation tool aiding in the data analysis is very important in handling such a data stream. MetAlign software-as described in this manuscript-handles a broad range of accurate mass and nominal mass GC/MS

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

    Science.gov (United States)

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

    2015-01-01

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

  8. Mask alignment system for semiconductor processing

    Science.gov (United States)

    Webb, Aaron P.; Carlson, Charles T.; Weaver, William T.; Grant, Christopher N.

    2017-02-14

    A mask alignment system for providing precise and repeatable alignment between ion implantation masks and workpieces. The system includes a mask frame having a plurality of ion implantation masks loosely connected thereto. The mask frame is provided with a plurality of frame alignment cavities, and each mask is provided with a plurality of mask alignment cavities. The system further includes a platen for holding workpieces. The platen may be provided with a plurality of mask alignment pins and frame alignment pins configured to engage the mask alignment cavities and frame alignment cavities, respectively. The mask frame can be lowered onto the platen, with the frame alignment cavities moving into registration with the frame alignment pins to provide rough alignment between the masks and workpieces. The mask alignment cavities are then moved into registration with the mask alignment pins, thereby shifting each individual mask into precise alignment with a respective workpiece.

  9. Precision alignment and calibration of optical systems using computer generated holograms

    Science.gov (United States)

    Coyle, Laura Elizabeth

    As techniques for manufacturing and metrology advance, optical systems are being designed with more complexity than ever before. Given these prescriptions, alignment and calibration can be a limiting factor in their final performance. Computer generated holograms (CGHs) have several unique properties that make them powerful tools for meeting these demanding tolerances. This work will present three novel methods for alignment and calibration of optical systems using computer generated holograms. Alignment methods using CGHs require that the optical wavefront created by the CGH be related to a mechanical datum to locate it space. An overview of existing methods is provided as background, then two new alignment methods are discussed in detail. In the first method, the CGH contact Ball Alignment Tool (CBAT) is used to align a ball or sphere mounted retroreflector (SMR) to a Fresnel zone plate pattern with micron level accuracy. The ball is bonded directly onto the CGH substrate and provides permanent, accurate registration between the optical wavefront and a mechanical reference to locate the CGH in space. A prototype CBAT was built and used to align and bond an SMR to a CGH. In the second method, CGH references are used to align axi-symmetric optics in four degrees of freedom with low uncertainty and real time feedback. The CGHs create simultaneous 3D optical references where the zero order reflection sets tilt and the first diffracted order sets centration. The flexibility of the CGH design can be used to accommodate a wide variety of optical systems and maximize sensitivity to misalignments. A 2-CGH prototype system was aligned multiplied times and the alignment uncertainty was quantified and compared to an error model. Finally, an enhanced calibration method is presented. It uses multiple perturbed measurements of a master sphere to improve the calibration of CGH-based Fizeau interferometers ultimately measuring aspheric test surfaces. The improvement in the

  10. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    M. Dallavalle

    2013-01-01

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

  11. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez

    2011-01-01

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

  12. Energy level alignment in Au/pentacene/PTCDA trilayer stacks

    OpenAIRE

    Sehati, P.; Braun, S.; Fahlman, M.

    2013-01-01

    Ultraviolet photoelectron spectroscopy is used to investigate the energy level alignment and molecular orientation at the interfaces in Au/pentacene/PTCDA trilayer stacks. We deduced a standing orientation for pentacene grown on Au while we conclude a flat lying geometry for PTCDA grown onto pentacene. We propose that the rough surface of polycrystalline Au induces the standing geometry in pentacene. It is further shown that in situ deposition of PTCDA on pentacene can influence the orientati...

  13. Band Alignment Determination of Two-Dimensional Heterojunctions and Their Electronic Applications

    KAUST Repository

    Chiu, Ming-Hui

    2018-05-09

    Two-dimensional (2D) layered materials such as MoS2 have been recognized as high on-off ratio semiconductors which are promising candidates for electronic and optoelectronic devices. In addition to the use of individual 2D materials, the accelerated field of 2D heterostructures enables even greater functionalities. Device designs differ, and they are strongly controlled by the electronic band alignment. For example, photovoltaic cells require type II heterostructures for light harvesting, and light-emitting diodes benefit from multiple quantum wells with the type I band alignment for high emission efficiency. The vertical tunneling field-effect transistor for next-generation electronics depends on nearly broken-gap band alignment for boosting its performance. To tailor these 2D layered materials toward possible future applications, the understanding of 2D heterostructure band alignment becomes critically important. In the first part of this thesis, we discuss the band alignment of 2D heterostructures. To do so, we firstly study the interlayer coupling between two dissimilar 2D materials. We conclude that a post-anneal process could enhance the interlayer coupling of as-transferred 2D heterostructures, and heterostructural stacking imposes similar symmetry changes as homostructural stacking. Later, we precisely determine the quasi particle bandgap and band alignment of the MoS2/WSe2 heterostructure by using scan tunneling microscopy/spectroscopy (STM/S) and micron-beam X-ray photoelectron spectroscopy (μ-XPS) techniques. Lastly, we prove that the band alignment of 2D heterojunctions can be accurately predicted by Anderson’s model, which has previously failed to predict conventional bulk heterostructures. In the second part of this thesis, we develop a new Chemical Vapor Deposition (CVD) method capable of precisely controlling the growth area of p- and n-type transition metal dichalcogenides (TMDCs) and further form lateral or vertical 2D heterostructures. This

  14. Polymer chain alignment and transistor properties of nanochannel-templated poly(3-hexylthiophene) nanowires

    Science.gov (United States)

    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.

  15. Reducing beam shaper alignment complexity: diagnostic techniques for alignment and tuning

    Science.gov (United States)

    Lizotte, Todd E.

    2011-10-01

    Safe and efficient optical alignment is a critical requirement for industrial laser systems used in a high volume manufacturing environment. Of specific interest is the development of techniques to align beam shaping optics within a beam line; having the ability to instantly verify by a qualitative means that each element is in its proper position as the beam shaper module is being aligned. There is a need to reduce these types of alignment techniques down to a level where even a newbie to optical alignment will be able to complete the task. Couple this alignment need with the fact that most laser system manufacturers ship their products worldwide and the introduction of a new set of variables including cultural and language barriers, makes this a top priority for manufacturers. Tools and methodologies for alignment of complex optical systems need to be able to cross these barriers to ensure the highest degree of up time and reduce the cost of maintenance on the production floor. Customers worldwide, who purchase production laser equipment, understand that the majority of costs to a manufacturing facility is spent on system maintenance and is typically the largest single controllable expenditure in a production plant. This desire to reduce costs is driving the trend these days towards predictive and proactive, not reactive maintenance of laser based optical beam delivery systems [10]. With proper diagnostic tools, laser system developers can develop proactive approaches to reduce system down time, safe guard operational performance and reduce premature or catastrophic optics failures. Obviously analytical data will provide quantifiable performance standards which are more precise than qualitative standards, but each have a role in determining overall optical system performance [10]. This paper will discuss the use of film and fluorescent mirror devices as diagnostic tools for beam shaper module alignment off line or in-situ. The paper will also provide an overview

  16. A fast fiducial marker tracking model for fully automatic alignment in electron tomography

    KAUST Repository

    Han, Renmin; Zhang, Fa; Gao, Xin

    2017-01-01

    Automatic alignment, especially fiducial marker-based alignment, has become increasingly important due to the high demand of subtomogram averaging and the rapid development of large-field electron microscopy. Among the alignment steps, fiducial marker tracking is a crucial one that determines the quality of the final alignment. Yet, it is still a challenging problem to track the fiducial markers accurately and effectively in a fully automatic manner.In this paper, we propose a robust and efficient scheme for fiducial marker tracking. Firstly, we theoretically prove the upper bound of the transformation deviation of aligning the positions of fiducial markers on two micrographs by affine transformation. Secondly, we design an automatic algorithm based on the Gaussian mixture model to accelerate the procedure of fiducial marker tracking. Thirdly, we propose a divide-and-conquer strategy against lens distortions to ensure the reliability of our scheme. To our knowledge, this is the first attempt that theoretically relates the projection model with the tracking model. The real-world experimental results further support our theoretical bound and demonstrate the effectiveness of our algorithm. This work facilitates the fully automatic tracking for datasets with a massive number of fiducial markers.The C/C ++ source code that implements the fast fiducial marker tracking is available at https://github.com/icthrm/gmm-marker-tracking. Markerauto 1.6 version or later (also integrated in the AuTom platform at http://ear.ict.ac.cn/) offers a complete implementation for fast alignment, in which fast fiducial marker tracking is available by the

  17. A fast fiducial marker tracking model for fully automatic alignment in electron tomography

    KAUST Repository

    Han, Renmin

    2017-10-20

    Automatic alignment, especially fiducial marker-based alignment, has become increasingly important due to the high demand of subtomogram averaging and the rapid development of large-field electron microscopy. Among the alignment steps, fiducial marker tracking is a crucial one that determines the quality of the final alignment. Yet, it is still a challenging problem to track the fiducial markers accurately and effectively in a fully automatic manner.In this paper, we propose a robust and efficient scheme for fiducial marker tracking. Firstly, we theoretically prove the upper bound of the transformation deviation of aligning the positions of fiducial markers on two micrographs by affine transformation. Secondly, we design an automatic algorithm based on the Gaussian mixture model to accelerate the procedure of fiducial marker tracking. Thirdly, we propose a divide-and-conquer strategy against lens distortions to ensure the reliability of our scheme. To our knowledge, this is the first attempt that theoretically relates the projection model with the tracking model. The real-world experimental results further support our theoretical bound and demonstrate the effectiveness of our algorithm. This work facilitates the fully automatic tracking for datasets with a massive number of fiducial markers.The C/C ++ source code that implements the fast fiducial marker tracking is available at https://github.com/icthrm/gmm-marker-tracking. Markerauto 1.6 version or later (also integrated in the AuTom platform at http://ear.ict.ac.cn/) offers a complete implementation for fast alignment, in which fast fiducial marker tracking is available by the

  18. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal; Salama, Khaled N.

    2011-01-01

    fast alignment algorithm, called 'Alignment By Scanning' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the 'GAP' (which is heuristic) and the 'Needleman

  19. Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment.

    Science.gov (United States)

    Nagar, Anurag; Hahsler, Michael

    2013-01-01

    Next Generation Sequencing techniques are producing enormous amounts of biological sequence data and analysis becomes a major computational problem. Currently, most analysis, especially the identification of conserved regions, relies heavily on Multiple Sequence Alignment and its various heuristics such as progressive alignment, whose run time grows with the square of the number and the length of the aligned sequences and requires significant computational resources. In this work, we present a method to efficiently discover regions of high similarity across multiple sequences without performing expensive sequence alignment. The method is based on approximating edit distance between segments of sequences using p-mer frequency counts. Then, efficient high-throughput data stream clustering is used to group highly similar segments into so called quasi-alignments. Quasi-alignments have numerous applications such as identifying species and their taxonomic class from sequences, comparing sequences for similarities, and, as in this paper, discovering conserved regions across related sequences. In this paper, we show that quasi-alignments can be used to discover highly similar segments across multiple sequences from related or different genomes efficiently and accurately. Experiments on a large number of unaligned 16S rRNA sequences obtained from the Greengenes database show that the method is able to identify conserved regions which agree with known hypervariable regions in 16S rRNA. Furthermore, the experiments show that the proposed method scales well for large data sets with a run time that grows only linearly with the number and length of sequences, whereas for existing multiple sequence alignment heuristics the run time grows super-linearly. Quasi-alignment-based algorithms can detect highly similar regions and conserved areas across multiple sequences. Since the run time is linear and the sequences are converted into a compact clustering model, we are able to

  20. CMASA: an accurate algorithm for detecting local protein structural similarity and its application to enzyme catalytic site annotation

    Directory of Open Access Journals (Sweden)

    Li Gong-Hua

    2010-08-01

    Full Text Available Abstract Background The rapid development of structural genomics has resulted in many "unknown function" proteins being deposited in Protein Data Bank (PDB, thus, the functional prediction of these proteins has become a challenge for structural bioinformatics. Several sequence-based and structure-based methods have been developed to predict protein function, but these methods need to be improved further, such as, enhancing the accuracy, sensitivity, and the computational speed. Here, an accurate algorithm, the CMASA (Contact MAtrix based local Structural Alignment algorithm, has been developed to predict unknown functions of proteins based on the local protein structural similarity. This algorithm has been evaluated by building a test set including 164 enzyme families, and also been compared to other methods. Results The evaluation of CMASA shows that the CMASA is highly accurate (0.96, sensitive (0.86, and fast enough to be used in the large-scale functional annotation. Comparing to both sequence-based and global structure-based methods, not only the CMASA can find remote homologous proteins, but also can find the active site convergence. Comparing to other local structure comparison-based methods, the CMASA can obtain the better performance than both FFF (a method using geometry to predict protein function and SPASM (a local structure alignment method; and the CMASA is more sensitive than PINTS and is more accurate than JESS (both are local structure alignment methods. The CMASA was applied to annotate the enzyme catalytic sites of the non-redundant PDB, and at least 166 putative catalytic sites have been suggested, these sites can not be observed by the Catalytic Site Atlas (CSA. Conclusions The CMASA is an accurate algorithm for detecting local protein structural similarity, and it holds several advantages in predicting enzyme active sites. The CMASA can be used in large-scale enzyme active site annotation. The CMASA can be available by the

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

    International Nuclear Information System (INIS)

    Houben, L.; Bar Sadan, M.

    2011-01-01

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

  2. DNA Translator and Aligner: HyperCard utilities to aid phylogenetic analysis of molecules.

    Science.gov (United States)

    Eernisse, D J

    1992-04-01

    DNA Translator and Aligner are molecular phylogenetics HyperCard stacks for Macintosh computers. They manipulate sequence data to provide graphical gene mapping, conversions, translations and manual multiple-sequence alignment editing. DNA Translator is able to convert documented GenBank or EMBL documented sequences into linearized, rescalable gene maps whose gene sequences are extractable by clicking on the corresponding map button or by selection from a scrolling list. Provided gene maps, complete with extractable sequences, consist of nine metazoan, one yeast, and one ciliate mitochondrial DNAs and three green plant chloroplast DNAs. Single or multiple sequences can be manipulated to aid in phylogenetic analysis. Sequences can be translated between nucleic acids and proteins in either direction with flexible support of alternate genetic codes and ambiguous nucleotide symbols. Multiple aligned sequence output from diverse sources can be converted to Nexus, Hennig86 or PHYLIP format for subsequent phylogenetic analysis. Input or output alignments can be examined with Aligner, a convenient accessory stack included in the DNA Translator package. Aligner is an editor for the manual alignment of up to 100 sequences that toggles between display of matched characters and normal unmatched sequences. DNA Translator also generates graphic displays of amino acid coding and codon usage frequency relative to all other, or only synonymous, codons for approximately 70 select organism-organelle combinations. Codon usage data is compatible with spreadsheet or UWGCG formats for incorporation of additional molecules of interest. The complete package is available via anonymous ftp and is free for non-commercial uses.

  3. Inverse Problem Approach for the Alignment of Electron Tomographic Series

    International Nuclear Information System (INIS)

    Tran, V.D.; Moreaud, M.; Thiebaut, E.; Denis, L.; Becker, J.M.

    2014-01-01

    In the refining industry, morphological measurements of particles have become an essential part in the characterization catalyst supports. Through these parameters, one can infer the specific physico-chemical properties of the studied materials. One of the main acquisition techniques is electron tomography (or nano-tomography). 3D volumes are reconstructed from sets of projections from different angles made by a Transmission Electron Microscope (TEM). This technique provides a real three-dimensional information at the nano-metric scale. A major issue in this method is the misalignment of the projections that contributes to the reconstruction. The current alignment techniques usually employ fiducial markers such as gold particles for a correct alignment of the images. When the use of markers is not possible, the correlation between adjacent projections is used to align them. However, this method sometimes fails. In this paper, we propose a new method based on the inverse problem approach where a certain criterion is minimized using a variant of the Nelder and Mead simplex algorithm. The proposed approach is composed of two steps. The first step consists of an initial alignment process, which relies on the minimization of a cost function based on robust statistics measuring the similarity of a projection to its previous projections in the series. It reduces strong shifts resulting from the acquisition between successive projections. In the second step, the pre-registered projections are used to initialize an iterative alignment-refinement process which alternates between (i) volume reconstructions and (ii) registrations of measured projections onto simulated projections computed from the volume reconstructed in (i). At the end of this process, we have a correct reconstruction of the volume, the projections being correctly aligned. Our method is tested on simulated data and shown to estimate accurately the translation, rotation and scale of arbitrary transforms. We

  4. Zipping, entanglement, and the elastic modulus of aligned single-walled carbon nanotube films

    Science.gov (United States)

    Won, Yoonjin; Gao, Yuan; Panzer, Matthew A.; Xiang, Rong; Maruyama, Shigeo; Kenny, Thomas W.; Cai, Wei; Goodson, Kenneth E.

    2013-01-01

    Reliably routing heat to and from conversion materials is a daunting challenge for a variety of innovative energy technologies––from thermal solar to automotive waste heat recovery systems––whose efficiencies degrade due to massive thermomechanical stresses at interfaces. This problem may soon be addressed by adhesives based on vertically aligned carbon nanotubes, which promise the revolutionary combination of high through-plane thermal conductivity and vanishing in-plane mechanical stiffness. Here, we report the data for the in-plane modulus of aligned single-walled carbon nanotube films using a microfabricated resonator method. Molecular simulations and electron microscopy identify the nanoscale mechanisms responsible for this property. The zipping and unzipping of adjacent nanotubes and the degree of alignment and entanglement are shown to govern the spatially varying local modulus, thereby providing the route to engineered materials with outstanding combinations of mechanical and thermal properties. PMID:24309375

  5. Automated quantification of aligned collagen for human breast carcinoma prognosis

    Directory of Open Access Journals (Sweden)

    Jeremy S Bredfeldt

    2014-01-01

    Full Text Available Background: Mortality in cancer patients is directly attributable to the ability of cancer cells to metastasize to distant sites from the primary tumor. This migration of tumor cells begins with a remodeling of the local tumor microenvironment, including changes to the extracellular matrix and the recruitment of stromal cells, both of which facilitate invasion of tumor cells into the bloodstream. In breast cancer, it has been proposed that the alignment of collagen fibers surrounding tumor epithelial cells can serve as a quantitative image-based biomarker for survival of invasive ductal carcinoma patients. Specific types of collagen alignment have been identified for their prognostic value and now these tumor associated collagen signatures (TACS are central to several clinical specimen imaging trials. Here, we implement the semi-automated acquisition and analysis of this TACS candidate biomarker and demonstrate a protocol that will allow consistent scoring to be performed throughout large patient cohorts. Methods: Using large field of view high resolution microscopy techniques, image processing and supervised learning methods, we are able to quantify and score features of collagen fiber alignment with respect to adjacent tumor-stromal boundaries. Results: Our semi-automated technique produced scores that have statistically significant correlation with scores generated by a panel of three human observers. In addition, our system generated classification scores that accurately predicted survival in a cohort of 196 breast cancer patients. Feature rank analysis reveals that TACS positive fibers are more well-aligned with each other, are of generally lower density, and terminate within or near groups of epithelial cells at larger angles of interaction. Conclusion: These results demonstrate the utility of a supervised learning protocol for streamlining the analysis of collagen alignment with respect to tumor stromal boundaries.

  6. Independent alignment of RNA for dynamic studies using residual dipolar couplings

    Energy Technology Data Exchange (ETDEWEB)

    Bardaro, Michael F.; Varani, Gabriele, E-mail: varani@chem.washington.edu [University of Washington, Department of Chemistry (United States)

    2012-09-15

    Molecular motion and dynamics play an essential role in the biological function of many RNAs. An important source of information on biomolecular motion can be found in residual dipolar couplings which contain dynamics information over the entire ms-ps timescale. However, these methods are not fully applicable to RNA because nucleic acid molecules tend to align in a highly collinear manner in different alignment media. As a consequence, information on dynamics that can be obtained with this method is limited. In order to overcome this limitation, we have generated a chimeric RNA containing both the wild type TAR RNA, the target of our investigation of dynamics, as well as the binding site for U1A protein. When U1A protein was bound to the portion of the chimeric RNA containing its binding site, we obtained independent alignment of TAR by exploiting the physical chemical characteristics of this protein. This technique can allow the extraction of new information on RNA dynamics, which is particularly important for time scales not covered by relaxation methods where important RNA motions occur.

  7. Alignment effects in two-photon double ionization of H{sub 2} in femtosecond xuv laser pulses

    Energy Technology Data Exchange (ETDEWEB)

    Guan Xiaoxu; Bartschat, Klaus [Department of Physics and Astronomy, Drake University, Des Moines, Iowa 50311 (United States); Schneider, Barry I. [Office of Cyberinfrastructure, National Science Foundation, Arlington, Virgina 22230 (United States)

    2011-09-15

    Triple-differential cross sections for two-photon double ionization of the aligned hydrogen molecule at the equilibrium distance are presented for a central photon energy of 30 eV. The temporal response of the laser-driven molecule is investigated by solving the time-dependent Schroedinger equation in full dimensionality using two-center elliptical coordinates and a finite-element discrete-variable-representation approach. The molecular orientation is found to have a strong effect on the emission modes of the two correlated photoelectrons. This molecular effect is most noticeable when the molecular axis and the laser polarization vector are oriented parallel to each other. For intermediate cases between the parallel and perpendicular geometries, the dominant emission modes for two-electron ejection oscillate between those for the two extreme cases. The contributions from different ionization channels are also analyzed in detail. Depending on the emission direction of the reference electron, the interference contributions from the various channels can be constructive or destructive at small alignment angles, while they always contribute constructively to the triple-differential cross sections near the perpendicular geometry.

  8. Molecular design for nonpolar chiral-axial quadratic nonlinear optics

    Science.gov (United States)

    Wiggers, Gregory A.

    In this thesis the hyperpolarizability of various multi-dimensional molecules is studied theoretically/computationally, with particular focus on the second-rank Kleinman-disallowed (KD) component of the hyperpolarizability. This component, which transforms as a second-rank traceless symmetric tensor, could be utilized in certain chiral-axial molecular alignment schemes to produce a bulk response. Nonpolar chiral-axial systems have been proposed in contrast to polar media, which utilize the vector component of the molecular hyperpolarizability and require parallel alignment of the molecular dipoles. Such parallel alignment of dipoles must be "frozen in" in order to overcome the natural tendency for dipoles to align anti-parallel. This limits the density of chromophores that can be loaded into a polar material. Nonpolar materials do not have such limits in theory. The two geometric classes of molecules that can most easily be incorporated into nonpolar chiral-uniaxial materials are propeller-shaped (C3 or D3 symmetry) and Λ-shaped (C2v symmetry). This work describes efforts to design molecules within these classes that would be suitable for bulk NLO materials. The sum-over-states (SOS) expression is used to model the molecular hyperpolarizability, and quantum chemical calculations, along with linear absorption data (when available) provide the necessary parameters to evaluate truncated forms of the SOS expression. A host of chemical and geometric modifications will be considered in order to elucidate important structure/function relationships. Also, the SOS model will be tested in some cases when experimental measurements (via Kleinman-disallowed hyper-Rayleigh scattering) are available. While a majority of this work focuses on multi-dimensional molecules, a small section deals with the question of optimizing the hyperpolarizability of a one-dimensional system. It is suggested that the recently-proposed idea of "modulated conjugation" as a means for improving

  9. A novel technique for reference point generation to aid in intraoral scan alignment.

    Science.gov (United States)

    Renne, Walter G; Evans, Zachary P; Mennito, Anthony; Ludlow, Mark

    2017-11-12

    When using a completely digital workflow on larger prosthetic cases it is often difficult to communicate to the laboratory or chairside Computer Aided Design and Computer Aided Manufacturing system the provisional prosthetic information. The problem arises when common hard tissue data points are limited or non-existent such as in complete arch cases in which the 3D model of the complete arch provisional restorations must be aligned perfectly with the 3D model of the complete arch preparations. In these instances, soft tissue is not enough to ensure an accurate automatic or manual alignment due to a lack of well-defined reference points. A new technique is proposed for the proper digital alignment of the 3D virtual model of the provisional prosthetic to the 3D virtual model of the prepared teeth in cases where common and coincident hard tissue data points are limited. Clinical considerations: A technique is described in which fiducial composite resin dots are temporarily placed on the intraoral keratinized tissue in strategic locations prior to final impressions. These fiducial dots provide coincident and clear 3D data points that when scanned into a digital impression allow superimposition of the 3D models. Composite resin dots on keratinized tissue were successful at allowing accurate merging of provisional restoration and post-preparation 3D models for the purpose of using the provisional restorations as a guide for final CLINICAL SIGNIFICANCE: Composite resin dots placed temporarily on attached tissue were successful at allowing accurate merging of the provisional restoration 3D models to the preparation 3D models for the purposes of using the provisional restorations as a guide for final restoration design and manufacturing. In this case, they allowed precise superimposition of the 3D models made in the absence of any other hard tissue reference points, resulting in the fabrication of ideal final restorations. © 2017 Wiley Periodicals, Inc.

  10. Clear aligners in orthodontic treatment.

    Science.gov (United States)

    Weir, T

    2017-03-01

    Since the introduction of the Tooth Positioner (TP Orthodontics) in 1944, removable appliances analogous to clear aligners have been employed for mild to moderate orthodontic tooth movements. Clear aligner therapy has been a part of orthodontic practice for decades, but has, particularly since the introduction of Invisalign appliances (Align Technology) in 1998, become an increasingly common addition to the orthodontic armamentarium. An internet search reveals at least 27 different clear aligner products currently on offer for orthodontic treatment. The present paper will highlight the increasing popularity of clear aligner appliances, as well as the clinical scope and the limitations of aligner therapy in general. Further, the paper will outline the differences between the various types of clear aligner products currently available. © 2017 Australian Dental Association.

  11. Balancing an accurate representation of the molecular surface in generalized Born formalisms with integrator stability in molecular dynamics simulations

    Czech Academy of Sciences Publication Activity Database

    Chocholoušová, Jana; Feig, M.

    2006-01-01

    Roč. 27, č. 6 (2006), s. 719-729 ISSN 0192-8651 Keywords : molecular surface * generalized Born formalisms * molecular dynamic simulations Subject RIV: CC - Organic Chemistry Impact factor: 4.893, year: 2006

  12. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    Gervasio Gomez

    2012-01-01

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

  13. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez

    2010-01-01

    For the last three months, the Muon Alignment group has focussed on providing a new, improved set of alignment constants for the end-of-year data reprocessing. These constants were delivered on time and approved by the CMS physics validation team on November 17. The new alignment incorporates several improvements over the previous one from March for nearly all sub-systems. Motivated by the loss of information from a hardware failure in May (an entire MAB was lost), the optical barrel alignment has moved from a modular, super-plane reconstruction, to a full, single loop calculation of the entire geometry for all DTs in stations 1, 2 and 3. This makes better use of the system redundancy, mitigating the effect of the information loss. Station 4 is factorised and added afterwards to make the system smaller (and therefore faster to run), and also because the MAB calibration at the MB4 zone is less precise. This new alignment procedure was tested at 0 T against photogrammetry resulting in precisions of the order...

  14. Influence of solvent and salt concentration on the alignment properties of acrylamide copolymer gels for the measurement of RDC.

    Science.gov (United States)

    Trigo-Mouriño, Pablo; Navarro-Vázquez, Armando; Sánchez-Pedregal, Víctor M

    2012-12-01

    The dependence of molecular alignment with solvent nature and salt concentration has been investigated for mechanically stretched polyacrylamide copolymer gels. Residual dipolar couplings (RDCs) were recorded for D(2)O, DMSO-d(6), and DMSO-d(6)/D(2)O solutions containing different proportions of the solvents and different sodium chloride concentrations. Alignment tensors were determined by fitting the experimental RDCs to the DFT-computed structure of N-methylcodeinium ion. Analysis of the tensors shows that the degree of alignment decreases with the proportion of DMSO-d(6) as well as with the concentration of sodium chloride, most likely due to enhanced ion-pair aggregation. Furthermore, rotation of the alignment tensor is observed when increasing the salt concentration. Copyright © 2012 John Wiley & Sons, Ltd.

  15. Thermal transport in semicrystalline polyethylene by molecular dynamics simulation

    Science.gov (United States)

    Lu, Tingyu; Kim, Kyunghoon; Li, Xiaobo; Zhou, Jun; Chen, Gang; Liu, Jun

    2018-01-01

    Recent research has highlighted the potential to achieve high-thermal-conductivity polymers by aligning their molecular chains. Combined with other merits, such as low-cost, corrosion resistance, and light weight, such polymers are attractive for heat transfer applications. Due to their quasi-one-dimensional structural nature, the understanding on the thermal transport in those ultra-drawn semicrystalline polymer fibers or films is still lacking. In this paper, we built the ideal repeating units of semicrystalline polyethylene and studied their dependence of thermal conductivity on different crystallinity and interlamellar topology using the molecular dynamics simulations. We found that the conventional models, such as the Choy-Young's model, the series model, and Takayanagi's model, cannot accurately predict the thermal conductivity of the quasi-one-dimensional semicrystalline polyethylene. A modified Takayanagi's model was proposed to explain the dependence of thermal conductivity on the bridge number at intermediate and high crystallinity. We also analyzed the heat transfer pathways and demonstrated the substantial role of interlamellar bridges in the thermal transport in the semicrystalline polyethylene. Our work could contribute to the understanding of the structure-property relationship in semicrystalline polymers and shed some light on the development of plastic heat sinks and thermal management in flexible electronics.

  16. Theory for the alignment of cortical feature maps during development.

    Science.gov (United States)

    Bressloff, Paul C; Oster, Andrew M

    2010-08-01

    We present a developmental model of ocular dominance column formation that takes into account the existence of an array of intrinsically specified cytochrome oxidase blobs. We assume that there is some molecular substrate for the blobs early in development, which generates a spatially periodic modulation of experience-dependent plasticity. We determine the effects of such a modulation on a competitive Hebbian mechanism for the modification of the feedforward afferents from the left and right eyes. We show how alternating left and right eye dominated columns can develop, in which the blobs are aligned with the centers of the ocular dominance columns and receive a greater density of feedforward connections, thus becoming defined extrinsically. More generally, our results suggest that the presence of periodically distributed anatomical markers early in development could provide a mechanism for the alignment of cortical feature maps.

  17. Electronic states of model hydrocarbon chromophores investigated by Synchrotron Radiation Linear Dichroism (SRLD) spectroscopy on aligned samples

    DEFF Research Database (Denmark)

    Nguyen, Duy Duc; Hoffmann, Søren Vrønning; Jones, Nykola

    2010-01-01

    Conventional UV-VIS absorption spectroscopy provides information on transition energies and intensities. Linear dichroism (LD) spectroscopy on aligned molecular samples yields additional information on transition moment directions, thereby frequently leading to resolution of otherwise overlapping...

  18. Strategic Alignment and New Product Development

    DEFF Research Database (Denmark)

    Acur, Nuran; Kandemir, Destan; Boer, Harry

    2012-01-01

    Strategic alignment is widely accepted as a prerequisite for a firm’s success, but insight into the role of alignment in, and its impact on, the new product evelopment (NPD) process and its performance is less well developed. Most publications on this topic either focus on one form of alignment...... of NPD performance indicators. Strategic planning and innovativeness appear to affect technological, market, and NPD-marketing alignment positively. Environmental munificence is negatively associated with NPD-marketing alignment, but has no effect on the two other forms of alignment. Technological change...... has a positive effect on technological alignment, a negative effect on NPD-marketing alignment, but no effect on market alignment. These findings suggest that internal capabilities are more likely to be associated with the development of strategic alignment than environmental factors are. Furthermore...

  19. Molecular Diagnostics

    OpenAIRE

    Choe, Hyonmin; Deirmengian, Carl A.; Hickok, Noreen J.; Morrison, Tiffany N.; Tuan, Rocky S.

    2015-01-01

    Orthopaedic infections are complex conditions that require immediate diagnosis and accurate identification of the causative organisms to facilitate appropriate management. Conventional methodologies for diagnosis of these infections sometimes lack accuracy or sufficient rapidity. Current molecular diagnostics are an emerging area of bench-to-bedside research in orthopaedic infections. Examples of promising molecular diagnostics include measurement of a specific biomarker in the synovial fluid...

  20. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal; Salama, Khaled N.

    2011-01-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the 'Needleman-Wunsch' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  1. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal

    2011-08-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  2. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal

    2011-11-01

    Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. We introduce fast alignment algorithm, called \\'Alignment By Scanning\\' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the \\'GAP\\' (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  3. Self-adapting denoising, alignment and reconstruction in electron tomography in materials science

    Energy Technology Data Exchange (ETDEWEB)

    Printemps, Tony, E-mail: tony.printemps@cea.fr [Université Grenoble Alpes, F-38000 Grenoble (France); CEA, LETI, MINATEC Campus, F-38054 Grenoble (France); Mula, Guido [Dipartimento di Fisica, Università di Cagliari, Cittadella Universitaria, S.P. 8km 0.700, 09042 Monserrato (Italy); Sette, Daniele; Bleuet, Pierre; Delaye, Vincent; Bernier, Nicolas; Grenier, Adeline; Audoit, Guillaume; Gambacorti, Narciso; Hervé, Lionel [Université Grenoble Alpes, F-38000 Grenoble (France); CEA, LETI, MINATEC Campus, F-38054 Grenoble (France)

    2016-01-15

    An automatic procedure for electron tomography is presented. This procedure is adapted for specimens that can be fashioned into a needle-shaped sample and has been evaluated on inorganic samples. It consists of self-adapting denoising, automatic and accurate alignment including detection and correction of tilt axis, and 3D reconstruction. We propose the exploitation of a large amount of information of an electron tomography acquisition to achieve robust and automatic mixed Poisson–Gaussian noise parameter estimation and denoising using undecimated wavelet transforms. The alignment is made by mixing three techniques, namely (i) cross-correlations between neighboring projections, (ii) common line algorithm to get a precise shift correction in the direction of the tilt axis and (iii) intermediate reconstructions to precisely determine the tilt axis and shift correction in the direction perpendicular to that axis. Mixing alignment techniques turns out to be very efficient and fast. Significant improvements are highlighted in both simulations and real data reconstructions of porous silicon in high angle annular dark field mode and agglomerated silver nanoparticles in incoherent bright field mode. 3D reconstructions obtained with minimal user-intervention present fewer artefacts and less noise, which permits easier and more reliable segmentation and quantitative analysis. After careful sample preparation and data acquisition, the denoising procedure, alignment and reconstruction can be achieved within an hour for a 3D volume of about a hundred million voxels, which is a step toward a more routine use of electron tomography. - Highlights: • Goal: perform a reliable and user-independent 3D electron tomography reconstruction. • Proposed method: self-adapting denoising and alignment prior to 3D reconstruction. • Noise estimation and denoising are performed using wavelet transform. • Tilt axis determination is done automatically as well as projection alignment.

  4. New overlay measurement technique with an i-line stepper using embedded standard field image alignment marks for wafer bonding applications

    Science.gov (United States)

    Kulse, P.; Sasai, K.; Schulz, K.; Wietstruck, M.

    2017-06-01

    In the last decades the semiconductor technology has been driven by Moore's law leading to high performance CMOS technologies with feature sizes of less than 10 nm [1]. It has been pointed out that not only scaling but also the integration of novel components and technology modules into CMOS/BiCMOS technologies is becoming more attractive to realize smart and miniaturized systems [2]. Driven by new applications in the area of communication, health and automation, new components and technology modules such as BiCMOS embedded RF-MEMS, high-Q passives, Sibased microfluidics and InP-SiGe BiCMOS heterointegration have been demonstrated [3-6]. In contrast to standard VLSI processes fabricated on front side of the silicon wafer, these new technology modules require addition backside processing of the wafer; thus an accurate alignment between the front and backside of the wafer is mandatory. In previous work an advanced back to front side alignment technique and implementation into IHP's 0.25/0.13 μm high performance SiGe:C BiCMOS backside process module has been presented [7]. The developed technique enables a high resolution and accurate lithography on the backside of BiCMOS wafer for additional backside processing. In addition to the aforementioned back side process technologies, new applications like Through-Silicon Vias (TSV) for interposers and advanced substrate technologies for 3D heterogeneous integration demand not only single wafer fabrication but also processing of wafer stacks provided by temporary and permanent wafer bonding [8]. Therefore, the available overlay measurement techniques are not suitable if overlay and alignment marks are realized at the bonding interface of a wafer stack which consists of both a silicon device and a silicon carrier wafer. The former used EVG 40NT automated overlay measurement system, which use two opposite positioned microscopes inspecting simultaneous the wafer back and front side, is not capable measuring embedded overlay

  5. Three dimensional extrusion printing induces polymer molecule alignment and cell organization within engineered cartilage.

    Science.gov (United States)

    Guo, Ting; Ringel, Julia P; Lim, Casey G; Bracaglia, Laura G; Noshin, Maeesha; Baker, Hannah B; Powell, Douglas A; Fisher, John P

    2018-04-16

    Proper cell-material interactions are critical to remain cell function and thus successful tissue regeneration. Many fabrication processes have been developed to create microenvironments to control cell attachment and organization on a three-dimensional (3D) scaffold. However, these approaches often involve heavy engineering and only the surface layer can be patterned. We found that 3D extrusion based printing at high temperature and pressure will result an aligned effect on the polymer molecules, and this molecular arrangement will further induce the cell alignment and different differentiation capacities. In particular, articular cartilage tissue is known to have zonal collagen fiber and cell orientation to support different functions, where collagen fibers and chondrocytes align parallel, randomly, and perpendicular, respectively, to the surface of the joint. Therefore, cell alignment was evaluated in a cartilage model in this study. We used small angle X-ray scattering analysis to substantiate the polymer molecule alignment phenomenon. The cellular response was evaluated both in vitro and in vivo. Seeded mesenchymal stem cells (MSCs) showed different morphology and orientation on scaffolds, as a combined result of polymer molecule alignment and printed scaffold patterns. Gene expression results showed improved superficial zonal chondrogenic marker expression in parallel-aligned group. The cell alignment was successfully maintained in the animal model after 7 days with distinct MSC morphology between the casted and parallel printed scaffolds. This 3D printing induced polymer and cell alignment will have a significant impact on developing scaffold with controlled cell-material interactions for complex tissue engineering while avoiding complicated surface treatment, and therefore provides new concept for effective tissue repairing in future clinical applications. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A, 2018. © 2018 Wiley Periodicals, Inc.

  6. Pareto optimal pairwise sequence alignment.

    Science.gov (United States)

    DeRonne, Kevin W; Karypis, George

    2013-01-01

    Sequence alignment using evolutionary profiles is a commonly employed tool when investigating a protein. Many profile-profile scoring functions have been developed for use in such alignments, but there has not yet been a comprehensive study of Pareto optimal pairwise alignments for combining multiple such functions. We show that the problem of generating Pareto optimal pairwise alignments has an optimal substructure property, and develop an efficient algorithm for generating Pareto optimal frontiers of pairwise alignments. All possible sets of two, three, and four profile scoring functions are used from a pool of 11 functions and applied to 588 pairs of proteins in the ce_ref data set. The performance of the best objective combinations on ce_ref is also evaluated on an independent set of 913 protein pairs extracted from the BAliBASE RV11 data set. Our dynamic-programming-based heuristic approach produces approximated Pareto optimal frontiers of pairwise alignments that contain comparable alignments to those on the exact frontier, but on average in less than 1/58th the time in the case of four objectives. Our results show that the Pareto frontiers contain alignments whose quality is better than the alignments obtained by single objectives. However, the task of identifying a single high-quality alignment among those in the Pareto frontier remains challenging.

  7. Energy level alignment at the methylammonium lead iodide/copper phthalocyanine interface

    Directory of Open Access Journals (Sweden)

    Shi Chen

    2014-08-01

    Full Text Available The energy level alignment at the CH3NH3PbI3/copper phthalocyanine (CuPc interface is investigated by X-ray photoelectron spectroscopy (XPS and ultraviolet photoelectron spectroscopy (UPS. XPS reveal a 0.3 eV downward band bending in the CuPc film. UPS validate this finding and further reveal negligible interfacial dipole formation – verifying the viability of vacuum level alignment. The highest occupied molecular orbital of CuPc is found to be closer to the Fermi level than the valance band maximum of CH3NH3PbI3, facilitating hole transfer from CH3NH3PbI3 to CuPc. However, subsequent hole extraction from CuPc may be impeded by the downward band bending in the CuPc layer.

  8. Alignment for CSR

    International Nuclear Information System (INIS)

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

    2002-01-01

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

  9. Reverse capillary flow of condensed water through aligned multiwalled carbon nanotubes

    International Nuclear Information System (INIS)

    Yun, Jongju; Jeon, Wonjae; Alam Khan, Fakhre; Lee, Jinkee; Baik, Seunghyun

    2015-01-01

    Molecular transport through nanopores has recently received considerable attention as a result of advances in nanofabrication and nanomaterial synthesis technologies. Surprisingly, water transport investigations through carbon nanochannels resulted in two contradicting observations: extremely fast transport or rejection of water molecules. In this paper, we elucidate the mechanism of impeded water vapor transport through the interstitial space of aligned multiwalled carbon nanotubes (aligned-MWCNTs)—capillary condensation, agglomeration, reverse capillary flow, and removal by superhydrophobicity at the tip of the nanotubes. The origin of separation comes from the water’s phase change from gas to liquid, followed by reverse capillary flow. First, the saturation water vapor pressure is decreased in a confined space, which is favorable for the phase change of incoming water vapor into liquid drops. Once continuous water meniscus is formed between the nanotubes by the adsoprtion and agglomeration of water molecules, a high reverse Laplace pressure is induced in the mushroom-shaped liquid meniscus at the entry region of the aligned-MWCNTs. The reverse Laplace pressure can be significantly enhanced by decreasing the pore size. Finally, the droplets pushed backward by the reverse Laplace pressure can be removed by superhydrophobicity at the tip of the aligned-MWCNTs. The analytical analysis was also supported by experiments carried out using 4 mm-long aligned-MWCNTs with different intertube distances. The water rejection rate and the separation factor increased as the intertube distance decreased, resulting in 90% and 10, respectively, at an intertube distance of 4 nm. This mechanism and nanotube membrane may be useful for energy-efficient water vapor separation and dehumidification. (paper)

  10. CUFID-query: accurate network querying through random walk based network flow estimation.

    Science.gov (United States)

    Jeong, Hyundoo; Qian, Xiaoning; Yoon, Byung-Jun

    2017-12-28

    Functional modules in biological networks consist of numerous biomolecules and their complicated interactions. Recent studies have shown that biomolecules in a functional module tend to have similar interaction patterns and that such modules are often conserved across biological networks of different species. As a result, such conserved functional modules can be identified through comparative analysis of biological networks. In this work, we propose a novel network querying algorithm based on the CUFID (Comparative network analysis Using the steady-state network Flow to IDentify orthologous proteins) framework combined with an efficient seed-and-extension approach. The proposed algorithm, CUFID-query, can accurately detect conserved functional modules as small subnetworks in the target network that are expected to perform similar functions to the given query functional module. The CUFID framework was recently developed for probabilistic pairwise global comparison of biological networks, and it has been applied to pairwise global network alignment, where the framework was shown to yield accurate network alignment results. In the proposed CUFID-query algorithm, we adopt the CUFID framework and extend it for local network alignment, specifically to solve network querying problems. First, in the seed selection phase, the proposed method utilizes the CUFID framework to compare the query and the target networks and to predict the probabilistic node-to-node correspondence between the networks. Next, the algorithm selects and greedily extends the seed in the target network by iteratively adding nodes that have frequent interactions with other nodes in the seed network, in a way that the conductance of the extended network is maximally reduced. Finally, CUFID-query removes irrelevant nodes from the querying results based on the personalized PageRank vector for the induced network that includes the fully extended network and its neighboring nodes. Through extensive

  11. A generalized global alignment algorithm.

    Science.gov (United States)

    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.

  12. HAL: a hierarchical format for storing and analyzing multiple genome alignments.

    Science.gov (United States)

    Hickey, Glenn; Paten, Benedict; Earl, Dent; Zerbino, Daniel; Haussler, David

    2013-05-15

    Large multiple genome alignments and inferred ancestral genomes are ideal resources for comparative studies of molecular evolution, and advances in sequencing and computing technology are making them increasingly obtainable. These structures can provide a rich understanding of the genetic relationships between all subsets of species they contain. Current formats for storing genomic alignments, such as XMFA and MAF, are all indexed or ordered using a single reference genome, however, which limits the information that can be queried with respect to other species and clades. This loss of information grows with the number of species under comparison, as well as their phylogenetic distance. We present HAL, a compressed, graph-based hierarchical alignment format for storing multiple genome alignments and ancestral reconstructions. HAL graphs are indexed on all genomes they contain. Furthermore, they are organized phylogenetically, which allows for modular and parallel access to arbitrary subclades without fragmentation because of rearrangements that have occurred in other lineages. HAL graphs can be created or read with a comprehensive C++ API. A set of tools is also provided to perform basic operations, such as importing and exporting data, identifying mutations and coordinate mapping (liftover). All documentation and source code for the HAL API and tools are freely available at http://github.com/glennhickey/hal. hickey@soe.ucsc.edu or haussler@soe.ucsc.edu Supplementary data are available at Bioinformatics online.

  13. Pairwise Sequence Alignment Library

    Energy Technology Data Exchange (ETDEWEB)

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

  14. Progressive multiple sequence alignments from triplets

    Directory of Open Access Journals (Sweden)

    Stadler Peter F

    2007-07-01

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

  15. Belt Aligning Revisited

    Directory of Open Access Journals (Sweden)

    Yurchenko Vadim

    2017-01-01

    parts of the conveyor, the sides of the belt wear intensively. This results in reducing the life of the belt. The reasons for this phenomenon are well investigated, but the difficulty lies in the fact that they all act simultaneously. The belt misalignment prevention can be carried out in two ways: by minimizing the effect of causes and by aligning the belt. The construction of aligning devices and errors encountered in practice are considered in this paper. Self-aligning roller supports rotational in plan view are recommended as a means of combating the belt misalignment.

  16. Antares beam-alignment-system performance

    International Nuclear Information System (INIS)

    Appert, Q.D.; Bender, S.C.

    1983-01-01

    The beam alignment system for the 24-beam-sector Antares CO 2 fusion laser automatically aligns more than 200 optical elements. A visible-wavelength alignment technique is employed which uses a telescope/TV system to view point-light sources appropriately located down the beamline. The centroids of the light spots are determined by a video tracker, which generates error signals used by the computer control system to move appropriate mirrors in a closed-loop system. Final touch-up alignment is accomplished by projecting a CO 2 alignment laser beam through the system and sensing its position at the target location. The techniques and control algorithms employed have resulted in alignment accuracies exceeding design requirements. By employing video processing to determine the centroids of diffraction images and by averaging over multiple TV frames, we achieve alignment accuracies better than 0.1 times system diffraction limits in the presence of air turbulence

  17. A UNIFIED MODEL OF GRAIN ALIGNMENT: RADIATIVE ALIGNMENT OF INTERSTELLAR GRAINS WITH MAGNETIC INCLUSIONS

    Energy Technology Data Exchange (ETDEWEB)

    Hoang, Thiem [Canadian Institute for Theoretical Astrophysics, University of Toronto, 60 St. George Street, Toronto, ON M5S 3H8 (Canada); Lazarian, A. [Department of Astronomy, University of Wisconsin-Madison (United States)

    2016-11-10

    The radiative torque (RAT) alignment of interstellar grains with ordinary paramagnetic susceptibilities has been supported by earlier studies. The alignment of such grains depends on the so-called RAT parameter q {sup max}, which is determined by the grain shape. In this paper, we elaborate on our model of RAT alignment for grains with enhanced magnetic susceptibility due to iron inclusions, such that RAT alignment is magnetically enhanced, which we term the MRAT mechanism. Such grains can be aligned with high angular momentum at the so-called high- J attractor points, achieving a high degree of alignment. Using our analytical model of RATs, we derive the critical value of the magnetic relaxation parameter δ {sub m} to produce high- J attractor points as functions of q {sup max} and the anisotropic radiation angle relative to the magnetic field ψ . We find that if about 10% of the total iron abundance present in silicate grains is forming iron clusters, this is sufficient to produce high- J attractor points for all reasonable values of q {sup max}. To calculate the degree of grain alignment, we carry out numerical simulations of MRAT alignment by including stochastic excitations from gas collisions and magnetic fluctuations. We show that large grains can achieve perfect alignment when the high- J attractor point is present, regardless of the values of q {sup max}. Our obtained results pave the way for the physical modeling of polarized thermal dust emission as well as magnetic dipole emission. We also find that millimeter-sized grains in accretion disks may be aligned with the magnetic field if they are incorporated with iron nanoparticles.

  18. Theory of the deformation of aligned polyethylene.

    Science.gov (United States)

    Hammad, A; Swinburne, T D; Hasan, H; Del Rosso, S; Iannucci, L; Sutton, A P

    2015-08-08

    Solitons are proposed as the agents of plastic and viscoelastic deformation in aligned polyethylene. Interactions between straight, parallel molecules are mapped rigorously onto the Frenkel-Kontorova model. It is shown that these molecular interactions distribute an applied load between molecules, with a characteristic transfer length equal to the soliton width. Load transfer leads to the introduction of tensile and compressive solitons at the chain ends to mark the onset of plasticity at a well-defined yield stress, which is much less than the theoretical pull-out stress. Interaction energies between solitons and an equation of motion for solitons are derived. The equation of motion is based on Langevin dynamics and the fluctuation-dissipation theorem and it leads to the rigorous definition of an effective mass for solitons. It forms the basis of a soliton dynamics in direct analogy to dislocation dynamics. Close parallels are drawn between solitons in aligned polymers and dislocations in crystals, including the configurational force on a soliton. The origins of the strain rate and temperature dependencies of the viscoelastic behaviour are discussed in terms of the formation energy of solitons. A failure mechanism is proposed involving soliton condensation under a tensile load.

  19. Alignment between Protostellar Outflows and Filamentary Structure

    Energy Technology Data Exchange (ETDEWEB)

    Stephens, Ian W.; Dunham, Michael M.; Myers, Philip C.; Pokhrel, Riwaj; Sadavoy, Sarah I.; Lee, Katherine I.; Goodman, Alyssa A. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA (United States); Vorobyov, Eduard I. [Institute of Fluid Mechanics and Heat Transfer, TU Wien, Vienna, A-1060 (Austria); Tobin, John J. [Homer L. Dodge Department of Physics and Astronomy, University of Oklahoma, 440 W. Brooks Street, Norman, OK 73019 (United States); Pineda, Jaime E. [Max-Planck-Institut für extraterrestrische Physik, Giessenbachstrasse 1, 85748 Garching (Germany); Offner, Stella S. R. [Department of Astronomy, University of Massachusetts, Amherst, MA 01003 (United States); Kristensen, Lars E. [Centre for Star and Planet Formation, Niels Bohr Institute and Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K (Denmark); Jørgensen, Jes K. [Niels Bohr Institute and Center for Star and Planet Formation, Copenhagen University, DK-1350 Copenhagen K. (Denmark); Bourke, Tyler L. [SKA Organization, Jodrell Bank Observatory, Lower Withington, Macclesfield, Cheshire SK11 9DL (United Kingdom); Arce, Héctor G. [Department of Astronomy, Yale University, New Haven, CT 06520 (United States); Plunkett, Adele L., E-mail: ian.stephens@cfa.harvard.edu [European Southern Observatory, Av. Alonso de Cordova 3107, Vitacura, Santiago de Chile (Chile)

    2017-09-01

    We present new Submillimeter Array (SMA) observations of CO(2–1) outflows toward young, embedded protostars in the Perseus molecular cloud as part of the Mass Assembly of Stellar Systems and their Evolution with the SMA (MASSES) survey. For 57 Perseus protostars, we characterize the orientation of the outflow angles and compare them with the orientation of the local filaments as derived from Herschel observations. We find that the relative angles between outflows and filaments are inconsistent with purely parallel or purely perpendicular distributions. Instead, the observed distribution of outflow-filament angles are more consistent with either randomly aligned angles or a mix of projected parallel and perpendicular angles. A mix of parallel and perpendicular angles requires perpendicular alignment to be more common by a factor of ∼3. Our results show that the observed distributions probably hold regardless of the protostar’s multiplicity, age, or the host core’s opacity. These observations indicate that the angular momentum axis of a protostar may be independent of the large-scale structure. We discuss the significance of independent protostellar rotation axes in the general picture of filament-based star formation.

  20. Substrate dependence of energy level alignment at the donor-acceptor interface in organic photovoltaic devices

    International Nuclear Information System (INIS)

    Zhou, Y.C.; Liu, Z.T.; Tang, J.X.; Lee, C.S.; Lee, S.T.

    2009-01-01

    The interface energy level alignment between copper phthalocyanine (CuPC) and fullerene (C60), the widely studied donor-acceptor pair in organic photovoltaics (OPVs), on indium-tin oxide (ITO) and Mg substrate was investigated. The CuPC/C60 interface formed on ITO shows a nearly common vacuum level, but a dipole and band bending exist, resulting in a 0.8 eV band offset at the same interface on Mg. This observation indicates that the energy difference between the highest occupied molecular orbital of CuPC and the lowest unoccupied molecular orbital of C60, which dictates the open circuit voltage of the CuPC/C60 OPV, can be tuned by the work function of the substrate. Furthermore, the substrate effect on the energy alignment at the donor/acceptor interface can satisfactorily explain that a device with an anode of a smaller work function can provide a higher open circuit voltage.

  1. Single crystalline growth of a soluble organic semiconductor in a parallel aligned liquid crystal solvent using rubbing-treated polyimide films

    Science.gov (United States)

    Matsuzaki, Tomoya; Shibata, Yosei; Takeda, Risa; Ishinabe, Takahiro; Fujikake, Hideo

    2017-01-01

    For directional control of organic single crystals, we propose a crystal growth method using liquid crystal as the solvent. In this study, we examined the formation of 2,7-dioctyl[1]benzothieno[3,2-b][1]benzothiophene (C8-BTBT) single crystals using a parallel aligned liquid crystal (LC) cell and rubbing-treated polyimide films in order to clarify the effects of LC alignment on anisotropic C8-BTBT crystal growth. Based on the results, we found that the crystal growth direction of C8-BTBT single crystals was related to the direction of the aligned LC molecules because of rubbing treatment. Moreover, by optical evaluation, we found that the C8-BTBT single crystals have a aligned molecular structure.

  2. Effects of backbone conformation and surface texture of polyimide alignment film on the pretilt angle of liquid crystals

    International Nuclear Information System (INIS)

    Chang, Chi-Jung; Chou, Ray-Lin; Lin, Yu-Chi; Liang, Bau-Jy; Chen, Jyun-Ji

    2011-01-01

    Polyimides (PIs) with different inclination angle of polymer backbones, together with polar hydroxyl group and/or nonpolar trifluoromethyl group at various sites of the backbone were synthesized and used as liquid crystal alignment layers. The molecular conformation, surface chemistry, surface energy, surface morphology, and pretilt angle of the PI film were investigated. The distributions of fluorinated group and hydroxyl group at different depths of the PI surfaces were analyzed by X-ray photoelectron spectroscopy. Effects of the conformation of the PI molecular backbone on the surface morphology of the rubbed PI layer, the pretilt angle and surface energy of the alignment film were studied. The PI which contains both nonpolar fluorinated groups sticking out of the surface and the polar hydroxyl groups on the surface exhibits high pretilt angle.

  3. Galaxy Alignments: Theory, Modelling & Simulations

    Science.gov (United States)

    Kiessling, Alina; Cacciato, Marcello; Joachimi, Benjamin; Kirk, Donnacha; Kitching, Thomas D.; Leonard, Adrienne; Mandelbaum, Rachel; Schäfer, Björn Malte; Sifón, Cristóbal; Brown, Michael L.; Rassat, Anais

    2015-11-01

    The shapes of galaxies are not randomly oriented on the sky. During the galaxy formation and evolution process, environment has a strong influence, as tidal gravitational fields in the large-scale structure tend to align nearby galaxies. Additionally, events such as galaxy mergers affect the relative alignments of both the shapes and angular momenta of galaxies throughout their history. These "intrinsic galaxy alignments" are known to exist, but are still poorly understood. This review will offer a pedagogical introduction to the current theories that describe intrinsic galaxy alignments, including the apparent difference in intrinsic alignment between early- and late-type galaxies and the latest efforts to model them analytically. It will then describe the ongoing efforts to simulate intrinsic alignments using both N-body and hydrodynamic simulations. Due to the relative youth of this field, there is still much to be done to understand intrinsic galaxy alignments and this review summarises the current state of the field, providing a solid basis for future work.

  4. The CMS Muon System Alignment

    CERN Document Server

    Martinez Ruiz-Del-Arbol, P

    2009-01-01

    The alignment of the muon system of CMS is performed using different techniques: photogrammetry measurements, optical alignment and alignment with tracks. For track-based alignment, several methods are employed, ranging from a hit and impact point (HIP) algorithm and a procedure exploiting chamber overlaps to a global fit method based on the Millepede approach. For start-up alignment as long as available integrated luminosity is still significantly limiting the size of the muon sample from collisions, cosmic muon and beam halo signatures play a very strong role. During the last commissioning runs in 2008 the first aligned geometries have been produced and validated with data. The CMS offline computing infrastructure has been used in order to perform improved reconstructions. We present the computational aspects related to the calculation of alignment constants at the CERN Analysis Facility (CAF), the production and population of databases and the validation and performance in the official reconstruction. Also...

  5. Theory for the alignment of cortical feature maps during development

    KAUST Repository

    Bressloff, Paul C.

    2010-08-23

    We present a developmental model of ocular dominance column formation that takes into account the existence of an array of intrinsically specified cytochrome oxidase blobs. We assume that there is some molecular substrate for the blobs early in development, which generates a spatially periodic modulation of experience-dependent plasticity. We determine the effects of such a modulation on a competitive Hebbian mechanism for the modification of the feedforward afferents from the left and right eyes. We show how alternating left and right eye dominated columns can develop, in which the blobs are aligned with the centers of the ocular dominance columns and receive a greater density of feedforward connections, thus becoming defined extrinsically. More generally, our results suggest that the presence of periodically distributed anatomical markers early in development could provide a mechanism for the alignment of cortical feature maps. © 2010 The American Physical Society.

  6. Electrospinning of aligned fibers with adjustable orientation using auxiliary electrodes

    International Nuclear Information System (INIS)

    Arras, Matthias M L; Grasl, Christian; Schima, Heinrich; Bergmeister, Helga

    2012-01-01

    A conventional electrospinning setup was upgraded by two turnable plate-like auxiliary high-voltage electrodes that allowed aligned fiber deposition in adjustable directions. Fiber morphology was analyzed by scanning electron microscopy and attenuated total reflection Fourier transform infrared spectroscopy (FTIR-ATR). The auxiliary electric field constrained the jet bending instability and the fiber deposition became controllable. At target speeds of 0.9 m s −1 90% of the fibers had aligned within 2°, whereas the angular spread was 70° without the use of auxiliary electrodes. It was even possible to orient fibers perpendicular to the rotational direction of the target. The fiber diameter became smaller and its distribution narrower, while according to the FTIR-ATR measurement the molecular orientation of the polymer was unaltered. This study comprehensively documents the feasibility of directed fiber deposition and offers an easy upgrade to existing electrospinning setups. (paper)

  7. Image alignment for tomography reconstruction from synchrotron X-ray microscopic images.

    Directory of Open Access Journals (Sweden)

    Chang-Chieh Cheng

    Full Text Available A synchrotron X-ray microscope is a powerful imaging apparatus for taking high-resolution and high-contrast X-ray images of nanoscale objects. A sufficient number of X-ray projection images from different angles is required for constructing 3D volume images of an object. Because a synchrotron light source is immobile, a rotational object holder is required for tomography. At a resolution of 10 nm per pixel, the vibration of the holder caused by rotating the object cannot be disregarded if tomographic images are to be reconstructed accurately. This paper presents a computer method to compensate for the vibration of the rotational holder by aligning neighboring X-ray images. This alignment process involves two steps. The first step is to match the "projected feature points" in the sequence of images. The matched projected feature points in the x-θ plane should form a set of sine-shaped loci. The second step is to fit the loci to a set of sine waves to compute the parameters required for alignment. The experimental results show that the proposed method outperforms two previously proposed methods, Xradia and SPIDER. The developed software system can be downloaded from the URL, http://www.cs.nctu.edu.tw/~chengchc/SCTA or http://goo.gl/s4AMx.

  8. Image alignment for tomography reconstruction from synchrotron X-ray microscopic images.

    Science.gov (United States)

    Cheng, Chang-Chieh; Chien, Chia-Chi; Chen, Hsiang-Hsin; Hwu, Yeukuang; Ching, Yu-Tai

    2014-01-01

    A synchrotron X-ray microscope is a powerful imaging apparatus for taking high-resolution and high-contrast X-ray images of nanoscale objects. A sufficient number of X-ray projection images from different angles is required for constructing 3D volume images of an object. Because a synchrotron light source is immobile, a rotational object holder is required for tomography. At a resolution of 10 nm per pixel, the vibration of the holder caused by rotating the object cannot be disregarded if tomographic images are to be reconstructed accurately. This paper presents a computer method to compensate for the vibration of the rotational holder by aligning neighboring X-ray images. This alignment process involves two steps. The first step is to match the "projected feature points" in the sequence of images. The matched projected feature points in the x-θ plane should form a set of sine-shaped loci. The second step is to fit the loci to a set of sine waves to compute the parameters required for alignment. The experimental results show that the proposed method outperforms two previously proposed methods, Xradia and SPIDER. The developed software system can be downloaded from the URL, http://www.cs.nctu.edu.tw/~chengchc/SCTA or http://goo.gl/s4AMx.

  9. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez

    Since September, the muon alignment system shifted from a mode of hardware installation and commissioning to operation and data taking. All three optical subsystems (Barrel, Endcap and Link alignment) have recorded data before, during and after CRAFT, at different magnetic fields and during ramps of the magnet. This first data taking experience has several interesting goals: •    study detector deformations and movements under the influence of the huge magnetic forces; •    study the stability of detector structures and of the alignment system over long periods, •    study geometry reproducibility at equal fields (specially at 0T and 3.8T); •    reconstruct B=0T geometry and compare to nominal/survey geometries; •    reconstruct B=3.8T geometry and provide DT and CSC alignment records for CMSSW. However, the main goal is to recons...

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

    Science.gov (United States)

    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.

  11. Nova laser alignment control system

    International Nuclear Information System (INIS)

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

    1984-01-01

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

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

    Science.gov (United States)

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

    2017-09-01

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

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

    Science.gov (United States)

    Houben, L; Bar Sadan, M

    2011-01-01

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

  14. Alignment engineering in liquid crystalline elastomers: Free-form microstructures with multiple functionalities

    Energy Technology Data Exchange (ETDEWEB)

    Zeng, Hao; Cerretti, Giacomo; Wiersma, Diederik S., E-mail: camilla.parmeggiani@lens.unifi.it, E-mail: wiersma@lens.unifi.it [European Laboratory for Non Linear Spectroscopy (LENS), University of Florence, via Nello Carrara 1, 50019 Sesto Fiorentino (Italy); Wasylczyk, Piotr [European Laboratory for Non Linear Spectroscopy (LENS), University of Florence, via Nello Carrara 1, 50019 Sesto Fiorentino (Italy); Faculty of Physics, Institute of Experimental Physics, University of Warsaw, ul. Hoza 69, Warszawa 00-681 (Poland); Martella, Daniele [European Laboratory for Non Linear Spectroscopy (LENS), University of Florence, via Nello Carrara 1, 50019 Sesto Fiorentino (Italy); Dipartimento di Chimica “Ugo Schiff,” University of Florence, via della Lastruccia 3-13, 50019 Sesto Fiorentino (Italy); Parmeggiani, Camilla, E-mail: camilla.parmeggiani@lens.unifi.it, E-mail: wiersma@lens.unifi.it [European Laboratory for Non Linear Spectroscopy (LENS), University of Florence, via Nello Carrara 1, 50019 Sesto Fiorentino (Italy); CNR-INO, via Nello Carrara 1, 50019 Sesto Fiorentino (Italy)

    2015-03-16

    We report a method to fabricate polymer microstructures with local control over the molecular orientation. Alignment control is achieved on molecular level in a structure of arbitrary form that can be from 1 to 100 μm in size, by fixing the local boundary conditions with micro-grating patterns. The method makes use of two-photon polymerization (Direct Laser Writing) and is demonstrated specifically in liquid-crystalline elastomers. This concept allows for the realization of free-form polymeric structures with multiple functionalities which are not possible to realize with existing techniques and which can be locally controlled by light in the micrometer scale.

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

    Energy Technology Data Exchange (ETDEWEB)

    Ovacik, Meric A. [Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States); Androulakis, Ioannis P., E-mail: yannis@rci.rutgers.edu [Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States); Biomedical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States)

    2013-09-15

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

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

    International Nuclear Information System (INIS)

    Ovacik, Meric A.; Androulakis, Ioannis P.

    2013-01-01

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

  17. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez and Y. Pakhotin

    2012-01-01

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

  18. On the field-induced switching of molecular organization in a biaxial nematic cell and its relaxation

    Science.gov (United States)

    Ricci, Matteo; Berardi, Roberto; Zannoni, Claudio

    2015-08-01

    We investigate the switching of a biaxial nematic filling a flat cell with planar homogeneous anchoring using a coarse-grained molecular dynamics simulation. We have found that an aligning field applied across the film, and acting on specific molecular axes, can drive the reorientation of the secondary biaxial director up to one order of magnitude faster than that for the principal director. While the π/2 switching of the secondary director does not affect the alignment of the long molecular axes, the field-driven reorientation of the principal director proceeds via a concerted rotation of the long and transversal molecular axes. More importantly, while upon switching off a (relatively) weak or intermediate field, the biaxial nematic liquid crystal is always able to relax to the initial surface aligned director state; this is not the case when using fields above a certain threshold. In that case, while the secondary director always recovers the initial state, the principal one remains, occasionally, trapped in a nonuniform director state due to the formation of domain walls.

  19. Accurate alpha sticking fractions from improved calculations relevant for muon catalyzed fusion

    International Nuclear Information System (INIS)

    Szalewicz, K.

    1990-05-01

    Recent experiments have shown that under proper conditions a single muon may catalyze almost two hundred fusions in its lifetime. This process proceeds through formation of muonic molecular ions. Properties of these ions are central to the understanding of the phenomenon. Our work included the most accurate calculations of the energy levels and Coulombic sticking fractions for tdμ and other muonic molecular ions, calculations of Auger transition rates, calculations of corrections to the energy levels due to interactions with the most molecule, and calculation of the reactivation of muons from α particles. The majority of our effort has been devoted to the theory and computation of the influence of the strong nuclear forces on fusion rates and sticking fractions. We have calculated fusion rates for tdμ including the effects of nuclear forces on the molecular wave functions. We have also shown that these results can be reproduced to almost four digit accuracy by using a very simple quasifactorizable expression which does not require modifications of the molecular wave functions. Our sticking fractions are more accurate than any other theoretical values. We have used a more sophisticated theory than any other work and our numerical calculations have converged to at least three significant digits

  20. Indexed variation graphs for efficient and accurate resistome profiling.

    Science.gov (United States)

    Rowe, Will P M; Winn, Martyn D

    2018-05-14

    Antimicrobial resistance remains a major threat to global health. Profiling the collective antimicrobial resistance genes within a metagenome (the "resistome") facilitates greater understanding of antimicrobial resistance gene diversity and dynamics. In turn, this can allow for gene surveillance, individualised treatment of bacterial infections and more sustainable use of antimicrobials. However, resistome profiling can be complicated by high similarity between reference genes, as well as the sheer volume of sequencing data and the complexity of analysis workflows. We have developed an efficient and accurate method for resistome profiling that addresses these complications and improves upon currently available tools. Our method combines a variation graph representation of gene sets with an LSH Forest indexing scheme to allow for fast classification of metagenomic sequence reads using similarity-search queries. Subsequent hierarchical local alignment of classified reads against graph traversals enables accurate reconstruction of full-length gene sequences using a scoring scheme. We provide our implementation, GROOT, and show it to be both faster and more accurate than a current reference-dependent tool for resistome profiling. GROOT runs on a laptop and can process a typical 2 gigabyte metagenome in 2 minutes using a single CPU. Our method is not restricted to resistome profiling and has the potential to improve current metagenomic workflows. GROOT is written in Go and is available at https://github.com/will-rowe/groot (MIT license). will.rowe@stfc.ac.uk. Supplementary data are available at Bioinformatics online.

  1. Alignment of CEBAF cryomodules

    International Nuclear Information System (INIS)

    Schneider, W.J.; Bisognano, J.J.; Fischer, J.

    1993-06-01

    CEBAF, the Continuous Electron Beam Accelerator Facility, when completed, will house a 4 GeV recirculating accelerator. Each of the accelerator's two linacs contains 160 superconducting radio frequency (SRF) 1497 MHz niobium cavities in 20 cryomodules. Alignments of the cavities within the cryomodule with respect to beam axis is critical to achieving the optimum accelerator performance. This paper discusses the rationale for the current specification on cavity mechanical alignment: 2 mrad (rms) applied to the 0.5 m active length cavities. We describe the tooling that was developed to achieve the tolerance at the time of cavity pair assembly, to preserve and integrate alignment during cryomodule assembly, and to translate alignment to appropriate installation in the beam line

  2. WAViS server for handling, visualization and presentation of multiple alignments of nucleotide or aminoacids sequences

    Czech Academy of Sciences Publication Activity Database

    Zíka, Radek; Pačes, Jan; Pavlíček, A.; Pačes, Václav

    2004-01-01

    Roč. 32, suppl 2 (2004), s. 48-49 ISSN 0305-1048 R&D Projects: GA MŠk LN00A079 Institutional research plan: CEZ:AV0Z5052915 Keywords : server * alignment * vizualization Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 7.260, year: 2004

  3. Molecular form factors in X-ray crystallography

    NARCIS (Netherlands)

    Groenewegen, P.P.M.; Feil, D.

    1969-01-01

    The calculation of molecular form factors from ab initio molecular electronic wavefunctions is discussed, and a scheme for application to X-ray diffraction structure analysis is given. The method is used to calculate the form factor of the NH+4 molecular ion from three accurate molecular

  4. Physician-Hospital Alignment in Orthopedic Surgery.

    Science.gov (United States)

    Bushnell, Brandon D

    2015-09-01

    The concept of "alignment" between physicians and hospitals is a popular buzzword in the age of health care reform. Despite their often tumultuous histories, physicians and hospitals find themselves under increasing pressures to work together toward common goals. However, effective alignment is more than just simple cooperation between parties. The process of achieving alignment does not have simple, universal steps. Alignment will differ based on individual situational factors and the type of specialty involved. Ultimately, however, there are principles that underlie the concept of alignment and should be a part of any physician-hospital alignment efforts. In orthopedic surgery, alignment involves the clinical, administrative, financial, and even personal aspects of a surgeon's practice. It must be based on the principles of financial interest, clinical authority, administrative participation, transparency, focus on the patient, and mutual necessity. Alignment can take on various forms as well, with popular models consisting of shared governance and comanagement, gainsharing, bundled payments, accountable care organizations, and other methods. As regulatory and financial pressures continue to motivate physicians and hospitals to develop alignment relationships, new and innovative methods of alignment will also appear. Existing models will mature and evolve, with individual variability based on local factors. However, certain trends seem to be appearing as time progresses and alignment relationships deepen, including regional and national collaboration, population management, and changes in the legal system. This article explores the history, principles, and specific methods of physician-hospital alignment and its critical importance for the future of health care delivery. Copyright 2015, SLACK Incorporated.

  5. Superstructure of self-aligned hexagonal GaN nanorods formed on nitrided Si(111) surface

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Praveen; Tuteja, Mohit; Kesaria, Manoj; Waghmare, U. V.; Shivaprasad, S. M. [Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560 064 (India)

    2012-09-24

    We present here the spontaneous formation of catalyst-free, self-aligned crystalline (wurtzite) nanorods on Si(111) surfaces modified by surface nitridation. Nanorods grown by molecular beam epitaxy on bare Si(111) and non-stoichiometric silicon nitride interface are found to be single crystalline but disoriented. Those grown on single crystalline Si{sub 3}N{sub 4} intermediate layer are highly dense c-oriented hexagonal shaped nanorods. The morphology and the self-assembly of the nanorods shows an ordered epitaxial hexagonal superstructure, suggesting that they are nucleated at screw dislocations at the interface and grow spirally in the c-direction. The aligned nanorod assembly shows high-quality structural and optical emission properties.

  6. The CMS Silicon Tracker Alignment

    CERN Document Server

    Castello, R

    2008-01-01

    The alignment of the Strip and Pixel Tracker of the Compact Muon Solenoid experiment, with its large number of independent silicon sensors and its excellent spatial resolution, is a complex and challenging task. Besides high precision mounting, survey measurements and the Laser Alignment System, track-based alignment is needed to reach the envisaged precision.\\\\ Three different algorithms for track-based alignment were successfully tested on a sample of cosmic-ray data collected at the Tracker Integration Facility, where 15\\% of the Tracker was tested. These results, together with those coming from the CMS global run, will provide the basis for the full-scale alignment of the Tracker, which will be carried out with the first \\emph{p-p} collisions.

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

    International Nuclear Information System (INIS)

    Chen Kang; Tjandra, Nico

    2007-01-01

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

  8. Unified Alignment of Protein-Protein Interaction Networks.

    Science.gov (United States)

    Malod-Dognin, Noël; Ban, Kristina; Pržulj, Nataša

    2017-04-19

    Paralleling the increasing availability of protein-protein interaction (PPI) network data, several network alignment methods have been proposed. Network alignments have been used to uncover functionally conserved network parts and to transfer annotations. However, due to the computational intractability of the network alignment problem, aligners are heuristics providing divergent solutions and no consensus exists on a gold standard, or which scoring scheme should be used to evaluate them. We comprehensively evaluate the alignment scoring schemes and global network aligners on large scale PPI data and observe that three methods, HUBALIGN, L-GRAAL and NATALIE, regularly produce the most topologically and biologically coherent alignments. We study the collective behaviour of network aligners and observe that PPI networks are almost entirely aligned with a handful of aligners that we unify into a new tool, Ulign. Ulign enables complete alignment of two networks, which traditional global and local aligners fail to do. Also, multiple mappings of Ulign define biologically relevant soft clusterings of proteins in PPI networks, which may be used for refining the transfer of annotations across networks. Hence, PPI networks are already well investigated by current aligners, so to gain additional biological insights, a paradigm shift is needed. We propose such a shift come from aligning all available data types collectively rather than any particular data type in isolation from others.

  9. A Comparison of Plain Radiography with Computer Tomography in Determining Coronal and Sagittal Alignments following Total Knee Arthroplasty

    Directory of Open Access Journals (Sweden)

    Solayar GN

    2017-07-01

    Full Text Available INTRODUCTION: Optimal coronal and sagittal component positioning is important in achieving a successful outcome following total knee arthroplasty (TKA. Modalities to determine post-operative alignment include plain radiography and computer tomography (CT imaging. This study aims to determine the accuracy and reliability of plain radiographs in measuring coronal and sagittal alignment following TKA. MATERIALS AND METHODS: A prospective, consecutive study of 58 patients undergoing TKA was performed comparing alignment data from plain radiographs and CT imaging. Hip- knee-angle (HKA, sagittal femoral angle (SFA and sagittal tibial angle (STA measurements were taken by two observers from plain radiographs and compared with CT alignment. Intra- and inter-observer correlation was calculated for each measurement. RESULTS: Intra-observer correlation was excellent for HKA (r>0.89 with a mean difference of 0.95 and STA (r>0.8 compared to SFA (r=0.5. When comparing modalities (radiographs vs CT, HKA estimations for both observers showed the least maximum and mean differences while SFA observations were the least accurate. CONCLUSION: Radiographic estimation of HKA showed excellent intra- and inter-observer correlation and corresponds well with CT imaging. However, radiographic estimation of sagittal plane alignment was less reliably measured and correlated less with CT imaging. Plain radiography was found to be inferior to CT for estimation of biplanar prosthetic alignment following TKA.

  10. Intrinsic work function of molecular films

    International Nuclear Information System (INIS)

    Ivančo, Ján

    2012-01-01

    The electronic properties of molecular films are analysed with the consideration of the molecular orientation. The study demonstrates that surfaces of electroactive oligomeric molecular films can be classified—analogously to the elemental surfaces—by their intrinsic work functions. The intrinsic work function of molecular films is correlated with their ionisation energies; again, the behaviour is analogous to the correlation existing between the first ionisation energy of elements and the work function of the corresponding elemental surfaces. The proposed intrinsic work-function concept suggests that the mechanism for the energy-level alignment at the interfaces associated with molecular films is virtually controlled by work functions of materials brought into the contact. - Highlights: ► Molecular films exhibit their own (intrinsic) work function. ► Intrinsic work function is correlated with ionisation energy of molecular films. ► Intrinsic work function determines dipole at interface with a particular surface. ► Surface vacuum-level change upon film growth does not relate to interfacial dipole.

  11. Molecular Frame Reconstruction Using Time-Domain Photoionization Interferometry.

    Science.gov (United States)

    Marceau, Claude; Makhija, Varun; Platzer, Dominique; Naumov, A Yu; Corkum, P B; Stolow, Albert; Villeneuve, D M; Hockett, Paul

    2017-08-25

    Photoionization of molecular species is, essentially, a multipath interferometer with both experimentally controllable and intrinsic molecular characteristics. In this work, XUV photoionization of impulsively aligned molecular targets (N_{2}) is used to provide a time-domain route to "complete" photoionization experiments, in which the rotational wave packet controls the geometric part of the photoionization interferometer. The data obtained is sufficient to determine the magnitudes and phases of the ionization matrix elements for all observed channels, and to reconstruct molecular frame interferograms from lab frame measurements. In principle, this methodology provides a time-domain route to complete photoionization experiments and the molecular frame, which is generally applicable to any molecule (no prerequisites), for all energies and ionization channels.

  12. Precision alignment device

    Science.gov (United States)

    Jones, N.E.

    1988-03-10

    Apparatus for providing automatic alignment of beam devices having an associated structure for directing, collimating, focusing, reflecting, or otherwise modifying the main beam. A reference laser is attached to the structure enclosing the main beam producing apparatus and produces a reference beam substantially parallel to the main beam. Detector modules containing optical switching devices and optical detectors are positioned in the path of the reference beam and are effective to produce an electrical output indicative of the alignment of the main beam. This electrical output drives servomotor operated adjustment screws to adjust the position of elements of the structure associated with the main beam to maintain alignment of the main beam. 5 figs.

  13. Curricular Alignment: A Re-examination.

    Science.gov (United States)

    Anderson, Lorin W.

    2002-01-01

    Examines key differences among content coverage, opportunity to learn, and curriculum alignment, suggesting that the revised Taxonomy provides a framework for analyzing curriculum alignment and illustrating how the Taxonomy Table can be used to estimate curriculum alignment. The paper notes that the revised Taxonomy enables educators to probe…

  14. Probing the Energy Level Alignment and the Correlation with Open-Circuit Voltage in Solution-Processed Polymeric Bulk Heterojunction Photovoltaic Devices.

    Science.gov (United States)

    Yang, Qing-Dan; Li, Ho-Wa; Cheng, Yuanhang; Guan, Zhiqiang; Liu, Taili; Ng, Tsz-Wai; Lee, Chun-Sing; Tsang, Sai-Wing

    2016-03-23

    Energy level alignment at the organic donor and acceptor interface is a key to determine the photovoltaic performance in organic solar cells, but direct probing of such energy alignment is still challenging especially for solution-processed bulk heterojunction (BHJ) thin films. Here we report a systematic investigation on probing the energy level alignment with different approaches in five commonly used polymer:[6,6]-phenyl-C71-butyric acid methyl ester (PCBM) BHJ systems. We find that by tuning the weight ratio of polymer to PCBM the electronic features from both polymer and PCBM can be obtained by photoemission spectroscopy. Using this approach, we find that some of the BHJ blends simply follow vacuum level alignment, but others show strong energy level shifting as a result of Fermi level pinning. Independently, by measuring the temperature-dependent open-circuit voltage (VOC), we find that the effective energy gap (Eeff), the energy difference between the highest occupied molecular orbital of the polymer donor (EHOMO-D) and lowest unoccupied molecular orbital of the PCBM acceptor (ELUMO-A), obtained by photoemission spectroscopy in all polymer:PCBM blends has an excellent agreement with the extrapolated VOC at 0 K. Consequently, the photovoltage loss of various organic BHJ photovoltaic devices at room temperature is in a range of 0.3-0.6 V. It is believed that the demonstrated direct measurement approach of the energy level alignment in solution-processed organic BHJ will bring deeper insight into the origin of the VOC and the corresponding photovoltage loss mechanism in organic photovoltaic cells.

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

    International Nuclear Information System (INIS)

    Almond, Andrew; Duus, Jens O.

    2001-01-01

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

  16. Accurate density-functional calculations on large systems: Fullerenes and magnetic clusters

    International Nuclear Information System (INIS)

    Dunlap, B.I.

    1996-01-01

    Efforts to accurately compute all-electron density-functional energies for large molecules and clusters using Gaussian basis sets will be reviewed. The foundation of this effort, variational fitting, will be described and followed by three applications of the method. The first application concerns fullerenes. When first discovered, C 60 is quite unstable relative to the higher fullerenes. In addition, to raising questions about the relative abundance of the various fullerenes, this work conflicted with the then state-of-the art density-funcitonal calculations on crystalline graphite. Now high accuracy molecular and band structure calculations are in fairly good agreement. Second, we have used these methods to design transition metal clusters having the highest magnetic moment by maximizing the symmetry-required degeneracy of the one-electron orbitals. Most recently, we have developed accurate, variational generalized-gradient approximation (GGA) forces for use in geometry optimization of clusters and in molecular-dynamics simulations of friction. The GGA optimized geometries of a number of large clusters will be given

  17. JavaScript DNA translator: DNA-aligned protein translations.

    Science.gov (United States)

    Perry, William L

    2002-12-01

    There are many instances in molecular biology when it is necessary to identify ORFs in a DNA sequence. While programs exist for displaying protein translations in multiple ORFs in alignment with a DNA sequence, they are often expensive, exist as add-ons to software that must be purchased, or are only compatible with a particular operating system. JavaScript DNA Translator is a shareware application written in JavaScript, a scripting language interpreted by the Netscape Communicator and Internet Explorer Web browsers, which makes it compatible with several different operating systems. While the program uses a familiar Web page interface, it requires no connection to the Internet since calculations are performed on the user's own computer. The program analyzes one or multiple DNA sequences and generates translations in up to six reading frames aligned to a DNA sequence, in addition to displaying translations as separate sequences in FASTA format. ORFs within a reading frame can also be displayed as separate sequences. Flexible formatting options are provided, including the ability to hide ORFs below a minimum size specified by the user. The program is available free of charge at the BioTechniques Software Library (www.Biotechniques.com).

  18. libgapmis: extending short-read alignments.

    Science.gov (United States)

    Alachiotis, Nikolaos; Berger, Simon; Flouri, Tomáš; Pissis, Solon P; Stamatakis, Alexandros

    2013-01-01

    A wide variety of short-read alignment programmes have been published recently to tackle the problem of mapping millions of short reads to a reference genome, focusing on different aspects of the procedure such as time and memory efficiency, sensitivity, and accuracy. These tools allow for a small number of mismatches in the alignment; however, their ability to allow for gaps varies greatly, with many performing poorly or not allowing them at all. The seed-and-extend strategy is applied in most short-read alignment programmes. After aligning a substring of the reference sequence against the high-quality prefix of a short read--the seed--an important problem is to find the best possible alignment between a substring of the reference sequence succeeding and the remaining suffix of low quality of the read--extend. The fact that the reads are rather short and that the gap occurrence frequency observed in various studies is rather low suggest that aligning (parts of) those reads with a single gap is in fact desirable. In this article, we present libgapmis, a library for extending pairwise short-read alignments. Apart from the standard CPU version, it includes ultrafast SSE- and GPU-based implementations. libgapmis is based on an algorithm computing a modified version of the traditional dynamic-programming matrix for sequence alignment. Extensive experimental results demonstrate that the functions of the CPU version provided in this library accelerate the computations by a factor of 20 compared to other programmes. The analogous SSE- and GPU-based implementations accelerate the computations by a factor of 6 and 11, respectively, compared to the CPU version. The library also provides the user the flexibility to split the read into fragments, based on the observed gap occurrence frequency and the length of the read, thereby allowing for a variable, but bounded, number of gaps in the alignment. We present libgapmis, a library for extending pairwise short-read alignments. We

  19. Alignment performance monitoring for ASML systems

    Science.gov (United States)

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

    2006-03-01

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

  20. Geodetic alignment of laser power installations

    International Nuclear Information System (INIS)

    Shtorm, V.V.; Gostev, A.M.; Drobikov, A.V.

    1989-01-01

    Main problems occuring in applied geodesy under initial alignment of laser power installation optical channel are considered. Attention is paid to alignment of lens beamguide telescopic pairs and alignment quality control. Methods and means of geodetic measurements under alignment are indicated. Conclusions are made about the degree of working through certain aspects of the problem

  1. Micro-vision servo control of a multi-axis alignment system for optical fiber assembly

    International Nuclear Information System (INIS)

    Chen, Weihai; Yu, Fei; Qu, Jianliang; Chen, Wenjie; Zhang, Jianbin

    2017-01-01

    This paper describes a novel optical fiber assembly system featuring a multi-axis alignment function based on micro-vision feedback control. It consists of an active parallel alignment mechanism, a passive compensation mechanism, a micro-gripper and a micro-vision servo control system. The active parallel alignment part is a parallelogram-based design with remote-center-of-motion (RCM) function to achieve precise rotation without fatal lateral motion. The passive mechanism, with five degrees of freedom (5-DOF), is used to implement passive compensation for multi-axis errors. A specially designed 1-DOF micro-gripper mounted onto the active parallel alignment platform is adopted to grasp and rotate the optical fiber. A micro-vision system equipped with two charge-coupled device (CCD) cameras is introduced to observe the small field of view and obtain multi-axis errors for servo feedback control. The two CCD cameras are installed in an orthogonal arrangement—thus the errors can be easily measured via the captured images. Meanwhile, a series of tracking and measurement algorithms based on specific features of the target objects are developed. Details of the force and displacement sensor information acquisition in the assembly experiment are also provided. An experiment demonstrates the validity of the proposed visual algorithm by achieving the task of eliminating errors and inserting an optical fiber to the U-groove accurately. (paper)

  2. GRAIN ALIGNMENT INDUCED BY RADIATIVE TORQUES: EFFECTS OF INTERNAL RELAXATION OF ENERGY AND COMPLEX RADIATION FIELD

    International Nuclear Information System (INIS)

    Hoang, Thiem; Lazarian, A.

    2009-01-01

    Earlier studies of grain alignment dealt mostly with interstellar grains that have strong internal relaxation of energy which aligns the grain axis of maximum moment of inertia (the axis of major inertia) with respect to the grain's angular momentum. In this paper, we study the alignment by radiative torques for large irregular grains, e.g., grains in accretion disks, for which internal relaxation is subdominant. We use both numerical calculations and the analytical model of a helical grain introduced by us earlier. We demonstrate that grains in such a regime exhibit more complex dynamics. In particular, if initially the grain axis of major inertia makes a small angle with angular momentum, then radiative torques can align the grain axis of major inertia with angular momentum, and both the axis of major inertia and angular momentum are aligned with the magnetic field when attractors with high angular momentum (high-J attractors) are available. For alignment without high-J attractors, beside the earlier studied attractors with low angular momentum (low-J attractors), there appear new low-J attractors. In addition, we also study the alignment of grains in the presence of strong internal relaxation, but induced not by a radiation beam as in earlier studies but instead induced by a complex radiation field that can be decomposed into dipole and quadrupole components. We found that in this situation the parameter space q max , for which high-J attractors exist in trajectory maps, is more extended, resulting in the higher degree of polarization expected. Our results are useful for modeling polarization arising from aligned dust grains in molecular clouds.

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

    Science.gov (United States)

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

    2011-01-01

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

  4. AlignNemo: a local network alignment method to integrate homology and topology.

    Directory of Open Access Journals (Sweden)

    Giovanni Ciriello

    Full Text Available Local network alignment is an important component of the analysis of protein-protein interaction networks that may lead to the identification of evolutionary related complexes. We present AlignNemo, a new algorithm that, given the networks of two organisms, uncovers subnetworks of proteins that relate in biological function and topology of interactions. The discovered conserved subnetworks have a general topology and need not to correspond to specific interaction patterns, so that they more closely fit the models of functional complexes proposed in the literature. The algorithm is able to handle sparse interaction data with an expansion process that at each step explores the local topology of the networks beyond the proteins directly interacting with the current solution. To assess the performance of AlignNemo, we ran a series of benchmarks using statistical measures as well as biological knowledge. Based on reference datasets of protein complexes, AlignNemo shows better performance than other methods in terms of both precision and recall. We show our solutions to be biologically sound using the concept of semantic similarity applied to Gene Ontology vocabularies. The binaries of AlignNemo and supplementary details about the algorithms and the experiments are available at: sourceforge.net/p/alignnemo.

  5. FMIT alignment cart

    International Nuclear Information System (INIS)

    Potter, R.C.; Dauelsberg, L.B.; Clark, D.C.; Grieggs, R.J.

    1981-01-01

    The Fusion Materials Irradiation Test (FMIT) Facility alignment cart must perform several functions. It must serve as a fixture to receive the drift-tube girder assembly when it is removed from the linac tank. It must transport the girder assembly from the linac vault to the area where alignment or disassembly is to take place. It must serve as a disassembly fixture to hold the girder while individual drift tubes are removed for repair. It must align the drift tube bores in a straight line parallel to the girder, using an optical system. These functions must be performed without violating any clearances found within the building. The bore tubes of the drift tubes will be irradiated, and shielding will be included in the system for easier maintenance

  6. Alignment method for parabolic trough solar concentrators

    Science.gov (United States)

    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.

  7. CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking.

    Directory of Open Access Journals (Sweden)

    Lei Hua

    Full Text Available RNA junctions are important structural elements of RNA molecules. They are formed when three or more helices come together in three-dimensional space. Recent studies have focused on the annotation and prediction of coaxial helical stacking (CHS motifs within junctions. Here we exploit such predictions to develop an efficient alignment tool to handle RNA secondary structures with CHS motifs. Specifically, we build upon our Junction-Explorer software for predicting coaxial stacking and RNAJAG for modelling junction topologies as tree graphs to incorporate constrained tree matching and dynamic programming algorithms into a new method, called CHSalign, for aligning the secondary structures of RNA molecules containing CHS motifs. Thus, CHSalign is intended to be an efficient alignment tool for RNAs containing similar junctions. Experimental results based on thousands of alignments demonstrate that CHSalign can align two RNA secondary structures containing CHS motifs more accurately than other RNA secondary structure alignment tools. CHSalign yields a high score when aligning two RNA secondary structures with similar CHS motifs or helical arrangement patterns, and a low score otherwise. This new method has been implemented in a web server, and the program is also made freely available, at http://bioinformatics.njit.edu/CHSalign/.

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

    Science.gov (United States)

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

    2017-11-01

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

  9. Probabilistic biological network alignment.

    Science.gov (United States)

    Todor, Andrei; Dobra, Alin; Kahveci, Tamer

    2013-01-01

    Interactions between molecules are probabilistic events. An interaction may or may not happen with some probability, depending on a variety of factors such as the size, abundance, or proximity of the interacting molecules. In this paper, we consider the problem of aligning two biological networks. Unlike existing methods, we allow one of the two networks to contain probabilistic interactions. Allowing interaction probabilities makes the alignment more biologically relevant at the expense of explosive growth in the number of alternative topologies that may arise from different subsets of interactions that take place. We develop a novel method that efficiently and precisely characterizes this massive search space. We represent the topological similarity between pairs of aligned molecules (i.e., proteins) with the help of random variables and compute their expected values. We validate our method showing that, without sacrificing the running time performance, it can produce novel alignments. Our results also demonstrate that our method identifies biologically meaningful mappings under a comprehensive set of criteria used in the literature as well as the statistical coherence measure that we developed to analyze the statistical significance of the similarity of the functions of the aligned protein pairs.

  10. Hybrid vehicle motor alignment

    Science.gov (United States)

    Levin, Michael Benjamin

    2001-07-03

    A rotor of an electric motor for a motor vehicle is aligned to an axis of rotation for a crankshaft of an internal combustion engine having an internal combustion engine and an electric motor. A locator is provided on the crankshaft, a piloting tool is located radially by the first locator to the crankshaft. A stator of the electric motor is aligned to a second locator provided on the piloting tool. The stator is secured to the engine block. The rotor is aligned to the crankshaft and secured thereto.

  11. Test procedure for calibration, grooming and alignment of the LDUA Optical Alignment Scope

    International Nuclear Information System (INIS)

    Potter, J.D.

    1995-01-01

    The Light Duty Utility Arm (LDUA) is a remotely operated manipulator used to enter into underground waste tanks through one of the tank risers. The LDUA must be carefully aligned with the tank riser during the installation process. The Optical Alignment Scope (OAS) is used to determine when optimum alignment has been achieved between the LDUA and the riser. This procedure is used to assure that the instrumentation and equipment comprising the OAS is properly adjusted in order to achieve its intended functions successfully

  12. STELLAR: fast and exact local alignments

    Directory of Open Access Journals (Sweden)

    Weese David

    2011-10-01

    Full Text Available Abstract Background Large-scale comparison of genomic sequences requires reliable tools for the search of local alignments. Practical local aligners are in general fast, but heuristic, and hence sometimes miss significant matches. Results We present here the local pairwise aligner STELLAR that has full sensitivity for ε-alignments, i.e. guarantees to report all local alignments of a given minimal length and maximal error rate. The aligner is composed of two steps, filtering and verification. We apply the SWIFT algorithm for lossless filtering, and have developed a new verification strategy that we prove to be exact. Our results on simulated and real genomic data confirm and quantify the conjecture that heuristic tools like BLAST or BLAT miss a large percentage of significant local alignments. Conclusions STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments between genomic sequences under the edit distance model. Binaries are freely available for Linux, Windows, and Mac OS X at http://www.seqan.de/projects/stellar. The source code is freely distributed with the SeqAn C++ library version 1.3 and later at http://www.seqan.de.

  13. DeepBound: accurate identification of transcript boundaries via deep convolutional neural fields

    KAUST Repository

    Shao, Mingfu; Ma, Jianzhu; Wang, Sheng

    2017-01-01

    Motivation: Reconstructing the full- length expressed transcripts (a. k. a. the transcript assembly problem) from the short sequencing reads produced by RNA-seq protocol plays a central role in identifying novel genes and transcripts as well as in studying gene expressions and gene functions. A crucial step in transcript assembly is to accurately determine the splicing junctions and boundaries of the expressed transcripts from the reads alignment. In contrast to the splicing junctions that can be efficiently detected from spliced reads, the problem of identifying boundaries remains open and challenging, due to the fact that the signal related to boundaries is noisy and weak.

  14. DeepBound: accurate identification of transcript boundaries via deep convolutional neural fields

    KAUST Repository

    Shao, Mingfu

    2017-04-20

    Motivation: Reconstructing the full- length expressed transcripts (a. k. a. the transcript assembly problem) from the short sequencing reads produced by RNA-seq protocol plays a central role in identifying novel genes and transcripts as well as in studying gene expressions and gene functions. A crucial step in transcript assembly is to accurately determine the splicing junctions and boundaries of the expressed transcripts from the reads alignment. In contrast to the splicing junctions that can be efficiently detected from spliced reads, the problem of identifying boundaries remains open and challenging, due to the fact that the signal related to boundaries is noisy and weak.

  15. Mechanisms of two-color laser-induced field-free molecular orientation.

    Science.gov (United States)

    Spanner, Michael; Patchkovskii, Serguei; Frumker, Eugene; Corkum, Paul

    2012-09-14

    Two mechanisms of two-color (ω+2ω) laser-induced field-free molecular orientation, based on the hyperpolarizability and ionization depletion, are explored and compared. The CO molecule is used as a computational example. While the hyperpolarizability mechanism generates small amounts of orientation at intensities below the ionization threshold, ionization depletion quickly becomes the dominant mechanism as soon as ionizing intensities are reached. Only the ionization mechanism leads to substantial orientation (e.g., on the order of ≳0.1). For intensities typical of laser-induced molecular alignment and orientation experiments, the two mechanisms lead to robust, characteristic timings of the field-free orientation wave-packet revivals relative to the alignment revivals and the revival time. The revival timings can be used to detect the active orientation mechanism experimentally.

  16. Dislocation mediated alignment during metal nanoparticle coalescence

    International Nuclear Information System (INIS)

    Lange, A.P.; Samanta, A.; Majidi, H.; Mahajan, S.; Ging, J.; Olson, T.Y.; Benthem, K. van; Elhadj, S.

    2016-01-01

    Dislocation mediated alignment processes during gold nanoparticle coalescence were studied at low and high temperatures using molecular dynamics simulations and transmission electron microscopy. Particles underwent rigid body rotations immediately following attachment in both low temperature (500 K) simulated coalescence events and low temperature (∼315 K) transmission electron microscopy beam heating experiments. In many low temperature simulations, some degree of misorientation between particles remained after rigid body rotations, which was accommodated by grain boundary dislocation nodes. These dislocations were either sessile and remained at the interface for the duration of the simulation or dissociated and cross-slipped through the adjacent particles, leading to improved co-alignment. Minimal rigid body rotations were observed during or immediately following attachment in high temperature (1100 K) simulations, which is attributed to enhanced diffusion at the particles' interface. However, rotation was eventually induced by {111} slip on planes parallel to the neck groove. These deformation modes led to the formation of single and multi-fold twins whose structures depended on the initial orientation of the particles. The driving force for {111} slip is attributed to high surface stresses near the intersection of low energy {111} facets in the neck region. The details of this twinning process were examined in detail using simulated trajectories, and the results reveal possible mechanisms for the nucleation and propagation of Shockley partials on consecutive planes. Deformation twinning was also observed in-situ using transmission electron microscopy, which resulted in the co-alignment of a set of the particles' {111} planes across their grain boundary and an increase in their dihedral angle. This constitutes the first detailed experimental observation of deformation twinning during nanoparticle coalescence, validating simulation results presented here and

  17. Modified alignment CGHs for aspheric surface test

    Science.gov (United States)

    Song, Jae-Bong; Yang, Ho-Soon; Rhee, Hyug-Gyo; Lee, Yun-Woo

    2009-08-01

    Computer Generated Holograms (CGH) for optical test are commonly consisted of one main pattern for testing aspheric surface and some alignment patterns for aligning the interferometer, CGH, and the test optics. To align the CGH plate and the test optics, we designed the alignment CGHs modified from the cat's eye alignment method, which are consisted of a couple of CGH patterns. The incident beam passed through the one part of the alignment CGH pattern is focused onto the one radius position of the test aspheric surface, and is reflected to the other part, and vice versa. This method has several merits compared to the conventional cat's eye alignment method. First, this method can be used in testing optics with a center hole, and the center part of CGH plate can be assigned to the alignment pattern. Second, the alignment pattern becomes a concentric circular arc pattern. The whole CGH patterns including the main pattern and alignment patterns are consisted of only concentric circular fringes. This concentric circular pattern can be easily made by the polar coordinated writer with circular scanning. The required diffraction angle becomes relatively small, so the 1st order diffraction beams instead of the 3rd order diffraction beam can be used as alignment beams, and the visibility can be improved. This alignment method also is more sensitive to the tilt and the lateral shift of the test aspheric surface. Using this alignment pattern, a 200 mm diameter F/0.5 aspheric mirror and a 600 mm diameter F/0.9 mirror were tested.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-05-20

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

  19. A Modified ELISA Accurately Measures Secretion of High Molecular Weight Hyaluronan (HA) by Graves' Disease Orbital Cells

    Science.gov (United States)

    Krieger, Christine C.

    2014-01-01

    Excess production of hyaluronan (hyaluronic acid [HA]) in the retro-orbital space is a major component of Graves' ophthalmopathy, and regulation of HA production by orbital cells is a major research area. In most previous studies, HA was measured by ELISAs that used HA-binding proteins for detection and rooster comb HA as standards. We show that the binding efficiency of HA-binding protein in the ELISA is a function of HA polymer size. Using gel electrophoresis, we show that HA secreted from orbital cells is primarily comprised of polymers more than 500 000. We modified a commercially available ELISA by using 1 million molecular weight HA as standard to accurately measure HA of this size. We demonstrated that IL-1β-stimulated HA secretion is at least 2-fold greater than previously reported, and activation of the TSH receptor by an activating antibody M22 from a patient with Graves' disease led to more than 3-fold increase in HA production in both fibroblasts/preadipocytes and adipocytes. These effects were not consistently detected with the commercial ELISA using rooster comb HA as standard and suggest that fibroblasts/preadipocytes may play a more prominent role in HA remodeling in Graves' ophthalmopathy than previously appreciated. PMID:24302624

  20. Aligning experimental design with bioinformatics analysis to meet discovery research objectives.

    Science.gov (United States)

    Kane, Michael D

    2002-01-01

    The utility of genomic technology and bioinformatic analytical support to provide new and needed insight into the molecular basis of disease, development, and diversity continues to grow as more research model systems and populations are investigated. Yet deriving results that meet a specific set of research objectives requires aligning or coordinating the design of the experiment, the laboratory techniques, and the data analysis. The following paragraphs describe several important interdependent factors that need to be considered to generate high quality data from the microarray platform. These factors include aligning oligonucleotide probe design with the sample labeling strategy if oligonucleotide probes are employed, recognizing that compromises are inherent in different sample procurement methods, normalizing 2-color microarray raw data, and distinguishing the difference between gene clustering and sample clustering. These factors do not represent an exhaustive list of technical variables in microarray-based research, but this list highlights those variables that span both experimental execution and data analysis. Copyright 2001 Wiley-Liss, Inc.

  1. Chromatic bifocus alignment system for SR stepper

    International Nuclear Information System (INIS)

    Miyatake, Tsutomu

    1991-01-01

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

  2. Alignment of the dye's molecular levels with the TiO2 band edges in dye-sensitized solar cells: a DFT-TDDFT study

    International Nuclear Information System (INIS)

    De Angelis, Filippo; Fantacci, Simona; Selloni, Annabella

    2008-01-01

    We present a theoretical study of the lineup of the LUMO of Ru(II)-polypyridyl (N3 and N719) molecular dyes with the conduction band edge of a TiO 2 anatase nanoparticle. We use density functional theory (DFT) and the Car-Parrinello scheme for efficient optimization of the dye-nanoparticle systems, followed by hybrid B3LYP functional calculations of the electronic structure and time-dependent DFT (TDDFT) determination of the lowest vertical excitation energies. The electronic structure and TDDFT calculations are performed in water solution, using a continuum model. Various approximate procedures to compute the excited state oxidation potential of dye sensitizers are discussed. Our calculations show that the level alignment for the interacting nanoparticle-sensitizer system is very similar, within about 0.1 eV, to that for the separated TiO 2 and dye. The excellent agreement of our results with available experimental data indicates that the approach of this work could be used as an efficient predictive tool to help the optimization of dye-sensitized solar cells.

  3. Molecular Imaging and nuclear medicine: expectations and requirements

    International Nuclear Information System (INIS)

    Rollo, F.D.

    2003-01-01

    Molecular Imaging with Nuclear Medicine offers earlier, more accurate and more specific diagnosis, as well as targeted molecular therapy, providing significant improvements in clinical outcomes. (orig.)

  4. DNAAlignEditor: DNA alignment editor tool

    Directory of Open Access Journals (Sweden)

    Guill Katherine E

    2008-03-01

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

  5. Advanced Alignment of the ATLAS Tracking System

    CERN Document Server

    Pedraza Lopez, S; The ATLAS collaboration

    2012-01-01

    In order to reconstruct trajectories of charged particles, ATLAS is equipped with a tracking system built using different technologies embedded in a 2T solenoidal magnetic field. ATLAS physics goals require high resolution, unbiased measurement of all charged particle kinematic parameters in order to assure accurate invariant mass reconstruction and interaction and decay vertex finding. These critically depend on the systematic effects related to the alignment of the tracking system. In order to eliminate malicious systematic deformations, various advanced tools and techniques have been put in place. These include information from known mass resonances, energy of electrons and positrons measured by the electromagnetic calorimeters, etc. Despite being stable under normal running conditions, ATLAS tracking system responses to sudden environ-mental changes (temperature, magnetic field) by small collective deformations. These have to be identified and corrected in order to assure uniform, highest quality tracking...

  6. Micropatterning stretched and aligned DNA for sequence-specific nanolithography

    Science.gov (United States)

    Petit, Cecilia Anna Paulette

    Techniques for fabricating nanostructured materials can be categorized as either "top-down" or "bottom-up". Top-down techniques use lithography and contact printing to create patterned surfaces and microfluidic channels that can corral and organize nanoscale structures, such as molecules and nanorods in contrast; bottom-up techniques use self-assembly or molecular recognition to direct the organization of materials. A central goal in nanotechnology is the integration of bottom-up and top-down assembly strategies for materials development, device design; and process integration. With this goal in mind, we have developed strategies that will allow this integration by using DNA as a template for nanofabrication; two top-down approaches allow the placement of these templates, while the bottom-up technique uses the specific sequence of bases to pattern materials along each strand of DNA. Our first top-down approach, termed combing of molecules in microchannels (COMMIC), produces microscopic patterns of stretched and aligned molecules of DNA on surfaces. This process consists of passing an air-water interface over end adsorbed molecules inside microfabricated channels. The geometry of the microchannel directs the placement of the DNA molecules, while the geometry of the airwater interface directs the local orientation and curvature of the molecules. We developed another top-down strategy for creating micropatterns of stretched and aligned DNA using surface chemistry. Because DNA stretching occurs on hydrophobic surfaces, this technique uses photolithography to pattern vinyl-terminated silanes on glass When these surface-, are immersed in DNA solution, molecules adhere preferentially to the silanized areas. This approach has also proven useful in patterning protein for cell adhesion studies. Finally, we describe the use of these stretched and aligned molecules of DNA as templates for the subsequent bottom-up construction of hetero-structures through hybridization

  7. MEMS Integrated Submount Alignment for Optoelectronics

    Science.gov (United States)

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

    2005-02-01

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

  8. A cross-species alignment tool (CAT)

    DEFF Research Database (Denmark)

    Li, Heng; Guan, Liang; Liu, Tao

    2007-01-01

    BACKGROUND: The main two sorts of automatic gene annotation frameworks are ab initio and alignment-based, the latter splitting into two sub-groups. The first group is used for intra-species alignments, among which are successful ones with high specificity and speed. The other group contains more...... sensitive methods which are usually applied in aligning inter-species sequences. RESULTS: Here we present a new algorithm called CAT (for Cross-species Alignment Tool). It is designed to align mRNA sequences to mammalian-sized genomes. CAT is implemented using C scripts and is freely available on the web...... at http://xat.sourceforge.net/. CONCLUSIONS: Examined from different angles, CAT outperforms other extant alignment tools. Tested against all available mouse-human and zebrafish-human orthologs, we demonstrate that CAT combines the specificity and speed of the best intra-species algorithms, like BLAT...

  9. Methods in ALFA Alignment

    CERN Document Server

    Melendez, Jordan

    2014-01-01

    This note presents two model-independent methods for use in the alignment of the ALFA forward detectors. Using a Monte Carlo simulated LHC run at \\beta = 90m and \\sqrt{s} = 7 TeV, the Kinematic Peak alignment method is utilized to reconstruct the Mandelstam momentum transfer variable t for single-diractive protons. The Hot Spot method uses fluctuations in the hitmap density to pinpoint particular regions in the detector that could signal a misalignment. Another method uses an error function fit to find the detector edge. With this information, the vertical alignment can be determined.

  10. Multiple Whole Genome Alignments Without a Reference Organism

    Energy Technology Data Exchange (ETDEWEB)

    Dubchak, Inna; Poliakov, Alexander; Kislyuk, Andrey; Brudno, Michael

    2009-01-16

    Multiple sequence alignments have become one of the most commonly used resources in genomics research. Most algorithms for multiple alignment of whole genomes rely either on a reference genome, against which all of the other sequences are laid out, or require a one-to-one mapping between the nucleotides of the genomes, preventing the alignment of recently duplicated regions. Both approaches have drawbacks for whole-genome comparisons. In this paper we present a novel symmetric alignment algorithm. The resulting alignments not only represent all of the genomes equally well, but also include all relevant duplications that occurred since the divergence from the last common ancestor. Our algorithm, implemented as a part of the VISTA Genome Pipeline (VGP), was used to align seven vertebrate and sixDrosophila genomes. The resulting whole-genome alignments demonstrate a higher sensitivity and specificity than the pairwise alignments previously available through the VGP and have higher exon alignment accuracy than comparable public whole-genome alignments. Of the multiple alignment methods tested, ours performed the best at aligning genes from multigene families?perhaps the most challenging test for whole-genome alignments. Our whole-genome multiple alignments are available through the VISTA Browser at http://genome.lbl.gov/vista/index.shtml.

  11. Alignment system for SGII-Up laser facility

    Science.gov (United States)

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

    2018-03-01

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

  12. Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features.

    Science.gov (United States)

    Iwata, Hiroaki; Gotoh, Osamu

    2012-11-01

    Spliced alignment plays a central role in the precise identification of eukaryotic gene structures. Even though many spliced alignment programs have been developed, recent rapid progress in DNA sequencing technologies demands further improvements in software tools. Benchmarking algorithms under various conditions is an indispensable task for the development of better software; however, there is a dire lack of appropriate datasets usable for benchmarking spliced alignment programs. In this study, we have constructed two types of datasets: simulated sequence datasets and actual cross-species datasets. The datasets are designed to correspond to various real situations, i.e. divergent eukaryotic species, different types of reference sequences, and the wide divergence between query and target sequences. In addition, we have developed an extended version of our program Spaln, which incorporates two additional features to the scoring scheme of the original version, and examined this extended version, Spaln2, together with the original Spaln and other representative aligners based on our benchmark datasets. Although the effects of the modifications are not individually striking, Spaln2 is consistently most accurate and reasonably fast in most practical cases, especially for plants and fungi and for increasingly divergent pairs of target and query sequences.

  13. W-curve alignments for HIV-1 genomic comparisons.

    Directory of Open Access Journals (Sweden)

    Douglas J Cork

    2010-06-01

    Full Text Available The W-curve was originally developed as a graphical visualization technique for viewing DNA and RNA sequences. Its ability to render features of DNA also makes it suitable for computational studies. Its main advantage in this area is utilizing a single-pass algorithm for comparing the sequences. Avoiding recursion during sequence alignments offers advantages for speed and in-process resources. The graphical technique also allows for multiple models of comparison to be used depending on the nucleotide patterns embedded in similar whole genomic sequences. The W-curve approach allows us to compare large numbers of samples quickly.We are currently tuning the algorithm to accommodate quirks specific to HIV-1 genomic sequences so that it can be used to aid in diagnostic and vaccine efforts. Tracking the molecular evolution of the virus has been greatly hampered by gap associated problems predominantly embedded within the envelope gene of the virus. Gaps and hypermutation of the virus slow conventional string based alignments of the whole genome. This paper describes the W-curve algorithm itself, and how we have adapted it for comparison of similar HIV-1 genomes. A treebuilding method is developed with the W-curve that utilizes a novel Cylindrical Coordinate distance method and gap analysis method. HIV-1 C2-V5 env sequence regions from a Mother/Infant cohort study are used in the comparison.The output distance matrix and neighbor results produced by the W-curve are functionally equivalent to those from Clustal for C2-V5 sequences in the mother/infant pairs infected with CRF01_AE.Significant potential exists for utilizing this method in place of conventional string based alignment of HIV-1 genomes, such as Clustal X. With W-curve heuristic alignment, it may be possible to obtain clinically useful results in a short time-short enough to affect clinical choices for acute treatment. A description of the W-curve generation process, including a comparison

  14. W-curve alignments for HIV-1 genomic comparisons.

    Science.gov (United States)

    Cork, Douglas J; Lembark, Steven; Tovanabutra, Sodsai; Robb, Merlin L; Kim, Jerome H

    2010-06-01

    The W-curve was originally developed as a graphical visualization technique for viewing DNA and RNA sequences. Its ability to render features of DNA also makes it suitable for computational studies. Its main advantage in this area is utilizing a single-pass algorithm for comparing the sequences. Avoiding recursion during sequence alignments offers advantages for speed and in-process resources. The graphical technique also allows for multiple models of comparison to be used depending on the nucleotide patterns embedded in similar whole genomic sequences. The W-curve approach allows us to compare large numbers of samples quickly. We are currently tuning the algorithm to accommodate quirks specific to HIV-1 genomic sequences so that it can be used to aid in diagnostic and vaccine efforts. Tracking the molecular evolution of the virus has been greatly hampered by gap associated problems predominantly embedded within the envelope gene of the virus. Gaps and hypermutation of the virus slow conventional string based alignments of the whole genome. This paper describes the W-curve algorithm itself, and how we have adapted it for comparison of similar HIV-1 genomes. A treebuilding method is developed with the W-curve that utilizes a novel Cylindrical Coordinate distance method and gap analysis method. HIV-1 C2-V5 env sequence regions from a Mother/Infant cohort study are used in the comparison. The output distance matrix and neighbor results produced by the W-curve are functionally equivalent to those from Clustal for C2-V5 sequences in the mother/infant pairs infected with CRF01_AE. Significant potential exists for utilizing this method in place of conventional string based alignment of HIV-1 genomes, such as Clustal X. With W-curve heuristic alignment, it may be possible to obtain clinically useful results in a short time-short enough to affect clinical choices for acute treatment. A description of the W-curve generation process, including a comparison technique of

  15. Numerical optimization of alignment reproducibility for customizable surgical guides.

    Science.gov (United States)

    Kroes, Thomas; Valstar, Edward; Eisemann, Elmar

    2015-10-01

    Computer-assisted orthopedic surgery aims at minimizing invasiveness, postoperative pain, and morbidity with computer-assisted preoperative planning and intra-operative guidance techniques, of which camera-based navigation and patient-specific templates (PST) are the most common. PSTs are one-time templates that guide the surgeon initially in cutting slits or drilling holes. This method can be extended to reusable and customizable surgical guides (CSG), which can be adapted to the patients' bone. Determining the right set of CSG input parameters by hand is a challenging task, given the vast amount of input parameter combinations and the complex physical interaction between the PST/CSG and the bone. This paper introduces a novel algorithm to solve the problem of choosing the right set of input parameters. Our approach predicts how well a CSG instance is able to reproduce the planned alignment based on a physical simulation and uses a genetic optimization algorithm to determine optimal configurations. We validate our technique with a prototype of a pin-based CSG and nine rapid prototyped distal femora. The proposed optimization technique has been compared to manual optimization by experts, as well as participants with domain experience. Using the optimization technique, the alignment errors remained within practical boundaries of 1.2 mm translation and [Formula: see text] rotation error. In all cases, the proposed method outperformed manual optimization. Manually optimizing CSG parameters turns out to be a counterintuitive task. Even after training, subjects with and without anatomical background fail in choosing appropriate CSG configurations. Our optimization algorithm ensures that the CSG is configured correctly, and we could demonstrate that the intended alignment of the CSG is accurately reproduced on all tested bone geometries.

  16. Stonehenge: A Simple and Accurate Predictor of Lunar Eclipses

    Science.gov (United States)

    Challener, S.

    1999-12-01

    Over the last century, much has been written about the astronomical significance of Stonehenge. The rage peaked in the mid to late 1960s when new computer technology enabled astronomers to make the first complete search for celestial alignments. Because there are hundreds of rocks or holes at Stonehenge and dozens of bright objects in the sky, the quest was fraught with obvious statistical problems. A storm of controversy followed and the subject nearly vanished from print. Only a handful of these alignments remain compelling. Today, few astronomers and still fewer archaeologists would argue that Stonehenge served primarily as an observatory. Instead, Stonehenge probably served as a sacred meeting place, which was consecrated by certain celestial events. These would include the sun's risings and settings at the solstices and possibly some lunar risings as well. I suggest that Stonehenge was also used to predict lunar eclipses. While Hawkins and Hoyle also suggested that Stonehenge was used in this way, their methods are complex and they make use of only early, minor, or outlying areas of Stonehenge. In contrast, I suggest a way that makes use of the imposing, central region of Stonehenge; the area built during the final phase of activity. To predict every lunar eclipse without predicting eclipses that do not occur, I use the less familiar lunar cycle of 47 lunar months. By moving markers about the Sarsen Circle, the Bluestone Circle, and the Bluestone Horseshoe, all umbral lunar eclipses can be predicted accurately.

  17. Biaxial magnetic grain alignment

    International Nuclear Information System (INIS)

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

    2000-01-01

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

  18. eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models.

    Directory of Open Access Journals (Sweden)

    Michal Brylinski

    2014-09-01

    Full Text Available Detecting similarities between ligand binding sites in the absence of global homology between target proteins has been recognized as one of the critical components of modern drug discovery. Local binding site alignments can be constructed using sequence order-independent techniques, however, to achieve a high accuracy, many current algorithms for binding site comparison require high-quality experimental protein structures, preferably in the bound conformational state. This, in turn, complicates proteome scale applications, where only various quality structure models are available for the majority of gene products. To improve the state-of-the-art, we developed eMatchSite, a new method for constructing sequence order-independent alignments of ligand binding sites in protein models. Large-scale benchmarking calculations using adenine-binding pockets in crystal structures demonstrate that eMatchSite generates accurate alignments for almost three times more protein pairs than SOIPPA. More importantly, eMatchSite offers a high tolerance to structural distortions in ligand binding regions in protein models. For example, the percentage of correctly aligned pairs of adenine-binding sites in weakly homologous protein models is only 4-9% lower than those aligned using crystal structures. This represents a significant improvement over other algorithms, e.g. the performance of eMatchSite in recognizing similar binding sites is 6% and 13% higher than that of SiteEngine using high- and moderate-quality protein models, respectively. Constructing biologically correct alignments using predicted ligand binding sites in protein models opens up the possibility to investigate drug-protein interaction networks for complete proteomes with prospective systems-level applications in polypharmacology and rational drug repositioning. eMatchSite is freely available to the academic community as a web-server and a stand-alone software distribution at http://www.brylinski.org/ematchsite.

  19. Band Alignment at GaN/Single-Layer WSe2 Interface

    KAUST Repository

    Tangi, Malleswararao

    2017-02-21

    We study the band discontinuity at the GaN/single-layer (SL) WSe2 heterointerface. The GaN thin layer is epitaxially grown by molecular beam epitaxy on chemically vapor deposited SL-WSe2/c-sapphire. We confirm that the WSe2 was formed as an SL from structural and optical analyses using atomic force microscopy, scanning transmission electron microscopy, micro-Raman, absorbance, and microphotoluminescence spectra. The determination of band offset parameters at the GaN/SL-WSe2 heterojunction is obtained by high-resolution X-ray photoelectron spectroscopy, electron affinities, and the electronic bandgap values of SL-WSe2 and GaN. The valence band and conduction band offset values are determined to be 2.25 ± 0.15 and 0.80 ± 0.15 eV, respectively, with type II band alignment. The band alignment parameters determined here provide a route toward the integration of group III nitride semiconducting materials with transition metal dichalcogenides (TMDs) for designing and modeling of their heterojunction-based electronic and optoelectronic devices.

  20. Band Alignment at GaN/Single-Layer WSe2 Interface

    KAUST Repository

    Tangi, Malleswararao; Mishra, Pawan; Tseng, Chien-Chih; Ng, Tien Khee; Hedhili, Mohamed N.; Anjum, Dalaver H.; Alias, Mohd Sharizal; Wei, Nini; Li, Lain-Jong; Ooi, Boon S.

    2017-01-01

    We study the band discontinuity at the GaN/single-layer (SL) WSe2 heterointerface. The GaN thin layer is epitaxially grown by molecular beam epitaxy on chemically vapor deposited SL-WSe2/c-sapphire. We confirm that the WSe2 was formed as an SL from structural and optical analyses using atomic force microscopy, scanning transmission electron microscopy, micro-Raman, absorbance, and microphotoluminescence spectra. The determination of band offset parameters at the GaN/SL-WSe2 heterojunction is obtained by high-resolution X-ray photoelectron spectroscopy, electron affinities, and the electronic bandgap values of SL-WSe2 and GaN. The valence band and conduction band offset values are determined to be 2.25 ± 0.15 and 0.80 ± 0.15 eV, respectively, with type II band alignment. The band alignment parameters determined here provide a route toward the integration of group III nitride semiconducting materials with transition metal dichalcogenides (TMDs) for designing and modeling of their heterojunction-based electronic and optoelectronic devices.

  1. Heuristics for multiobjective multiple sequence alignment.

    Science.gov (United States)

    Abbasi, Maryam; Paquete, Luís; Pereira, Francisco B

    2016-07-15

    Aligning multiple sequences arises in many tasks in Bioinformatics. However, the alignments produced by the current software packages are highly dependent on the parameters setting, such as the relative importance of opening gaps with respect to the increase of similarity. Choosing only one parameter setting may provide an undesirable bias in further steps of the analysis and give too simplistic interpretations. In this work, we reformulate multiple sequence alignment from a multiobjective point of view. The goal is to generate several sequence alignments that represent a trade-off between maximizing the substitution score and minimizing the number of indels/gaps in the sum-of-pairs score function. This trade-off gives to the practitioner further information about the similarity of the sequences, from which she could analyse and choose the most plausible alignment. We introduce several heuristic approaches, based on local search procedures, that compute a set of sequence alignments, which are representative of the trade-off between the two objectives (substitution score and indels). Several algorithm design options are discussed and analysed, with particular emphasis on the influence of the starting alignment and neighborhood search definitions on the overall performance. A perturbation technique is proposed to improve the local search, which provides a wide range of high-quality alignments. The proposed approach is tested experimentally on a wide range of instances. We performed several experiments with sequences obtained from the benchmark database BAliBASE 3.0. To evaluate the quality of the results, we calculate the hypervolume indicator of the set of score vectors returned by the algorithms. The results obtained allow us to identify reasonably good choices of parameters for our approach. Further, we compared our method in terms of correctly aligned pairs ratio and columns correctly aligned ratio with respect to reference alignments. Experimental results show

  2. Magnetic field-aligned particle precipitation

    International Nuclear Information System (INIS)

    Carlson, W.

    1985-01-01

    Magnetic field-aligned particle fluxes are a common auroral phenomenon. Precipitating field-aligned electrons are seen in the vicinity of auroral arcs as suprathermal bursts, as well as superimposed on the more isotropic inverted V electron precipitation. Electron distribution functions reveal two distinct source populations for the inverted V and field-aligned electron components, and also suggest possible acceleration mechanisms. The inverted V electrons are a hot, boundary plasma sheet population that gains the full parallel acceleration. The field-aligned component appears to originate from cold ionospheric electrons that may be distributed throughout the acceleration region. A turbulent parallel field might explain the apparent lifetime of cold electrons in the acceleration region

  3. XRD alignment, calibration and performance

    International Nuclear Information System (INIS)

    Davy, L.

    2002-01-01

    Full text: The quality of any diffractometer system is very much dependent on the alignment, calibration and performance. The three subjects are very much related. Firstly, you must know how to carry out the full diffractometer alignment. XRD alignment is easy once you know how. The presentation will show you step by step to carry out the full alignment. Secondly, you need to know how to calibrate the diffractometer system. The presentation will show you how to calibrate the goniometer, detector etc. Thirdly, to prove the system is working within the manufacturer specification. The presentation will show you how to carry out the resolution, reproducibility and linearity test. Copyright (2002) Australian X-ray Analytical Association Inc

  4. Sales Territory Alignment: A Review and Model

    OpenAIRE

    Andris A. Zoltners; Prabhakant Sinha

    1983-01-01

    The sales territory alignment problem may be viewed as the problem of grouping small geographic sales coverage units into larger geographic clusters called sales territories in a way that the sales territories are acceptable according to managerially relevant alignment criteria. This paper first reviews sales territory alignment models which have appeared in the marketing literature. A framework for sales territory alignment and several properties of a good sales territory alignment are devel...

  5. SU-E-J-33: Comparison Between Soft Tissue Alignment and Bony Alignment for Pancreatic Cancer Radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Suh, Y; Crane, C; Krishnan, S; Das, P; Koay, E; Beddar, S [UT MD Anderson Cancer Center, Houston, TX (United States)

    2015-06-15

    Purpose An IGRT modality for pancreatic cancer treatment with dose escalation at our institution is in-room daily CT imaging. The purpose of this study is to assess the difference between soft tissue alignment and bony alignment for pancreatic tumor localization. Methods Eighteen patients with pancreatic tumors who underwent IMRT treatment with an inspiration breath-hold technique between July 2012 and February 2015 are included in this study. Prior to each treatment, a CT scan was acquired. The CT image guidance started with auto-alignment to either the bony anatomy (vertebral bodies) or fiducials (for the six patients with the stent in/near the tumor) and then, when necessary, manual adjustments were made based on soft tissue alignment using clinical software (CT-Assisted Targeting system). The difference between soft tissue alignment and bony/fiducial alignment was evaluated. Results Of all 380 treatments, manual adjustment was made in 225 treatments, ranging from 11% (3 treatments out of 28) to 96% (27 treatments out of 28) per patient. The mean of the difference between soft tissue alignment and bony/fiducial alignment per patient ranged from −3.6 to 0.3 mm, −1.5 to 2.8 mm, and −3.3 to 3.4 mm in the AP, SI, and RL directions, respectively. The maximum difference over all treatments was −9.5, −14.6, and −14.6 mm in the AP, SI, and RL directions, respectively. Conclusion About 60% of the time, manual adjustment based on soft tissue alignment was required. The extent of manual adjustment was usually small but varied significantly from patient to patient. The ultimate goal of the IGRT modality using daily CT imaging is not to fully cover the target but to spare organs-at-risk as much as possible to avoid them moving into higher dose gradients than accepted in the treatment plan. To this end, manual adjustment based on soft tissue alignment is critically important.

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

    Directory of Open Access Journals (Sweden)

    Jakob H Havgaard

    2007-10-01

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

  7. Modelling dust polarization observations of molecular clouds through MHD simulations

    Science.gov (United States)

    King, Patrick K.; Fissel, Laura M.; Chen, Che-Yu; Li, Zhi-Yun

    2018-03-01

    The BLASTPol observations of Vela C have provided the most detailed characterization of the polarization fraction p and dispersion in polarization angles S for a molecular cloud. We compare the observed distributions of p and S with those obtained in synthetic observations of simulations of molecular clouds, assuming homogeneous grain alignment. We find that the orientation of the mean magnetic field relative to the observer has a significant effect on the p and S distributions. These distributions for Vela C are most consistent with synthetic observations where the mean magnetic field is close to the line of sight. Our results point to apparent magnetic disorder in the Vela C molecular cloud, although it can be due to either an inclination effect (i.e. observing close to the mean field direction) or significant field tangling from strong turbulence/low magnetization. The joint correlations of p with column density and of S with column density for the synthetic observations generally agree poorly with the Vela C joint correlations, suggesting that understanding these correlations requires a more sophisticated treatment of grain alignment physics.

  8. Controllable deposition distance of aligned pattern via dual-nozzle near-field electrospinning

    Science.gov (United States)

    Wang, Zhifeng; Chen, Xindu; Zeng, Jun; Liang, Feng; Wu, Peixuan; Wang, Han

    2017-03-01

    For large area micro/nano pattern printing, multi-nozzle electrohydrodynamic (EHD) printing setup is an efficient method to boost productivity in near-field electrospinning (NFES) process. And controlling EHD multi-jet accurate deposition under the interaction of nozzles and other parameters are crucial concerns during the process. The influence and sensitivity of various parameters such as the needle length, needle spacing, electrode-to-collector distance, voltage etc. on the direct-write patterning performance was investigated by orthogonal experiments with dual-nozzle NFES setup, and then the deposition distance estimated based on a novel model was compared with measurement results and proven. More controllable deposition distance and much denser of aligned naofiber can be achieved by rotating the dual-nozzle setup. This study can be greatly contributed to estimate the deposition distance and helpful to guide the multi-nozzle NFES process to accurate direct-write pattern in manufacturing process in future.

  9. BuddySuite: Command-Line Toolkits for Manipulating Sequences, Alignments, and Phylogenetic Trees.

    Science.gov (United States)

    Bond, Stephen R; Keat, Karl E; Barreira, Sofia N; Baxevanis, Andreas D

    2017-06-01

    The ability to manipulate sequence, alignment, and phylogenetic tree files has become an increasingly important skill in the life sciences, whether to generate summary information or to prepare data for further downstream analysis. The command line can be an extremely powerful environment for interacting with these resources, but only if the user has the appropriate general-purpose tools on hand. BuddySuite is a collection of four independent yet interrelated command-line toolkits that facilitate each step in the workflow of sequence discovery, curation, alignment, and phylogenetic reconstruction. Most common sequence, alignment, and tree file formats are automatically detected and parsed, and over 100 tools have been implemented for manipulating these data. The project has been engineered to easily accommodate the addition of new tools, is written in the popular programming language Python, and is hosted on the Python Package Index and GitHub to maximize accessibility. Documentation for each BuddySuite tool, including usage examples, is available at http://tiny.cc/buddysuite_wiki. All software is open source and freely available through http://research.nhgri.nih.gov/software/BuddySuite. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution 2017. This work is written by US Government employees and is in the public domain in the US.

  10. An Alignment of J-PARC Linac

    CERN Document Server

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

    2005-01-01

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

  11. Hydration free energies of cyanide and hydroxide ions from molecular dynamics simulations with accurate force fields

    Science.gov (United States)

    Lee, M.W.; Meuwly, M.

    2013-01-01

    The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories.

  12. RNA Structural Alignments, Part I

    DEFF Research Database (Denmark)

    Havgaard, Jakob Hull; Gorodkin, Jan

    2014-01-01

    Simultaneous alignment and secondary structure prediction of RNA sequences is often referred to as "RNA structural alignment." A class of the methods for structural alignment is based on the principles proposed by Sankoff more than 25 years ago. The Sankoff algorithm simultaneously folds and aligns...... is so high that it took more than a decade before the first implementation of a Sankoff style algorithm was published. However, with the faster computers available today and the improved heuristics used in the implementations the Sankoff-based methods have become practical. This chapter describes...... the methods based on the Sankoff algorithm. All the practical implementations of the algorithm use heuristics to make them run in reasonable time and memory. These heuristics are also described in this chapter....

  13. Fixture for aligning motor assembly

    Science.gov (United States)

    Shervington, Roger M.; Vaghani, Vallabh V.; Vanek, Laurence D.; Christensen, Scott A.

    2009-12-08

    An alignment fixture includes a rotor fixture, a stator fixture and a sensor system which measures a rotational displacement therebetween. The fixture precisely measures rotation of a generator stator assembly away from a NULL position referenced by a unique reference spline on the rotor shaft. By providing an adjustable location of the stator assembly within the housing, the magnetic axes within each generator shall be aligned to a predetermined and controlled tolerance between the generator interface mounting pin and the reference spline on the rotor shaft. Once magnetically aligned, each generator is essentially a line replaceable unit which may be readily mounted to any input of a multi-generator gearbox assembly with the assurance that the magnetic alignment will be within a predetermined tolerance.

  14. Molecular stopwatches, cogwheels and ``spinflakes'': studying the dynamics of molecular superrotors

    Science.gov (United States)

    Korobenko, Aleksey; Milner, Alexander; Hepburn, John; Milner, Valery

    2015-05-01

    Using the technique of an optical centrifuge, we excite diatomic molecules to ultrafast synchronous rotation. Femtosecond velocity-map imaging allows us to visualize and study the coherent dynamics of molecular superrotors under field free conditions and in external magnetic field. We demonstrate that when the created rotational wave packet is narrow, its free evolution is nondispersing and follows the motion of a classically rotating dumbbell or a hand of the smallest natural stopwatch. For wider rotational distributions, we observe the breakdown of classical rotation, when a dumbbell shape changes to that of a ``quantum cogwheel'' - a molecular state simultaneously aligned along multiple direction. Our measurements in external magnetic field reveal other peculiar aspects of the rich dynamics of molecular superrotors. The rotation of a non-magnetic molecule interacts with the applied field only weakly, giving rise to slow precession of the molecular angular momentum around the field direction. In contrast, the electronic spin of a paramagnetic superrotor mediates this interaction, causing the initial disk-like angular distribution to split into several spatial components, each precessing with its own frequency determined by the spin projection.

  15. Practical Photoemission Characterization Of Molecular Films And Related Interfaces

    International Nuclear Information System (INIS)

    Ivanco, J.

    2013-01-01

    Even though the term ‘organic electronics’ evokes rather organic devices, a significant part of its scope deals with physical properties of ‘active elements’ such as organic films and interfaces. Examination of the film growth and the evolution of the interface formation are particularly needful for the understanding a mechanism controlling their final properties. Performing such experiments in an ultra-high vacuum allows both to ‘stretch’ the time scale for pseudo real-time observations and to control properties of the probed systems on the atomic level. Photoemission technique probes directly electronic and chemical structure and it has thereby established among major tools employed in the field.This review primarily focuses to electronic properties of oligomeric molecular films and their interfaces examined by photoemission. Yet, it does not aspire after a complete overview on the topic; it rather aims to otherwise standard issues encountered at the photoemission characterization and analysis of the organic materials, though requiring to consider particularities of molecular films in terms of the growth, electronic properties, and their characterization and analysis. In particular, the fundamental electronic parameters of molecular films such as the work function, the ionization energy, and the interfacial energy level alignment, and their interplay, will be pursued with considering often neglected influence of the molecular orientation. Further, the implication on the band bending in molecular films based on photoemission characterization, and a model on the driving mechanism for the interfacial energy level alignment will be addressed. (author)

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

    Science.gov (United States)

    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 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) 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.

  17. VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences.

    Science.gov (United States)

    Xu, Duo; Jaber, Yousef; Pavlidis, Pavlos; Gokcumen, Omer

    2017-09-26

    Constructing alignments and phylogenies for a given locus from large genome sequencing studies with relevant outgroups allow novel evolutionary and anthropological insights. However, no user-friendly tool has been developed to integrate thousands of recently available and anthropologically relevant genome sequences to construct complete sequence alignments and phylogenies. Here, we provide VCFtoTree, a user friendly tool with a graphical user interface that directly accesses online databases to download, parse and analyze genome variation data for regions of interest. Our pipeline combines popular sequence datasets and tree building algorithms with custom data parsing to generate accurate alignments and phylogenies using all the individuals from the 1000 Genomes Project, Neanderthal and Denisovan genomes, as well as reference genomes of Chimpanzee and Rhesus Macaque. It can also be applied to other phased human genomes, as well as genomes from other species. The output of our pipeline includes an alignment in FASTA format and a tree file in newick format. VCFtoTree fulfills the increasing demand for constructing alignments and phylogenies for a given loci from thousands of available genomes. Our software provides a user friendly interface for a wider audience without prerequisite knowledge in programming. VCFtoTree can be accessed from https://github.com/duoduoo/VCFtoTree_3.0.0 .

  18. A shear-induced network of aligned wormlike micelles in a sugar-based molecular gel. From gelation to biocompatibility assays.

    Science.gov (United States)

    Fitremann, Juliette; Lonetti, Barbara; Fratini, Emiliano; Fabing, Isabelle; Payré, Bruno; Boulé, Christelle; Loubinoux, Isabelle; Vaysse, Laurence; Oriol, Luis

    2017-10-15

    A new low molecular weight hydrogelator with a saccharide (lactobionic) polar head linked by azide-alkyne click chemistry was prepared in three steps. It was obtained in high purity without chromatography, by phase separation and ultrafiltration of the aqueous gel. Gelation was not obtained reproducibly by conventional heating-cooling cycles and instead was obtained by shearing the aqueous solutions, from 2 wt% to 0.25 wt%. This method of preparation favored the formation of a quite unusual network of interconnected large but thin 2D-sheets (7nm-thick) formed by the association side-by-side of long and aligned 7nm diameter wormlike micelles. It was responsible for the reproducible gelation at the macroscopic scale. A second network made of helical fibres with a 10-13nm diameter, more or less intertwined was also formed but was scarcely able to sustain a macroscopic gel on its own. The gels were analysed by TEM (Transmission Electronic Microscopy), cryo-TEM and SAXS (Small Angle X-ray Scattering). Molecular modelling was also used to highlight the possible conformations the hydrogelator can take. The gels displayed a weak and reversible transition near 20°C, close to room temperature, ascribed to the wormlike micelles 2D-sheets network. Heating over 30°C led to the loss of the gel macroscopic integrity, but gel fragments were still observed in suspension. A second transition near 50°C, ascribed to the network of helical fibres, finally dissolved completely these fragments. The gels showed thixotropic behaviour, recovering slowly their initial elastic modulus, in few hours, after injection through a needle. Stable gels were tested as scaffold for neural cell line culture, showing a reduced biocompatibility. This new gelator is a clear illustration of how controlling the pathway was critical for gel formation and how a new kind of self-assembly was obtained by shearing. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Molecular Orientation in Two Component Vapor-Deposited Glasses: Effect of Substrate Temperature and Molecular Shape

    Science.gov (United States)

    Powell, Charles; Jiang, Jing; Walters, Diane; Ediger, Mark

    Vapor-deposited glasses are widely investigated for use in organic electronics including the emitting layers of OLED devices. These materials, while macroscopically homogenous, have anisotropic packing and molecular orientation. By controlling this orientation, outcoupling efficiency can be increased by aligning the transition dipole moment of the light-emitting molecules parallel to the substrate. Light-emitting molecules are typically dispersed in a host matrix, as such, it is imperative to understand molecular orientation in two-component systems. In this study we examine two-component vapor-deposited films and the orientations of the constituent molecules using spectroscopic ellipsometry, UV-vis and IR spectroscopy. The role of temperature, composition and molecular shape as it effects molecular orientation is examined for mixtures of DSA-Ph in Alq3 and in TPD. Deposition temperature relative to the glass transition temperature of the two-component mixture is the primary controlling factor for molecular orientation. In mixtures of DSA-Ph in Alq3, the linear DSA-Ph has a horizontal orientation at low temperatures and slight vertical orientation maximized at 0.96Tg,mixture, analogous to one-component films.

  20. Molecular characterization of Prunus necrotic ringspot virus isolated from rose in Brazil.

    OpenAIRE

    FAJARDO, T. V. M.; NASCIMENTO, M. B.; EIRAS, M.; NICKEL, O.; PIO-RIBEIRO, G.

    2016-01-01

    ABSTRACT: There is no molecular characterization of Brazilian isolates of Prunus necrotic ringspot virus (PNRSV), except for those infecting peach. In this research, the causal agent of rose mosaic was determined and the movement (MP) and coat (CP) protein genes of a PNRSV isolate from rose were molecularly characterized for the first time in Brazil. The nucleotide and deduced amino acid sequences of MP and CP complete genes were aligned and compared with other isolates. Molecular analysis of...

  1. Self-Aligned Metal Electrodes in Fully Roll-to-Roll Processed Organic Transistors

    Directory of Open Access Journals (Sweden)

    Marja Vilkman

    2016-01-01

    Full Text Available We demonstrate the production of organic bottom gate transistors with self-aligned electrodes, using only continuous roll-to-roll (R2R techniques. The self-alignment allows accurate <5 µm layer-to-layer registration, which is usually a challenge in high-speed R2R environments as the standard registration methods are limited to the millimeter range—or, at best, to tens of µm if online cameras and automatic web control are utilized. The improved registration enables minimizing the overlap between the source/drain electrodes and the gate electrode, which is essential for minimizing the parasitic capacitance. The complete process is a combination of several techniques, including evaporation, reverse gravure, flexography, lift-off, UV exposure and development methods—all transferred to a continuous R2R pilot line. Altogether, approximately 80 meters of devices consisting of thousands of transistors were manufactured in a roll-to-roll fashion. Finally, a cost analysis is presented in order to ascertain the main costs and to predict whether the process would be feasible for the industrial production of organic transistors.

  2. Sparse alignment for robust tensor learning.

    Science.gov (United States)

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

    2014-10-01

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

  3. Subset of Kappa and Lambda Germline Sequences Result in Light Chains with a Higher Molecular Mass Phenotype.

    Science.gov (United States)

    Barnidge, David R; Lundström, Susanna L; Zhang, Bo; Dasari, Surendra; Murray, David L; Zubarev, Roman A

    2015-12-04

    In our previous work, we showed that electrospray ionization of intact polyclonal kappa and lambda light chains isolated from normal serum generates two distinct, Gaussian-shaped, molecular mass distributions representing the light-chain repertoire. During the analysis of a large (>100) patient sample set, we noticed a low-intensity molecular mass distribution with a mean of approximately 24 250 Da, roughly 800 Da higher than the mean of the typical kappa molecular-mass distribution mean of 23 450 Da. We also observed distinct clones in this region that did not appear to contain any typical post-translational modifications that would account for such a large mass shift. To determine the origin of the high molecular mass clones, we performed de novo bottom-up mass spectrometry on a purified IgM monoclonal light chain that had a calculated molecular mass of 24 275.03 Da. The entire sequence of the monoclonal light chain was determined using multienzyme digestion and de novo sequence-alignment software and was found to belong to the germline allele IGKV2-30. The alignment of kappa germline sequences revealed ten IGKV2 and one IGKV4 sequences that contained additional amino acids in their CDR1 region, creating the high-molecular-mass phenotype. We also performed an alignment of lambda germline sequences, which showed additional amino acids in the CDR2 region, and the FR3 region of functional germline sequences that result in a high-molecular-mass phenotype. The work presented here illustrates the ability of mass spectrometry to provide information on the diversity of light-chain molecular mass phenotypes in circulation, which reflects the germline sequences selected by the immunoglobulin-secreting B-cell population.

  4. Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions

    DEFF Research Database (Denmark)

    Seemann, Ernst Stefan; Richter, Andreas S.; Gorodkin, Jan

    2010-01-01

    of that used for individual multiple alignments. Results: We derived a rather extensive algorithm. One of the advantages of our approach (in contrast to other RNARNA interaction prediction methods) is the application of covariance detection and prediction of pseudoknots between intra- and inter-molecular base...... pairs. As a proof of concept, we show an example and discuss the strengths and weaknesses of the approach....

  5. Tasting soil fungal diversity with earth tongues: phylogenetic test of SATe alignments for environmental ITS data.

    Directory of Open Access Journals (Sweden)

    Zheng Wang

    Full Text Available An abundance of novel fungal lineages have been indicated by DNA sequencing of the nuclear ribosomal ITS region from environmental samples such as soil and wood. Although phylogenetic analysis of these novel lineages is a key component of unveiling the structure and diversity of complex communities, such analyses are rare for environmental ITS data due to the difficulties of aligning this locus across significantly divergent taxa. One potential approach to this issue is simultaneous alignment and tree estimation. We targeted divergent ITS sequences of the earth tongue fungi (Geoglossomycetes, a basal class in the Ascomycota, to assess the performance of SATé, recent software that combines progressive alignment and tree building. We found that SATé performed well in generating high-quality alignments and in accurately estimating the phylogeny of earth tongue fungi. Drawing from a data set of 300 sequences of earth tongues and progressively more distant fungal lineages, 30 insufficiently identified ITS sequences from the public sequence databases were assigned to the Geoglossomycetes. The association between earth tongues and plants has been hypothesized for a long time, but hard evidence is yet to be collected. The ITS phylogeny showed that four ectomycorrhizal isolates shared a clade with Geoglossum but not with Trichoglossum earth tongues, pointing to the significant potential inherent to ecological data mining of environmental samples. Environmental sampling holds the key to many focal questions in mycology, and simultaneous alignment and tree estimation, as performed by SATé, can be a highly efficient companion in that pursuit.

  6. Assessing Lower Limb Alignment: Comparison of Standard Knee Xray vs Long Leg View.

    Science.gov (United States)

    Zampogna, Biagio; Vasta, Sebastiano; Amendola, Annunziato; Uribe-Echevarria Marbach, Bastian; Gao, Yubo; Papalia, Rocco; Denaro, Vincenzo

    2015-01-01

    High tibial osteotomy (HTO) is a well-established and commonly utilized technique in medial knee osteoarthritis secondary to varus malalignment. Accurate measurement of the preoperative limb alignment, and the amount of correction required are essential when planning limb realignment surgery. The hip-knee-ankle angle (HKA) measured on a full length weightbearing (FLWB) X-ray in the standing position is considered the gold standard, since it allows for reliable and accurate measurement of the mechanical axis of the whole lower extremity. In general practice, alignment is often evaluated on standard anteroposterior weightbearing (APWB) X-rays, as the angle between the femur and tibial anatomic axis (TFa). It is, therefore, of value to establish if measuring the anatomical axis from limited APWB is an effective measure of knee alignment especially in patients undergoing osteotomy about the knee. Three independent observers measured preoperative and postoperative FTa with standard method (FTa1) and with circles method (FTa2) on APWB X-ray and the HKA on FLWB X-ray at three different time-points separated by a two-week period. Intra-observer and inter-observer reliabilities and the comparison and relationship between anatomical and mechanical alignment were calculated. Intra- and interclass coefficients for all the three methods indicated excellent reliability, having all the values above 0.80. Using the mean of paired t-student test, the comparison of HKA versus TFa1 and TFa2 showed a statistically significant difference (p<.0001) both for the pre-operative and post-operative sets of values. The correlation between the HKA and FTal was found poor for the preoperative set (R=0.26) and fair for the postoperative one (R=0.53), while the new circles method showed a higher correlation in both the preoperative (R=0.71) and postoperative sets (R=0.79). Intra-observer reliability was high for HKA, FTal and FTa2 on APWB x-rays in the pre- and post-operative setting. Inter

  7. New theoretical approaches to atomic and molecular dynamics triggered by ultrashort light pulses on the atto- to picosecond time scale

    International Nuclear Information System (INIS)

    Pabst, Stefan Ulf

    2013-04-01

    The concept of atoms as the building blocks of matter has existed for over 3000 years. A revolution in the understanding and the description of atoms and molecules has occurred in the last century with the birth of quantum mechanics. After the electronic structure was understood, interest in studying the dynamics of electrons, atoms, and molecules increased. However, time-resolved investigations of these ultrafast processes were not possible until recently. The typical time scale of atomic and molecular processes is in the picosecond to attosecond realm. Tremendous technological progress in recent years makes it possible to generate light pulses on these time scales. With such ultrashort pulses, atomic and molecular dynamics can be triggered, watched, and controlled. Simultaneously, the need rises for theoretical models describing the underlying mechanisms. This doctoral thesis focuses on the development of theoretical models which can be used to study the dynamical behavior of electrons, atoms, and molecules in the presence of ultrashort light pulses. Several examples are discussed illustrating how light pulses can trigger and control electronic, atomic, and molecular motions. In the first part of this work, I focus on the rotational motion of asymmetric molecules, which happens on picosecond and femtosecond time scales. Here, the aim is to align all three axes of the molecule as well as possible. To investigate theoretically alignment dynamics, I developed a program that can describe alignment motion ranging from the impulsive to the adiabatic regime. The asymmetric molecule SO 2 is taken as an example to discuss strategies of optimizing 3D alignment without the presence of an external field (i.e., field-free alignment). Field-free alignment is particularly advantageous because subsequent experiments on the aligned molecule are not perturbed by the aligning light pulse. Wellaligned molecules in the gas phase are suitable for diffraction experiments. From the

  8. New theoretical approaches to atomic and molecular dynamics triggered by ultrashort light pulses on the atto- to picosecond time scale

    Energy Technology Data Exchange (ETDEWEB)

    Pabst, Stefan Ulf

    2013-04-15

    The concept of atoms as the building blocks of matter has existed for over 3000 years. A revolution in the understanding and the description of atoms and molecules has occurred in the last century with the birth of quantum mechanics. After the electronic structure was understood, interest in studying the dynamics of electrons, atoms, and molecules increased. However, time-resolved investigations of these ultrafast processes were not possible until recently. The typical time scale of atomic and molecular processes is in the picosecond to attosecond realm. Tremendous technological progress in recent years makes it possible to generate light pulses on these time scales. With such ultrashort pulses, atomic and molecular dynamics can be triggered, watched, and controlled. Simultaneously, the need rises for theoretical models describing the underlying mechanisms. This doctoral thesis focuses on the development of theoretical models which can be used to study the dynamical behavior of electrons, atoms, and molecules in the presence of ultrashort light pulses. Several examples are discussed illustrating how light pulses can trigger and control electronic, atomic, and molecular motions. In the first part of this work, I focus on the rotational motion of asymmetric molecules, which happens on picosecond and femtosecond time scales. Here, the aim is to align all three axes of the molecule as well as possible. To investigate theoretically alignment dynamics, I developed a program that can describe alignment motion ranging from the impulsive to the adiabatic regime. The asymmetric molecule SO{sub 2} is taken as an example to discuss strategies of optimizing 3D alignment without the presence of an external field (i.e., field-free alignment). Field-free alignment is particularly advantageous because subsequent experiments on the aligned molecule are not perturbed by the aligning light pulse. Wellaligned molecules in the gas phase are suitable for diffraction experiments. From the

  9. Photoresist thin-film effects on alignment process capability

    Science.gov (United States)

    Flores, Gary E.; Flack, Warren W.

    1993-08-01

    Two photoresists were selected for alignment characterization based on their dissimilar coating properties and observed differences on alignment capability. The materials are Dynachem OFPR-800 and Shipley System 8. Both photoresists were examined on two challenging alignment levels in a submicron CMOS process, a nitride level and a planarized second level metal. An Ultratech Stepper model 1500 which features a darkfield alignment system with a broadband green light for alignment signal detection was used for this project. Initially, statistically designed linear screening experiments were performed to examine six process factors for each photoresist: viscosity, spin acceleration, spin speed, spin time, softbake time, and softbake temperature. Using the results derived from the screening experiments, a more thorough examination of the statistically significant process factors was performed. A full quadratic experimental design was conducted to examine viscosity, spin speed, and spin time coating properties on alignment. This included a characterization of both intra and inter wafer alignment control and alignment process capability. Insight to the different alignment behavior is analyzed in terms of photoresist material properties and the physical nature of the alignment detection system.

  10. Aligning with New Digital Strategy

    DEFF Research Database (Denmark)

    Yeow, Adrian; Soh, Christina; Hansen, Rina

    2018-01-01

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

  11. Antares automatic beam alignment system

    International Nuclear Information System (INIS)

    Appert, Q.; Swann, T.; Sweatt, W.; Saxman, A.

    1980-01-01

    Antares is a 24-beam-line CO 2 laser system for controlled fusion research, under construction at Los Alamos Scientific Laboratory (LASL). Rapid automatic alignment of this system is required prior to each experiment shot. The alignment requirements, operational constraints, and a developed prototype system are discussed. A visible-wavelength alignment technique is employed that uses a telescope/TV system to view point light sources appropriately located down the beamline. Auto-alignment is accomplished by means of a video centroid tracker, which determines the off-axis error of the point sources. The error is nulled by computer-driven, movable mirrors in a closed-loop system. The light sources are fiber-optic terminations located at key points in the optics path, primarily at the center of large copper mirrors, and remotely illuminated to reduce heating effects

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

    Science.gov (United States)

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

    2013-11-01

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

  13. Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq.

    Science.gov (United States)

    Liu, Ruolin; Dickerson, Julie

    2017-11-01

    We propose a novel method and software tool, Strawberry, for transcript reconstruction and quantification from RNA-Seq data under the guidance of genome alignment and independent of gene annotation. Strawberry consists of two modules: assembly and quantification. The novelty of Strawberry is that the two modules use different optimization frameworks but utilize the same data graph structure, which allows a highly efficient, expandable and accurate algorithm for dealing large data. The assembly module parses aligned reads into splicing graphs, and uses network flow algorithms to select the most likely transcripts. The quantification module uses a latent class model to assign read counts from the nodes of splicing graphs to transcripts. Strawberry simultaneously estimates the transcript abundances and corrects for sequencing bias through an EM algorithm. Based on simulations, Strawberry outperforms Cufflinks and StringTie in terms of both assembly and quantification accuracies. Under the evaluation of a real data set, the estimated transcript expression by Strawberry has the highest correlation with Nanostring probe counts, an independent experiment measure for transcript expression. Strawberry is written in C++14, and is available as open source software at https://github.com/ruolin/strawberry under the MIT license.

  14. FACT. Bokeh alignment for Cherenkov telescopes

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, Sebastian Achim [ETH Zurich (Switzerland); Buss, Jens [TU Dortmund (Germany)

    2016-07-01

    Imaging Atmospheric Cherenkov Telescopes (IACTs) need fast and large imaging optics to map the faint Cherenkov light emitted in cosmic ray air showers onto their image sensors. Segmented reflectors are inexpensive, lightweight and offer good image quality. However, alignment of the mirror facets remains a challenge. A good alignment is crucial in IACT observations to separate gamma rays from hadronic cosmic rays. We present a simple, yet extendable method, to align segmented reflectors using their Bokeh. Bokeh alignment does not need a star or good weather nights but can be done anytime, even during the day. Bokeh alignment optimizes the facet orientations by comparing the segmented reflector's Bokeh to a predefined template. The Bokeh is observed using the out of focus image of a nearby point like light source in a distance of about ten times the focal lengths. We introduce Bokeh alignment on segmented reflectors and present its use on the First Geiger-mode Avalanche Cherenkov Telescope (FACT) on Canary Island La Palma, as well as on the Cherenkov Telescope Array (CTA) Medium Size Telescope (MST) prototype in Berlin Adlershof.

  15. MICA: Multiple interval-based curve alignment

    Science.gov (United States)

    Mann, Martin; Kahle, Hans-Peter; Beck, Matthias; Bender, Bela Johannes; Spiecker, Heinrich; Backofen, Rolf

    2018-01-01

    MICA enables the automatic synchronization of discrete data curves. To this end, characteristic points of the curves' shapes are identified. These landmarks are used within a heuristic curve registration approach to align profile pairs by mapping similar characteristics onto each other. In combination with a progressive alignment scheme, this enables the computation of multiple curve alignments. Multiple curve alignments are needed to derive meaningful representative consensus data of measured time or data series. MICA was already successfully applied to generate representative profiles of tree growth data based on intra-annual wood density profiles or cell formation data. The MICA package provides a command-line and graphical user interface. The R interface enables the direct embedding of multiple curve alignment computation into larger analyses pipelines. Source code, binaries and documentation are freely available at https://github.com/BackofenLab/MICA

  16. Nanoparticle amount, and not size, determines chain alignment and nonlinear hardening in polymer nanocomposites

    Science.gov (United States)

    Varol, H. Samet; Meng, Fanlong; Hosseinkhani, Babak; Malm, Christian; Bonn, Daniel; Bonn, Mischa; Zaccone, Alessio

    2017-01-01

    Polymer nanocomposites—materials in which a polymer matrix is blended with nanoparticles (or fillers)—strengthen under sufficiently large strains. Such strain hardening is critical to their function, especially for materials that bear large cyclic loads such as car tires or bearing sealants. Although the reinforcement (i.e., the increase in the linear elasticity) by the addition of filler particles is phenomenologically understood, considerably less is known about strain hardening (the nonlinear elasticity). Here, we elucidate the molecular origin of strain hardening using uniaxial tensile loading, microspectroscopy of polymer chain alignment, and theory. The strain-hardening behavior and chain alignment are found to depend on the volume fraction, but not on the size of nanofillers. This contrasts with reinforcement, which depends on both volume fraction and size of nanofillers, potentially allowing linear and nonlinear elasticity of nanocomposites to be tuned independently. PMID:28377517

  17. Alignment of whole genomes.

    Science.gov (United States)

    Delcher, A L; Kasif, S; Fleischmann, R D; Peterson, J; White, O; Salzberg, S L

    1999-01-01

    A new system for aligning whole genome sequences is described. Using an efficient data structure called a suffix tree, the system is able to rapidly align sequences containing millions of nucleotides. Its use is demonstrated on two strains of Mycoplasma tuberculosis, on two less similar species of Mycoplasma bacteria and on two syntenic sequences from human chromosome 12 and mouse chromosome 6. In each case it found an alignment of the input sequences, using between 30 s and 2 min of computation time. From the system output, information on single nucleotide changes, translocations and homologous genes can easily be extracted. Use of the algorithm should facilitate analysis of syntenic chromosomal regions, strain-to-strain comparisons, evolutionary comparisons and genomic duplications. PMID:10325427

  18. Semiautomated improvement of RNA alignments

    DEFF Research Database (Denmark)

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

    2007-01-01

    connects to external tools to provide a flexible semiautomatic editing environment. A new method, Pcluster, is introduced for dividing the sequences of an RNA alignment into subgroups with secondary structure differences. Pcluster was used to evaluate 574 seed alignments obtained from the Rfam database...... and we identified 71 alignments with significant prediction of inconsistent base pairs and 102 alignments with significant prediction of novel base pairs. Four RNA families were used to illustrate how SARSE can be used to manually or automatically correct the inconsistent base pairs detected by Pcluster......: the mir-399 RNA, vertebrate telomase RNA (vert-TR), bacterial transfer-messenger RNA (tmRNA), and the signal recognition particle (SRP) RNA. The general use of the method is illustrated by the ability to accommodate pseudoknots and handle even large and divergent RNA families. The open architecture...

  19. Alignment technology and applications of liquid crystal devices

    CERN Document Server

    Takatoh, Kohki; Hasegawa, Ray; Koden, Mitsushiro; Itoh, Nobuyuki; Hasegawa, Masaki

    2005-01-01

    Alignment phenomena are characteristic of liquid crystalline materials, and understanding them is critically important in understanding the essential features and behavior of liquid crystals and the performance of Liquid Crystal Devices (LCDs). Furthermore, in LCD production lines, the alignment process is of practical importance. Alignment Technologies and Applications of Liquid Crystal Devices demonstrates both the fundamental and practical aspects of alignment phenomena in liquid crystals. The physical basis of alignment phenomena is first introduced in order to aid the understanding of the various physical phenomena observed in the interface between liquid crystalline materials and alignment layer surfaces. Methods for the characterization of surfaces, which induce the alignment phenomena, and of the alignment layer itself are introduced. These methods are useful for the research of liquid crystalline materials and devices in academic research as well as in industry. In the practical sections, the alignme...

  20. Combined CT-based and image-free navigation systems in TKA reduces postoperative outliers of rotational alignment of the tibial component.

    Science.gov (United States)

    Mitsuhashi, Shota; Akamatsu, Yasushi; Kobayashi, Hideo; Kusayama, Yoshihiro; Kumagai, Ken; Saito, Tomoyuki

    2018-02-01

    Rotational malpositioning of the tibial component can lead to poor functional outcome in TKA. Although various surgical techniques have been proposed, precise rotational placement of the tibial component was difficult to accomplish even with the use of a navigation system. The purpose of this study is to assess whether combined CT-based and image-free navigation systems replicate accurately the rotational alignment of tibial component that was preoperatively planned on CT, compared with the conventional method. We compared the number of outliers for rotational alignment of the tibial component using combined CT-based and image-free navigation systems (navigated group) with those of conventional method (conventional group). Seventy-two TKAs were performed between May 2012 and December 2014. In the navigated group, the anteroposterior axis was prepared using CT-based navigation system and the tibial component was positioned under control of the navigation. In the conventional group, the tibial component was placed with reference to the Akagi line that was determined visually. Fisher's exact probability test was performed to evaluate the results. There was a significant difference between the two groups with regard to the number of outliers: 3 outliers in the navigated group compared with 12 outliers in the conventional group (P image-free navigation systems decreased the number of rotational outliers of tibial component, and was helpful for the replication of the accurate rotational alignment of the tibial component that was preoperatively planned.